Starting phenix.real_space_refine on Tue Feb 13 19:27:10 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9f_15930/02_2024/8b9f_15930_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9f_15930/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9f_15930/02_2024/8b9f_15930.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9f_15930/02_2024/8b9f_15930.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9f_15930/02_2024/8b9f_15930_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8b9f_15930/02_2024/8b9f_15930_updated.pdb" } 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 Residue "E GLU 222": "OE1" <-> "OE2" Residue "C ASP 66": "OD1" <-> "OD2" Residue "A PHE 266": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 5533 Number of models: 1 Model: "" Number of chains: 4 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: 507 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 507 Unusual residues: {'SPH': 1} Classifications: {'peptide': 59, 'undetermined': 1} Link IDs: {'PTRANS': 5, 'TRANS': 53, None: 1} Not linked: pdbres="PRO A 287 " pdbres="SPH A 300 " Chain breaks: 1 Time building chain proxies: 3.71, per 1000 atoms: 0.67 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.02 Conformation dependent library (CDL) restraints added in 901.6 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... running ksdssp... Secondary structure from input PDB file: 10 helices and 18 sheets defined 7.8% alpha, 22.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.02 Creating SS restraints... Processing helix chain 'E' and resid 113 through 115 No H-bonds generated for 'chain 'E' and resid 113 through 115' Processing helix chain 'B' and resid 84 through 86 No H-bonds generated for 'chain 'B' and resid 84 through 86' Processing helix chain 'B' and resid 90 through 98 Processing helix chain 'B' and resid 143 through 146 No H-bonds generated for 'chain 'B' and resid 143 through 146' Processing helix chain 'B' and resid 179 through 184 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 47 No H-bonds generated for 'chain 'C' and resid 44 through 47' Processing helix chain 'C' and resid 66 through 68 No H-bonds generated for 'chain 'C' and resid 66 through 68' Processing helix chain 'C' and resid 99 through 106 removed outlier: 3.772A pdb=" N TYR C 106 " --> pdb=" O GLU C 102 " (cutoff:3.500A) Processing helix chain 'C' and resid 145 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 101 through 109 removed outlier: 3.592A pdb=" N MET A 109 " --> pdb=" O ARG A 105 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'E' and resid 45 through 47 Processing sheet with id= B, first strand: chain 'E' and resid 60 through 62 Processing sheet with id= C, first strand: chain 'E' and resid 107 through 109 Processing sheet with id= D, first strand: chain 'E' and resid 124 through 126 Processing sheet with id= E, first strand: chain 'E' and resid 133 through 135 Processing sheet with id= F, first strand: chain 'E' and resid 172 through 176 Processing sheet with id= G, first strand: chain 'E' and resid 194 through 197 Processing sheet with id= H, first strand: chain 'E' and resid 204 through 207 Processing sheet with id= I, first strand: chain 'E' and resid 234 through 236 Processing sheet with id= J, first strand: chain 'E' and resid 248 through 250 Processing sheet with id= K, first strand: chain 'E' and resid 267 through 270 Processing sheet with id= L, first strand: chain 'B' and resid 63 through 65 Processing sheet with id= M, first strand: chain 'B' and resid 69 through 71 removed outlier: 4.495A pdb=" N VAL B 239 " --> pdb=" O TRP B 71 " (cutoff:3.500A) Processing sheet with id= N, first strand: chain 'B' and resid 78 through 82 Processing sheet with id= O, first strand: chain 'B' and resid 101 through 103 Processing sheet with id= P, first strand: chain 'C' and resid 70 through 73 Processing sheet with id= Q, 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= R, first strand: chain 'C' and resid 109 through 111 122 hydrogen bonds defined for protein. 312 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: 1.34 Time building geometry restraints manager: 2.15 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=" 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 bond pdb=" N VAL B 141 " pdb=" CA VAL B 141 " ideal model delta sigma weight residual 1.457 1.491 -0.035 1.15e-02 7.56e+03 9.04e+00 ... (remaining 5673 not shown) Histogram of bond angle deviations from ideal: 98.55 - 105.65: 174 105.65 - 112.75: 2983 112.75 - 119.85: 1845 119.85 - 126.94: 2632 126.94 - 134.04: 93 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 - 24.34: 3251 24.34 - 48.68: 112 48.68 - 73.02: 22 73.02 - 97.36: 6 97.36 - 121.70: 1 Dihedral angle restraints: 3392 sinusoidal: 1345 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=" C5 SPH A 300 " pdb=" C3 SPH A 300 " pdb=" C4 SPH A 300 " pdb=" O3 SPH A 300 " ideal model delta sinusoidal sigma weight residual -68.94 52.76 -121.70 1 2.00e+01 2.50e-03 3.66e+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 ... (remaining 3389 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.059: 667 0.059 - 0.118: 144 0.118 - 0.176: 30 0.176 - 0.235: 7 0.235 - 0.294: 3 Chirality restraints: 851 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 848 not shown) Planarity restraints: 994 Sorted by residual: 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 delta sigma weight rms_deltas residual plane pdb=" CA PRO E 177 " 0.014 2.00e-02 2.50e+03 2.69e-02 7.26e+00 pdb=" C PRO E 177 " -0.047 2.00e-02 2.50e+03 pdb=" O PRO E 177 " 0.017 2.00e-02 2.50e+03 pdb=" N GLY E 178 " 0.016 2.00e-02 2.50e+03 ... (remaining 991 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 351 2.73 - 3.27: 5333 3.27 - 3.81: 9028 3.81 - 4.36: 11705 4.36 - 4.90: 19260 Nonbonded interactions: 45677 Sorted by model distance: nonbonded pdb=" OG SER E 214 " pdb=" OD1 ASP E 215 " model vdw 2.185 2.440 nonbonded pdb=" OE1 GLU A 108 " pdb=" OH TYR A 258 " model vdw 2.238 2.440 nonbonded pdb=" OD1 ASP C 182 " pdb=" OG1 THR C 185 " model vdw 2.257 2.440 nonbonded pdb=" O GLY E 132 " pdb=" N LYS E 161 " model vdw 2.313 2.520 nonbonded pdb=" OG1 THR B 183 " pdb=" O ASP C 50 " model vdw 2.326 2.440 ... (remaining 45672 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 2.960 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: 0.000 Extract box with map and model: 13.310 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.280 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.650 ------------------------------------------------------------------------------- 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 : 0.005 0.052 5678 Z= 0.349 Angle : 0.736 10.559 7727 Z= 0.460 Chirality : 0.056 0.294 851 Planarity : 0.005 0.047 994 Dihedral : 13.425 121.702 2054 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 fitting. rotamer outliers: 9 poor density : 246 time to evaluate : 0.604 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: 0.1845 time to fit residues: 57.9060 Evaluate side-chains 167 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 163 time to evaluate : 0.611 ------------------------------------------------------------------------------- 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: 70 random chunks: chunk 59 optimal weight: 0.7980 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 18 optimal weight: 10.0000 chunk 35 optimal weight: 0.9980 chunk 28 optimal weight: 0.7980 chunk 54 optimal weight: 1.9990 chunk 21 optimal weight: 10.0000 chunk 33 optimal weight: 0.9980 chunk 40 optimal weight: 0.0570 chunk 63 optimal weight: 2.9990 overall best weight: 0.7298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 113 ASN C 97 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6511 moved from start: 0.3060 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 5678 Z= 0.230 Angle : 0.569 5.714 7727 Z= 0.300 Chirality : 0.046 0.207 851 Planarity : 0.005 0.065 994 Dihedral : 7.020 108.373 785 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer: Outliers : 4.85 % Allowed : 17.29 % Favored : 77.87 % 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: -0.63 (0.29), residues: 699 helix: -0.50 (0.79), residues: 44 sheet: 0.27 (0.38), residues: 177 loop : -0.69 (0.25), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP B 80 HIS 0.004 0.001 HIS C 97 PHE 0.019 0.002 PHE B 226 TYR 0.030 0.002 TYR C 194 ARG 0.004 0.001 ARG C 177 *********************** 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 206 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 0.574 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 105 ASN cc_start: 0.7796 (m-40) cc_final: 0.7482 (m-40) REVERT: E 135 ARG cc_start: 0.6215 (ttt-90) cc_final: 0.4727 (tpp-160) REVERT: E 136 GLU cc_start: 0.6891 (tp30) cc_final: 0.6404 (tp30) REVERT: B 64 TYR cc_start: 0.8630 (m-80) cc_final: 0.8334 (m-80) REVERT: B 70 THR cc_start: 0.9015 (m) cc_final: 0.8611 (p) REVERT: B 72 GLU cc_start: 0.8173 (mp0) cc_final: 0.7831 (mp0) REVERT: B 74 ASP cc_start: 0.8127 (p0) cc_final: 0.7730 (p0) REVERT: B 84 ASP cc_start: 0.7832 (t0) cc_final: 0.7541 (t0) REVERT: B 87 LYS cc_start: 0.8240 (pttt) cc_final: 0.7679 (ptpt) REVERT: B 100 TYR cc_start: 0.7808 (t80) cc_final: 0.6495 (t80) REVERT: B 129 GLU cc_start: 0.6875 (mm-30) cc_final: 0.6422 (mm-30) REVERT: B 132 MET cc_start: 0.9189 (mtt) cc_final: 0.8587 (mtt) REVERT: B 213 MET cc_start: 0.7799 (mmm) cc_final: 0.7471 (mtt) REVERT: B 215 ARG cc_start: 0.6916 (ttp-170) cc_final: 0.4784 (mmt180) REVERT: B 218 ASN cc_start: 0.8450 (m-40) cc_final: 0.7903 (m110) REVERT: B 256 ARG cc_start: 0.7234 (ppt90) cc_final: 0.6169 (mtp-110) REVERT: C 44 MET cc_start: 0.7303 (mmt) cc_final: 0.6851 (tpp) REVERT: C 61 LYS cc_start: 0.8198 (mtmt) cc_final: 0.7915 (mtmt) REVERT: C 102 GLU cc_start: 0.7309 (mm-30) cc_final: 0.7106 (mm-30) REVERT: C 134 TYR cc_start: 0.8180 (t80) cc_final: 0.7749 (t80) REVERT: C 155 ILE cc_start: 0.8109 (mt) cc_final: 0.7904 (tt) REVERT: A 265 ASN cc_start: 0.7848 (m-40) cc_final: 0.7565 (m-40) outliers start: 30 outliers final: 22 residues processed: 194 average time/residue: 0.1816 time to fit residues: 44.5788 Evaluate side-chains 172 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 150 time to evaluate : 0.613 ------------------------------------------------------------------------------- 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 225 CYS Chi-restraints excluded: chain E residue 236 ILE Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain B residue 65 THR 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 228 SER Chi-restraints excluded: chain C residue 50 ASP 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: 70 random chunks: chunk 35 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 52 optimal weight: 0.8980 chunk 43 optimal weight: 3.9990 chunk 17 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 68 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 62 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 173 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 95 ASN B 218 ASN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.3917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5678 Z= 0.227 Angle : 0.550 6.256 7727 Z= 0.288 Chirality : 0.045 0.177 851 Planarity : 0.004 0.034 994 Dihedral : 5.925 87.001 777 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 5.49 % Allowed : 17.45 % Favored : 77.06 % 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: -0.54 (0.29), residues: 699 helix: -0.47 (0.78), residues: 39 sheet: 0.53 (0.40), residues: 161 loop : -0.67 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP E 276 HIS 0.004 0.001 HIS B 109 PHE 0.030 0.002 PHE B 219 TYR 0.033 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 190 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 156 time to evaluate : 0.601 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: 0.3648 (OUTLIER) cc_final: 0.2716 (tt) REVERT: E 105 ASN cc_start: 0.7962 (m-40) cc_final: 0.7617 (m-40) REVERT: E 135 ARG cc_start: 0.6009 (ttt-90) cc_final: 0.4603 (tpp-160) REVERT: E 205 LEU cc_start: 0.6337 (OUTLIER) cc_final: 0.6091 (mm) REVERT: B 64 TYR cc_start: 0.8583 (m-80) cc_final: 0.8145 (m-80) REVERT: B 70 THR cc_start: 0.9094 (m) cc_final: 0.8647 (p) REVERT: B 72 GLU cc_start: 0.8429 (mp0) cc_final: 0.7900 (mp0) REVERT: B 74 ASP cc_start: 0.8187 (p0) cc_final: 0.7729 (p0) REVERT: B 84 ASP cc_start: 0.7889 (t0) cc_final: 0.7463 (t0) REVERT: B 87 LYS cc_start: 0.8400 (pttt) cc_final: 0.7743 (ptpt) REVERT: B 129 GLU cc_start: 0.7170 (mm-30) cc_final: 0.6688 (mm-30) REVERT: B 132 MET cc_start: 0.8859 (mtt) cc_final: 0.8632 (mtt) REVERT: B 167 GLN cc_start: 0.6888 (tp-100) cc_final: 0.6433 (tp-100) REVERT: B 175 MET cc_start: 0.8334 (mtp) cc_final: 0.8124 (mtp) REVERT: B 215 ARG cc_start: 0.6646 (ttp-170) cc_final: 0.4765 (mmt180) REVERT: B 218 ASN cc_start: 0.8453 (m110) cc_final: 0.8189 (m-40) REVERT: B 226 PHE cc_start: 0.8620 (m-10) cc_final: 0.7988 (m-10) REVERT: B 256 ARG cc_start: 0.7431 (ppt90) cc_final: 0.6094 (mtp-110) REVERT: C 44 MET cc_start: 0.7623 (mmt) cc_final: 0.7228 (tpp) REVERT: C 61 LYS cc_start: 0.8231 (mtmt) cc_final: 0.7988 (mtmt) REVERT: C 86 GLN cc_start: 0.8567 (mt0) cc_final: 0.8101 (pt0) REVERT: C 134 TYR cc_start: 0.8228 (t80) cc_final: 0.7775 (t80) REVERT: C 155 ILE cc_start: 0.8046 (mt) cc_final: 0.7600 (pt) REVERT: A 98 ARG cc_start: 0.6919 (mtt90) cc_final: 0.6664 (mtm-85) outliers start: 34 outliers final: 25 residues processed: 171 average time/residue: 0.1977 time to fit residues: 42.2590 Evaluate side-chains 172 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 145 time to evaluate : 0.542 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 71 LYS 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 191 ASN Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 205 LEU 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 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 170 VAL Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 50 ASP 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 231 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 47 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 chunk 7 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 63 optimal weight: 0.5980 chunk 67 optimal weight: 0.6980 chunk 60 optimal weight: 0.9980 chunk 18 optimal weight: 0.9980 chunk 56 optimal weight: 0.0870 chunk 38 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 78 GLN ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6579 moved from start: 0.4343 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= 0.181 Angle : 0.521 6.504 7727 Z= 0.271 Chirality : 0.045 0.172 851 Planarity : 0.004 0.029 994 Dihedral : 5.134 68.258 776 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.00 % Favored : 98.00 % Rotamer: Outliers : 4.85 % Allowed : 20.03 % Favored : 75.12 % 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: -0.43 (0.80), residues: 39 sheet: 0.53 (0.40), residues: 168 loop : -0.65 (0.26), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP E 276 HIS 0.003 0.001 HIS C 97 PHE 0.031 0.002 PHE B 219 TYR 0.024 0.002 TYR C 194 ARG 0.004 0.001 ARG E 221 *********************** 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 fitting. rotamer outliers: 30 poor density : 158 time to evaluate : 0.550 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 105 ASN cc_start: 0.8015 (m-40) cc_final: 0.7668 (m-40) REVERT: E 135 ARG cc_start: 0.5889 (ttt-90) cc_final: 0.4900 (tpp-160) REVERT: E 205 LEU cc_start: 0.6391 (mp) cc_final: 0.6132 (mm) REVERT: E 246 ARG cc_start: 0.7588 (ptp-170) cc_final: 0.7113 (ptp-170) REVERT: B 64 TYR cc_start: 0.8561 (m-80) cc_final: 0.8077 (m-80) REVERT: B 74 ASP cc_start: 0.8221 (p0) cc_final: 0.7724 (p0) REVERT: B 84 ASP cc_start: 0.7907 (t0) cc_final: 0.7661 (t0) REVERT: B 87 LYS cc_start: 0.8430 (pttt) cc_final: 0.7887 (ptpt) REVERT: B 96 MET cc_start: 0.8393 (ttp) cc_final: 0.7747 (ttm) REVERT: B 129 GLU cc_start: 0.7286 (mm-30) cc_final: 0.6683 (mm-30) REVERT: B 132 MET cc_start: 0.8838 (mtt) cc_final: 0.8631 (mtt) REVERT: B 167 GLN cc_start: 0.7084 (tp-100) cc_final: 0.6584 (tp-100) REVERT: B 215 ARG cc_start: 0.6552 (ttp-170) cc_final: 0.4739 (mmt180) REVERT: B 226 PHE cc_start: 0.8576 (m-80) cc_final: 0.8055 (m-10) REVERT: C 44 MET cc_start: 0.7664 (mmt) cc_final: 0.7238 (tpp) REVERT: C 61 LYS cc_start: 0.8151 (mtmt) cc_final: 0.7915 (mtmt) REVERT: C 134 TYR cc_start: 0.8215 (t80) cc_final: 0.7841 (t80) REVERT: C 155 ILE cc_start: 0.7970 (mt) cc_final: 0.7487 (pt) outliers start: 30 outliers final: 24 residues processed: 171 average time/residue: 0.1776 time to fit residues: 38.7651 Evaluate side-chains 169 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 145 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 109 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 225 CYS Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain B residue 60 THR 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 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 50 ASP Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 164 CYS Chi-restraints excluded: chain C residue 199 VAL Chi-restraints excluded: chain C residue 224 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 0 optimal weight: 20.0000 chunk 50 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 57 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 chunk 22 optimal weight: 20.0000 chunk 13 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 86 GLN ** C 181 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 195 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6657 moved from start: 0.4737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 5678 Z= 0.275 Angle : 0.553 6.696 7727 Z= 0.290 Chirality : 0.044 0.165 851 Planarity : 0.004 0.029 994 Dihedral : 5.045 58.646 776 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 11.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.98 % Allowed : 20.68 % Favored : 73.34 % 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 (0.30), residues: 699 helix: -0.86 (0.77), residues: 39 sheet: 0.38 (0.40), residues: 171 loop : -0.67 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 80 HIS 0.003 0.001 HIS C 77 PHE 0.033 0.002 PHE B 219 TYR 0.038 0.002 TYR C 194 ARG 0.005 0.001 ARG B 62 *********************** 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 183 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 146 time to evaluate : 0.593 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 105 ASN cc_start: 0.8065 (m-40) cc_final: 0.7709 (m-40) REVERT: E 205 LEU cc_start: 0.6459 (mp) cc_final: 0.6207 (mm) REVERT: B 64 TYR cc_start: 0.8633 (m-80) cc_final: 0.8052 (m-80) REVERT: B 72 GLU cc_start: 0.8262 (mp0) cc_final: 0.8051 (mp0) REVERT: B 74 ASP cc_start: 0.8255 (p0) cc_final: 0.7716 (p0) REVERT: B 84 ASP cc_start: 0.7974 (t0) cc_final: 0.7669 (t0) REVERT: B 87 LYS cc_start: 0.8488 (pttt) cc_final: 0.7972 (ptpt) REVERT: B 129 GLU cc_start: 0.7512 (mm-30) cc_final: 0.6903 (mm-30) REVERT: B 132 MET cc_start: 0.8896 (mtt) cc_final: 0.8511 (mtt) REVERT: B 215 ARG cc_start: 0.6918 (ttp-170) cc_final: 0.4809 (mmt180) REVERT: B 226 PHE cc_start: 0.8649 (m-80) cc_final: 0.8266 (m-10) REVERT: B 256 ARG cc_start: 0.7781 (ppt90) cc_final: 0.6250 (mtt-85) REVERT: C 44 MET cc_start: 0.7760 (mmt) cc_final: 0.7411 (tpp) REVERT: C 134 TYR cc_start: 0.8297 (t80) cc_final: 0.7966 (t80) REVERT: C 155 ILE cc_start: 0.8038 (mt) cc_final: 0.7707 (pt) outliers start: 37 outliers final: 29 residues processed: 164 average time/residue: 0.1883 time to fit residues: 39.1681 Evaluate side-chains 168 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 139 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 71 LYS Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain B residue 60 THR 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 140 THR Chi-restraints excluded: chain B residue 146 ILE Chi-restraints excluded: chain B residue 170 VAL Chi-restraints excluded: chain B residue 171 THR 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 50 ASP Chi-restraints excluded: chain C residue 66 ASP 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 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 16 optimal weight: 9.9990 chunk 67 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 5 optimal weight: 20.0000 chunk 22 optimal weight: 7.9990 chunk 35 optimal weight: 0.9980 chunk 65 optimal weight: 1.9990 chunk 7 optimal weight: 9.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.1980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6659 moved from start: 0.5049 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5678 Z= 0.251 Angle : 0.564 6.913 7727 Z= 0.293 Chirality : 0.045 0.164 851 Planarity : 0.004 0.028 994 Dihedral : 4.968 53.202 776 Min Nonbonded Distance : 2.229 Molprobity Statistics. All-atom Clashscore : 12.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.72 % Favored : 97.28 % Rotamer: Outliers : 5.65 % Allowed : 21.32 % Favored : 73.02 % 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: -0.69 (0.30), residues: 699 helix: -1.24 (0.76), residues: 41 sheet: 0.50 (0.42), residues: 154 loop : -0.72 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 80 HIS 0.006 0.001 HIS E 242 PHE 0.033 0.002 PHE B 219 TYR 0.031 0.002 TYR C 194 ARG 0.005 0.001 ARG B 62 *********************** 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 181 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 146 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 105 ASN cc_start: 0.8058 (m-40) cc_final: 0.7698 (m-40) REVERT: E 113 TYR cc_start: 0.7366 (m-80) cc_final: 0.6554 (m-10) REVERT: E 135 ARG cc_start: 0.6064 (ttt-90) cc_final: 0.5259 (tpp-160) REVERT: E 205 LEU cc_start: 0.6472 (mp) cc_final: 0.6247 (mm) REVERT: E 246 ARG cc_start: 0.7614 (ptp-170) cc_final: 0.7389 (ptp-170) REVERT: B 64 TYR cc_start: 0.8557 (m-80) cc_final: 0.8016 (m-80) REVERT: B 72 GLU cc_start: 0.8310 (mp0) cc_final: 0.7938 (mp0) REVERT: B 74 ASP cc_start: 0.8260 (p0) cc_final: 0.7682 (p0) REVERT: B 84 ASP cc_start: 0.7999 (t0) cc_final: 0.7622 (t0) REVERT: B 87 LYS cc_start: 0.8440 (pttt) cc_final: 0.7911 (ptpt) REVERT: B 100 TYR cc_start: 0.7281 (t80) cc_final: 0.6276 (t80) REVERT: B 129 GLU cc_start: 0.7628 (mm-30) cc_final: 0.7003 (mm-30) REVERT: B 132 MET cc_start: 0.8903 (mtt) cc_final: 0.8409 (mtt) REVERT: B 154 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7703 (mtmm) REVERT: B 215 ARG cc_start: 0.6586 (ttp-170) cc_final: 0.4638 (mmt180) REVERT: B 226 PHE cc_start: 0.8577 (m-80) cc_final: 0.8077 (m-10) REVERT: B 256 ARG cc_start: 0.7693 (OUTLIER) cc_final: 0.6362 (mtt-85) REVERT: C 44 MET cc_start: 0.7860 (mmt) cc_final: 0.7511 (tpp) REVERT: C 88 GLN cc_start: 0.7657 (OUTLIER) cc_final: 0.6866 (mp10) REVERT: C 134 TYR cc_start: 0.8258 (t80) cc_final: 0.7901 (t80) REVERT: C 155 ILE cc_start: 0.8070 (mt) cc_final: 0.7648 (pt) outliers start: 35 outliers final: 26 residues processed: 165 average time/residue: 0.1948 time to fit residues: 40.3702 Evaluate side-chains 168 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 140 time to evaluate : 0.650 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 155 VAL Chi-restraints excluded: chain E residue 191 ASN Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain E residue 266 TYR Chi-restraints excluded: chain B residue 60 THR 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 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain B residue 256 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 66 ASP Chi-restraints excluded: chain C residue 88 GLN 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 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 227 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 0.0270 chunk 37 optimal weight: 0.5980 chunk 67 optimal weight: 3.9990 chunk 42 optimal weight: 0.2980 chunk 41 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 0.9980 chunk 20 optimal weight: 10.0000 chunk 13 optimal weight: 0.3980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6591 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5678 Z= 0.172 Angle : 0.540 7.018 7727 Z= 0.279 Chirality : 0.044 0.169 851 Planarity : 0.004 0.030 994 Dihedral : 4.658 48.671 776 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 11.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.00 % Favored : 97.00 % Rotamer: Outliers : 4.85 % Allowed : 23.26 % Favored : 71.89 % 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 (0.30), residues: 699 helix: -0.99 (0.78), residues: 41 sheet: 0.57 (0.42), residues: 154 loop : -0.69 (0.26), residues: 504 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 78 HIS 0.006 0.001 HIS B 109 PHE 0.027 0.001 PHE B 219 TYR 0.023 0.001 TYR E 127 ARG 0.004 0.001 ARG E 135 *********************** 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 185 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 155 time to evaluate : 0.639 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 113 TYR cc_start: 0.7387 (m-80) cc_final: 0.6369 (m-10) REVERT: E 135 ARG cc_start: 0.6011 (ttt-90) cc_final: 0.5324 (tpp-160) REVERT: E 203 PHE cc_start: 0.7368 (m-80) cc_final: 0.7092 (m-10) REVERT: E 205 LEU cc_start: 0.6479 (mp) cc_final: 0.6225 (mm) REVERT: B 64 TYR cc_start: 0.8601 (m-80) cc_final: 0.8043 (m-80) REVERT: B 72 GLU cc_start: 0.8327 (mp0) cc_final: 0.7910 (mp0) REVERT: B 74 ASP cc_start: 0.8210 (p0) cc_final: 0.7615 (p0) REVERT: B 81 LYS cc_start: 0.8655 (mttp) cc_final: 0.8131 (mttt) REVERT: B 84 ASP cc_start: 0.7932 (t0) cc_final: 0.7706 (t0) REVERT: B 87 LYS cc_start: 0.8448 (pttt) cc_final: 0.7936 (ptpt) REVERT: B 129 GLU cc_start: 0.7511 (mm-30) cc_final: 0.6915 (mm-30) REVERT: B 132 MET cc_start: 0.8860 (mtt) cc_final: 0.8250 (mtt) REVERT: B 154 LYS cc_start: 0.7942 (mtmm) cc_final: 0.7647 (mtmm) REVERT: B 213 MET cc_start: 0.7296 (mtt) cc_final: 0.7026 (mpp) REVERT: B 215 ARG cc_start: 0.6649 (ttp-170) cc_final: 0.4629 (mmt180) REVERT: B 226 PHE cc_start: 0.8607 (m-80) cc_final: 0.8140 (m-10) REVERT: C 44 MET cc_start: 0.7974 (mmt) cc_final: 0.7573 (tpp) REVERT: C 88 GLN cc_start: 0.7372 (OUTLIER) cc_final: 0.6907 (mp10) REVERT: C 134 TYR cc_start: 0.8173 (t80) cc_final: 0.7787 (t80) REVERT: C 155 ILE cc_start: 0.8008 (mt) cc_final: 0.7554 (pt) outliers start: 30 outliers final: 25 residues processed: 170 average time/residue: 0.1850 time to fit residues: 39.8764 Evaluate side-chains 173 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 147 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 35 ASP Chi-restraints excluded: chain E residue 100 VAL Chi-restraints excluded: chain E residue 117 ASN Chi-restraints excluded: chain E residue 119 PHE 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 60 THR 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 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 104 LEU 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 227 ASP 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: 70 random chunks: chunk 13 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 45 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 6 optimal weight: 30.0000 chunk 53 optimal weight: 0.9980 chunk 61 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 58 optimal weight: 4.9990 chunk 62 optimal weight: 0.6980 chunk 37 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6635 moved from start: 0.5455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5678 Z= 0.216 Angle : 0.563 7.249 7727 Z= 0.291 Chirality : 0.045 0.226 851 Planarity : 0.005 0.082 994 Dihedral : 4.692 44.871 776 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer: Outliers : 5.33 % Allowed : 22.78 % Favored : 71.89 % 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: -0.60 (0.30), residues: 699 helix: -0.94 (0.79), residues: 41 sheet: 0.56 (0.43), residues: 153 loop : -0.69 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 80 HIS 0.004 0.001 HIS B 109 PHE 0.035 0.002 PHE C 68 TYR 0.024 0.002 TYR C 194 ARG 0.012 0.001 ARG A 254 *********************** 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 183 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 150 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3722 (OUTLIER) cc_final: 0.2764 (tt) REVERT: E 135 ARG cc_start: 0.6232 (ttt-90) cc_final: 0.5450 (tpp-160) REVERT: E 203 PHE cc_start: 0.7397 (m-80) cc_final: 0.7115 (m-10) REVERT: E 205 LEU cc_start: 0.6486 (mp) cc_final: 0.6265 (mm) REVERT: B 64 TYR cc_start: 0.8595 (m-80) cc_final: 0.7999 (m-80) REVERT: B 72 GLU cc_start: 0.8338 (mp0) cc_final: 0.7921 (mp0) REVERT: B 74 ASP cc_start: 0.8275 (p0) cc_final: 0.7669 (p0) REVERT: B 81 LYS cc_start: 0.8673 (OUTLIER) cc_final: 0.7847 (mmtp) REVERT: B 84 ASP cc_start: 0.8001 (t0) cc_final: 0.7652 (t0) REVERT: B 87 LYS cc_start: 0.8495 (pttt) cc_final: 0.7958 (ptpt) REVERT: B 129 GLU cc_start: 0.7571 (mm-30) cc_final: 0.7034 (mm-30) REVERT: B 132 MET cc_start: 0.8874 (mtt) cc_final: 0.8338 (mtt) REVERT: B 154 LYS cc_start: 0.8100 (mtmm) cc_final: 0.7875 (mtmm) REVERT: B 213 MET cc_start: 0.7416 (mtt) cc_final: 0.7068 (mpp) REVERT: B 215 ARG cc_start: 0.7044 (ttp-170) cc_final: 0.4966 (mmt180) REVERT: B 226 PHE cc_start: 0.8590 (m-80) cc_final: 0.8117 (m-10) REVERT: B 256 ARG cc_start: 0.7658 (ppt90) cc_final: 0.6285 (mtt-85) REVERT: C 44 MET cc_start: 0.8055 (mmt) cc_final: 0.7677 (tpp) REVERT: C 88 GLN cc_start: 0.7308 (OUTLIER) cc_final: 0.6484 (mp10) REVERT: C 134 TYR cc_start: 0.8252 (t80) cc_final: 0.7842 (t80) REVERT: C 155 ILE cc_start: 0.8023 (mt) cc_final: 0.7575 (pt) outliers start: 33 outliers final: 27 residues processed: 167 average time/residue: 0.1905 time to fit residues: 40.4033 Evaluate side-chains 172 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 142 time to evaluate : 0.686 ------------------------------------------------------------------------------- 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 117 ASN Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 197 PHE Chi-restraints excluded: chain E residue 211 VAL Chi-restraints excluded: chain E residue 233 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 81 LYS Chi-restraints excluded: chain B residue 88 ASP 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 170 VAL 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 50 ASP Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 104 LEU Chi-restraints excluded: chain C residue 127 THR Chi-restraints excluded: chain C residue 198 ILE 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 227 ASP Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 27 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 19 optimal weight: 5.9990 chunk 56 optimal weight: 0.9980 chunk 59 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 41 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 31 optimal weight: 0.8980 chunk 46 optimal weight: 0.2980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 57 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6632 moved from start: 0.5594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5678 Z= 0.218 Angle : 0.592 8.766 7727 Z= 0.302 Chirality : 0.046 0.242 851 Planarity : 0.004 0.031 994 Dihedral : 4.673 43.352 776 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 5.17 % Allowed : 23.26 % Favored : 71.57 % 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 (0.30), residues: 699 helix: -0.70 (0.79), residues: 41 sheet: 0.60 (0.43), residues: 153 loop : -0.69 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 78 HIS 0.002 0.001 HIS E 242 PHE 0.039 0.002 PHE C 68 TYR 0.034 0.002 TYR E 127 ARG 0.006 0.001 ARG E 240 *********************** 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 175 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 143 time to evaluate : 0.610 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3717 (OUTLIER) cc_final: 0.2762 (tt) REVERT: E 203 PHE cc_start: 0.7384 (m-80) cc_final: 0.7102 (m-10) REVERT: E 205 LEU cc_start: 0.6458 (mp) cc_final: 0.6231 (mm) REVERT: B 64 TYR cc_start: 0.8581 (m-80) cc_final: 0.7988 (m-80) REVERT: B 72 GLU cc_start: 0.8347 (mp0) cc_final: 0.7956 (mp0) REVERT: B 74 ASP cc_start: 0.8193 (p0) cc_final: 0.7588 (p0) REVERT: B 81 LYS cc_start: 0.8679 (OUTLIER) cc_final: 0.7817 (mmtp) REVERT: B 84 ASP cc_start: 0.8018 (t0) cc_final: 0.7613 (t0) REVERT: B 87 LYS cc_start: 0.8515 (pttt) cc_final: 0.7935 (ptpt) REVERT: B 129 GLU cc_start: 0.7563 (mm-30) cc_final: 0.7008 (mm-30) REVERT: B 132 MET cc_start: 0.8852 (mtt) cc_final: 0.8360 (mtt) REVERT: B 154 LYS cc_start: 0.8066 (mtmm) cc_final: 0.7810 (mtmm) REVERT: B 213 MET cc_start: 0.7366 (mtt) cc_final: 0.6965 (mpp) REVERT: B 215 ARG cc_start: 0.7064 (ttp-170) cc_final: 0.5032 (mmt180) REVERT: B 226 PHE cc_start: 0.8706 (m-80) cc_final: 0.8254 (m-10) REVERT: B 256 ARG cc_start: 0.7690 (ppt90) cc_final: 0.6289 (mtt-85) REVERT: C 44 MET cc_start: 0.8103 (mmt) cc_final: 0.7887 (tpp) REVERT: C 88 GLN cc_start: 0.7389 (OUTLIER) cc_final: 0.6509 (mp10) REVERT: C 134 TYR cc_start: 0.8232 (t80) cc_final: 0.7825 (t80) REVERT: C 155 ILE cc_start: 0.7999 (mt) cc_final: 0.7537 (pt) REVERT: C 211 MET cc_start: 0.6961 (ttp) cc_final: 0.6698 (ttm) outliers start: 32 outliers final: 26 residues processed: 162 average time/residue: 0.1857 time to fit residues: 37.9575 Evaluate side-chains 173 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 144 time to evaluate : 0.557 ------------------------------------------------------------------------------- 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 117 ASN Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 127 TYR 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 233 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 81 LYS 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 170 VAL 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 88 GLN 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 210 ILE Chi-restraints excluded: chain C residue 224 LEU Chi-restraints excluded: chain C residue 227 ASP Chi-restraints excluded: chain A residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 69 optimal weight: 2.9990 chunk 64 optimal weight: 0.1980 chunk 55 optimal weight: 0.0980 chunk 5 optimal weight: 20.0000 chunk 42 optimal weight: 3.9990 chunk 34 optimal weight: 0.6980 chunk 44 optimal weight: 5.9990 chunk 59 optimal weight: 0.6980 chunk 17 optimal weight: 0.0170 chunk 51 optimal weight: 1.9990 chunk 8 optimal weight: 20.0000 overall best weight: 0.3418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6585 moved from start: 0.5674 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 5678 Z= 0.186 Angle : 0.581 7.463 7727 Z= 0.296 Chirality : 0.046 0.210 851 Planarity : 0.004 0.030 994 Dihedral : 4.590 41.885 776 Min Nonbonded Distance : 2.176 Molprobity Statistics. All-atom Clashscore : 12.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.58 % Favored : 97.42 % Rotamer: Outliers : 4.52 % Allowed : 23.59 % Favored : 71.89 % 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: -0.32 (0.80), residues: 41 sheet: 0.61 (0.43), residues: 153 loop : -0.65 (0.26), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 78 HIS 0.007 0.001 HIS B 109 PHE 0.028 0.002 PHE C 68 TYR 0.026 0.002 TYR E 127 ARG 0.004 0.000 ARG C 69 ********************** 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 176 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 148 time to evaluate : 0.645 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: E 82 LEU cc_start: 0.3715 (OUTLIER) cc_final: 0.2780 (tt) REVERT: E 113 TYR cc_start: 0.7151 (m-80) cc_final: 0.6208 (m-10) REVERT: E 203 PHE cc_start: 0.7378 (m-80) cc_final: 0.7068 (m-10) REVERT: E 205 LEU cc_start: 0.6452 (mp) cc_final: 0.6242 (mm) REVERT: B 64 TYR cc_start: 0.8592 (m-80) cc_final: 0.8038 (m-80) REVERT: B 72 GLU cc_start: 0.8345 (mp0) cc_final: 0.8069 (mp0) REVERT: B 74 ASP cc_start: 0.8184 (p0) cc_final: 0.7601 (p0) REVERT: B 81 LYS cc_start: 0.8608 (mttp) cc_final: 0.8215 (mttt) REVERT: B 84 ASP cc_start: 0.7954 (t0) cc_final: 0.7605 (t0) REVERT: B 87 LYS cc_start: 0.8506 (pttt) cc_final: 0.7971 (ptpt) REVERT: B 111 GLN cc_start: 0.7628 (mm-40) cc_final: 0.7333 (mm-40) REVERT: B 129 GLU cc_start: 0.7471 (mm-30) cc_final: 0.6902 (mm-30) REVERT: B 132 MET cc_start: 0.8805 (mtt) cc_final: 0.8310 (mtt) REVERT: B 154 LYS cc_start: 0.8016 (mtmm) cc_final: 0.7789 (mtmm) REVERT: B 213 MET cc_start: 0.7210 (mtt) cc_final: 0.6827 (mpp) REVERT: B 215 ARG cc_start: 0.7030 (ttp-170) cc_final: 0.4963 (mmt180) REVERT: B 226 PHE cc_start: 0.8615 (m-80) cc_final: 0.8175 (m-10) REVERT: B 256 ARG cc_start: 0.7614 (ppt90) cc_final: 0.6244 (mtt-85) REVERT: C 44 MET cc_start: 0.8088 (mmt) cc_final: 0.7876 (tpp) REVERT: C 63 ASP cc_start: 0.6991 (t0) cc_final: 0.6688 (t0) REVERT: C 88 GLN cc_start: 0.7223 (OUTLIER) cc_final: 0.6456 (mp10) REVERT: C 134 TYR cc_start: 0.8185 (t80) cc_final: 0.7830 (t80) REVERT: C 155 ILE cc_start: 0.7959 (mt) cc_final: 0.7485 (pt) REVERT: C 211 MET cc_start: 0.6865 (ttp) cc_final: 0.6592 (ttm) outliers start: 28 outliers final: 24 residues processed: 164 average time/residue: 0.1895 time to fit residues: 39.2276 Evaluate side-chains 170 residues out of total 619 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 144 time to evaluate : 0.615 ------------------------------------------------------------------------------- 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 117 ASN Chi-restraints excluded: chain E residue 119 PHE Chi-restraints excluded: chain E residue 127 TYR 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 233 ASN Chi-restraints excluded: chain B residue 60 THR Chi-restraints excluded: chain B residue 88 ASP 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 175 MET Chi-restraints excluded: chain B residue 177 VAL Chi-restraints excluded: chain B residue 228 SER Chi-restraints excluded: chain C residue 50 ASP Chi-restraints excluded: chain C residue 88 GLN Chi-restraints excluded: chain C residue 127 THR 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 A residue 113 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 70 random chunks: chunk 15 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 23 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 7 optimal weight: 9.9990 chunk 10 optimal weight: 9.9990 chunk 48 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 63 optimal weight: 0.0980 chunk 37 optimal weight: 0.9980 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 212 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 247 GLN ** E 271 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 109 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 111 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 119 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 195 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 233 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4353 r_free = 0.4353 target = 0.213194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.143722 restraints weight = 7165.133| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3702 r_free = 0.3702 target = 0.148555 restraints weight = 4468.890| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.151990 restraints weight = 3174.804| |-----------------------------------------------------------------------------| r_work (final): 0.3768 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6984 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.058 5678 Z= 0.303 Angle : 0.639 7.283 7727 Z= 0.331 Chirality : 0.047 0.197 851 Planarity : 0.004 0.035 994 Dihedral : 4.890 40.224 776 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 15.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer: Outliers : 4.68 % Allowed : 24.56 % Favored : 70.76 % 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: -0.66 (0.30), residues: 699 helix: -0.65 (0.82), residues: 41 sheet: 0.44 (0.42), residues: 159 loop : -0.74 (0.26), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP B 78 HIS 0.007 0.001 HIS B 109 PHE 0.035 0.002 PHE C 68 TYR 0.034 0.002 TYR C 194 ARG 0.006 0.001 ARG B 62 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1812.66 seconds wall clock time: 33 minutes 16.00 seconds (1996.00 seconds total)