Starting phenix.real_space_refine on Sun Mar 10 22:37:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vad_31837/03_2024/7vad_31837.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vad_31837/03_2024/7vad_31837.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.41 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vad_31837/03_2024/7vad_31837.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vad_31837/03_2024/7vad_31837.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vad_31837/03_2024/7vad_31837.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7vad_31837/03_2024/7vad_31837.pdb" } resolution = 3.41 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 43 5.16 5 C 3676 2.51 5 N 912 2.21 5 O 1066 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 128": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 156": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 10": "OE1" <-> "OE2" Residue "H TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 17": "OE1" <-> "OE2" Residue "L TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 5697 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 2344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 306, 2344 Classifications: {'peptide': 306} Link IDs: {'PTRANS': 17, 'TRANS': 288} Chain: "H" Number of atoms: 1669 Number of conformers: 1 Conformer: "" Number of residues, atoms: 221, 1669 Classifications: {'peptide': 221} Link IDs: {'PTRANS': 15, 'TRANS': 205} Chain: "L" Number of atoms: 1684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1684 Classifications: {'peptide': 216} Link IDs: {'PTRANS': 9, 'TRANS': 206} Time building chain proxies: 3.70, per 1000 atoms: 0.65 Number of scatterers: 5697 At special positions: 0 Unit cell: (87.15, 70.965, 143.175, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 43 16.00 O 1066 8.00 N 912 7.00 C 3676 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 203 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 94 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.22 Conformation dependent library (CDL) restraints added in 1.1 seconds 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1376 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 11 sheets defined 37.4% alpha, 20.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.63 Creating SS restraints... Processing helix chain 'A' and resid 15 through 20 Processing helix chain 'A' and resid 21 through 44 Processing helix chain 'A' and resid 47 through 57 removed outlier: 3.870A pdb=" N ILE A 51 " --> pdb=" O GLU A 47 " (cutoff:3.500A) Processing helix chain 'A' and resid 58 through 70 Processing helix chain 'A' and resid 71 through 83 Processing helix chain 'A' and resid 86 through 99 Processing helix chain 'A' and resid 102 through 113 removed outlier: 4.080A pdb=" N ASN A 106 " --> pdb=" O GLY A 102 " (cutoff:3.500A) removed outlier: 3.608A pdb=" N VAL A 107 " --> pdb=" O ASN A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 115 through 142 Proline residue: A 135 - end of helix Processing helix chain 'A' and resid 156 through 180 Proline residue: A 169 - end of helix Processing helix chain 'A' and resid 183 through 211 removed outlier: 3.569A pdb=" N VAL A 187 " --> pdb=" O TYR A 183 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA A 207 " --> pdb=" O THR A 203 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N ILE A 208 " --> pdb=" O VAL A 204 " (cutoff:3.500A) removed outlier: 3.875A pdb=" N GLY A 211 " --> pdb=" O ALA A 207 " (cutoff:3.500A) Processing helix chain 'A' and resid 214 through 218 removed outlier: 3.856A pdb=" N MET A 218 " --> pdb=" O MET A 215 " (cutoff:3.500A) Processing helix chain 'A' and resid 219 through 244 Proline residue: A 230 - end of helix Processing helix chain 'A' and resid 247 through 260 removed outlier: 3.550A pdb=" N ARG A 252 " --> pdb=" O GLY A 248 " (cutoff:3.500A) removed outlier: 4.770A pdb=" N THR A 253 " --> pdb=" O ARG A 249 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N VAL A 254 " --> pdb=" O CYS A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 263 through 274 Processing helix chain 'A' and resid 280 through 283 removed outlier: 3.588A pdb=" N PHE A 283 " --> pdb=" O GLY A 280 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 280 through 283' Processing helix chain 'A' and resid 284 through 308 removed outlier: 3.663A pdb=" N ILE A 291 " --> pdb=" O LEU A 287 " (cutoff:3.500A) Processing helix chain 'H' and resid 28 through 32 removed outlier: 3.828A pdb=" N TYR H 32 " --> pdb=" O PHE H 29 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.937A pdb=" N SER H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'L' and resid 126 through 132 removed outlier: 3.621A pdb=" N LEU L 130 " --> pdb=" O SER L 126 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N THR L 131 " --> pdb=" O SER L 127 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.555A pdb=" N ILE H 34 " --> pdb=" O TYR H 50 " (cutoff:3.500A) removed outlier: 4.426A pdb=" N TYR H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.813A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 10 through 12 removed outlier: 3.795A pdb=" N TYR H 110 " --> pdb=" O ARG H 98 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 128 through 131 Processing sheet with id=AA5, first strand: chain 'H' and resid 143 through 146 removed outlier: 6.713A pdb=" N THR H 184 " --> pdb=" O ALA H 176 " (cutoff:3.500A) removed outlier: 4.567A pdb=" N ALA H 176 " --> pdb=" O THR H 184 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N SER H 186 " --> pdb=" O PHE H 174 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 159 through 161 removed outlier: 3.932A pdb=" N CYS H 203 " --> pdb=" O LYS H 216 " (cutoff:3.500A) removed outlier: 4.300A pdb=" N LYS H 216 " --> pdb=" O CYS H 203 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'L' and resid 10 through 12 removed outlier: 6.848A pdb=" N LEU L 11 " --> pdb=" O GLU L 110 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'L' and resid 40 through 43 removed outlier: 6.598A pdb=" N TRP L 41 " --> pdb=" O LEU L 53 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 69 through 73 Processing sheet with id=AB1, first strand: chain 'L' and resid 119 through 123 removed outlier: 3.854A pdb=" N ASN L 143 " --> pdb=" O TYR L 178 " (cutoff:3.500A) removed outlier: 6.253A pdb=" N TYR L 178 " --> pdb=" O ASN L 143 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 158 through 159 281 hydrogen bonds defined for protein. 762 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: 1.63 Time building geometry restraints manager: 2.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1733 1.34 - 1.46: 1408 1.46 - 1.58: 2629 1.58 - 1.70: 0 1.70 - 1.82: 65 Bond restraints: 5835 Sorted by residual: bond pdb=" CB PRO H 126 " pdb=" CG PRO H 126 " ideal model delta sigma weight residual 1.492 1.577 -0.085 5.00e-02 4.00e+02 2.88e+00 bond pdb=" C LYS H 13 " pdb=" N PRO H 14 " ideal model delta sigma weight residual 1.337 1.346 -0.009 9.80e-03 1.04e+04 8.60e-01 bond pdb=" CB PRO A 276 " pdb=" CG PRO A 276 " ideal model delta sigma weight residual 1.492 1.536 -0.044 5.00e-02 4.00e+02 7.80e-01 bond pdb=" C SER L 7 " pdb=" N PRO L 8 " ideal model delta sigma weight residual 1.334 1.353 -0.019 2.34e-02 1.83e+03 6.58e-01 bond pdb=" CG PRO H 126 " pdb=" CD PRO H 126 " ideal model delta sigma weight residual 1.503 1.530 -0.027 3.40e-02 8.65e+02 6.31e-01 ... (remaining 5830 not shown) Histogram of bond angle deviations from ideal: 99.09 - 106.09: 169 106.09 - 113.08: 3194 113.08 - 120.07: 1938 120.07 - 127.06: 2558 127.06 - 134.06: 70 Bond angle restraints: 7929 Sorted by residual: angle pdb=" C ALA H 16 " pdb=" CA ALA H 16 " pdb=" CB ALA H 16 " ideal model delta sigma weight residual 115.89 110.41 5.48 1.32e+00 5.74e-01 1.73e+01 angle pdb=" CA PRO H 126 " pdb=" N PRO H 126 " pdb=" CD PRO H 126 " ideal model delta sigma weight residual 112.00 106.55 5.45 1.40e+00 5.10e-01 1.52e+01 angle pdb=" N LEU A 150 " pdb=" CA LEU A 150 " pdb=" CB LEU A 150 " ideal model delta sigma weight residual 113.65 109.57 4.08 1.47e+00 4.63e-01 7.71e+00 angle pdb=" CB MET A 133 " pdb=" CG MET A 133 " pdb=" SD MET A 133 " ideal model delta sigma weight residual 112.70 120.57 -7.87 3.00e+00 1.11e-01 6.89e+00 angle pdb=" N GLY A 132 " pdb=" CA GLY A 132 " pdb=" C GLY A 132 " ideal model delta sigma weight residual 112.77 115.95 -3.18 1.28e+00 6.10e-01 6.19e+00 ... (remaining 7924 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.79: 3022 13.79 - 27.58: 318 27.58 - 41.37: 116 41.37 - 55.16: 23 55.16 - 68.95: 2 Dihedral angle restraints: 3481 sinusoidal: 1329 harmonic: 2152 Sorted by residual: dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 94 " pdb=" CB CYS L 94 " ideal model delta sinusoidal sigma weight residual 93.00 161.95 -68.95 1 1.00e+01 1.00e-02 6.15e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 96 " pdb=" CB CYS H 96 " ideal model delta sinusoidal sigma weight residual 93.00 65.54 27.46 1 1.00e+01 1.00e-02 1.08e+01 dihedral pdb=" CA GLU A 277 " pdb=" CB GLU A 277 " pdb=" CG GLU A 277 " pdb=" CD GLU A 277 " ideal model delta sinusoidal sigma weight residual -60.00 -114.46 54.46 3 1.50e+01 4.44e-03 9.28e+00 ... (remaining 3478 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 555 0.029 - 0.059: 241 0.059 - 0.088: 71 0.088 - 0.117: 45 0.117 - 0.147: 6 Chirality restraints: 918 Sorted by residual: chirality pdb=" CA ILE H 104 " pdb=" N ILE H 104 " pdb=" C ILE H 104 " pdb=" CB ILE H 104 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.38e-01 chirality pdb=" CA MET A 133 " pdb=" N MET A 133 " pdb=" C MET A 133 " pdb=" CB MET A 133 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.40e-01 chirality pdb=" CB VAL L 19 " pdb=" CA VAL L 19 " pdb=" CG1 VAL L 19 " pdb=" CG2 VAL L 19 " both_signs ideal model delta sigma weight residual False -2.63 -2.76 0.13 2.00e-01 2.50e+01 4.04e-01 ... (remaining 915 not shown) Planarity restraints: 980 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR H 125 " 0.086 5.00e-02 4.00e+02 1.29e-01 2.64e+01 pdb=" N PRO H 126 " -0.222 5.00e-02 4.00e+02 pdb=" CA PRO H 126 " 0.069 5.00e-02 4.00e+02 pdb=" CD PRO H 126 " 0.067 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 275 " 0.030 5.00e-02 4.00e+02 4.49e-02 3.23e+00 pdb=" N PRO A 276 " -0.078 5.00e-02 4.00e+02 pdb=" CA PRO A 276 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 276 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA MET A 290 " 0.007 2.00e-02 2.50e+03 1.38e-02 1.90e+00 pdb=" C MET A 290 " -0.024 2.00e-02 2.50e+03 pdb=" O MET A 290 " 0.009 2.00e-02 2.50e+03 pdb=" N ILE A 291 " 0.008 2.00e-02 2.50e+03 ... (remaining 977 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 856 2.76 - 3.30: 5560 3.30 - 3.83: 9163 3.83 - 4.37: 10150 4.37 - 4.90: 17934 Nonbonded interactions: 43663 Sorted by model distance: nonbonded pdb=" OE1 GLN L 6 " pdb=" OG1 THR L 107 " model vdw 2.227 2.440 nonbonded pdb=" OG1 THR L 69 " pdb=" OG1 THR L 80 " model vdw 2.253 2.440 nonbonded pdb=" OG SER A 105 " pdb=" OE1 GLU A 257 " model vdw 2.275 2.440 nonbonded pdb=" OG1 THR H 28 " pdb=" OG SER H 31 " model vdw 2.287 2.440 nonbonded pdb=" OD1 ASP H 102 " pdb=" N GLY H 103 " model vdw 2.302 2.520 ... (remaining 43658 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 2.060 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 19.910 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: 0.010 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: 25.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7569 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 : 0.002 0.085 5835 Z= 0.147 Angle : 0.592 7.872 7929 Z= 0.294 Chirality : 0.040 0.147 918 Planarity : 0.006 0.129 980 Dihedral : 13.009 60.281 2096 Min Nonbonded Distance : 2.227 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 0.00 % Allowed : 0.46 % Favored : 99.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.31), residues: 737 helix: 1.37 (0.33), residues: 236 sheet: 0.80 (0.41), residues: 168 loop : -0.92 (0.34), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 111 HIS 0.004 0.001 HIS L 194 PHE 0.017 0.001 PHE A 244 TYR 0.007 0.001 TYR A 69 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 284 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 284 time to evaluate : 0.639 Fit side-chains revert: symmetry clash REVERT: A 40 LEU cc_start: 0.8328 (tp) cc_final: 0.8022 (tp) REVERT: A 153 LYS cc_start: 0.8373 (mttm) cc_final: 0.8132 (ttmm) REVERT: A 251 ARG cc_start: 0.7777 (ptp90) cc_final: 0.7564 (ptp90) REVERT: L 162 ASN cc_start: 0.7902 (t0) cc_final: 0.7676 (m-40) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.1410 time to fit residues: 53.6840 Evaluate side-chains 235 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 235 time to evaluate : 0.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 61 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 18 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 42 optimal weight: 20.0000 chunk 66 optimal weight: 1.9990 overall best weight: 1.1782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN L 37 ASN L 44 GLN L 129 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7855 moved from start: 0.2600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5835 Z= 0.264 Angle : 0.673 10.379 7929 Z= 0.328 Chirality : 0.044 0.163 918 Planarity : 0.005 0.082 980 Dihedral : 3.895 15.873 794 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 4.33 % Allowed : 18.42 % Favored : 77.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.31), residues: 737 helix: 1.84 (0.33), residues: 243 sheet: 0.72 (0.40), residues: 180 loop : -0.98 (0.34), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 56 HIS 0.006 0.001 HIS L 194 PHE 0.015 0.002 PHE A 231 TYR 0.018 0.002 TYR A 289 ARG 0.005 0.001 ARG L 67 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 242 time to evaluate : 0.658 Fit side-chains revert: symmetry clash REVERT: A 251 ARG cc_start: 0.7953 (ptp90) cc_final: 0.7725 (ttp-110) REVERT: H 100 TYR cc_start: 0.8505 (t80) cc_final: 0.8250 (t80) REVERT: L 44 GLN cc_start: 0.8766 (OUTLIER) cc_final: 0.8325 (tt0) REVERT: L 123 PHE cc_start: 0.8494 (m-80) cc_final: 0.8268 (m-80) REVERT: L 162 ASN cc_start: 0.8050 (t0) cc_final: 0.7847 (t0) outliers start: 28 outliers final: 22 residues processed: 254 average time/residue: 0.1402 time to fit residues: 47.7505 Evaluate side-chains 253 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 230 time to evaluate : 0.625 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 82 VAL Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 241 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 294 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 56 ASP Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 36 optimal weight: 3.9990 chunk 20 optimal weight: 0.0770 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 18 optimal weight: 4.9990 chunk 66 optimal weight: 0.5980 chunk 71 optimal weight: 7.9990 chunk 59 optimal weight: 2.9990 chunk 65 optimal weight: 4.9990 chunk 22 optimal weight: 0.5980 chunk 53 optimal weight: 0.9990 overall best weight: 1.0542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 172 HIS ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 129 GLN L 143 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.3143 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 5835 Z= 0.233 Angle : 0.636 9.915 7929 Z= 0.309 Chirality : 0.042 0.158 918 Planarity : 0.005 0.065 980 Dihedral : 4.003 15.916 794 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 13.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.06 % Favored : 92.94 % Rotamer: Outliers : 5.26 % Allowed : 23.22 % Favored : 71.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.31), residues: 737 helix: 1.84 (0.33), residues: 250 sheet: 0.75 (0.40), residues: 180 loop : -1.07 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 305 HIS 0.008 0.001 HIS L 194 PHE 0.021 0.002 PHE A 231 TYR 0.014 0.002 TYR A 289 ARG 0.010 0.001 ARG L 35 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 275 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 241 time to evaluate : 0.699 Fit side-chains revert: symmetry clash REVERT: H 100 TYR cc_start: 0.8603 (t80) cc_final: 0.8336 (t80) REVERT: H 130 TYR cc_start: 0.7981 (m-80) cc_final: 0.7709 (m-80) REVERT: H 159 THR cc_start: 0.9034 (OUTLIER) cc_final: 0.8708 (p) REVERT: L 44 GLN cc_start: 0.8834 (OUTLIER) cc_final: 0.8492 (tt0) REVERT: L 144 PHE cc_start: 0.8140 (p90) cc_final: 0.7920 (p90) outliers start: 34 outliers final: 28 residues processed: 255 average time/residue: 0.1347 time to fit residues: 46.7596 Evaluate side-chains 263 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 233 time to evaluate : 0.598 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 130 LEU Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 2.9990 chunk 49 optimal weight: 0.3980 chunk 34 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 0.4980 chunk 70 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 58 optimal weight: 0.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 129 GLN L 194 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7978 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 5835 Z= 0.255 Angle : 0.655 9.366 7929 Z= 0.321 Chirality : 0.043 0.152 918 Planarity : 0.005 0.057 980 Dihedral : 4.189 16.378 794 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.19 % Allowed : 24.61 % Favored : 69.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.54 (0.31), residues: 737 helix: 1.83 (0.33), residues: 252 sheet: 0.65 (0.40), residues: 180 loop : -1.10 (0.35), residues: 305 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 305 HIS 0.002 0.001 HIS L 194 PHE 0.021 0.002 PHE A 108 TYR 0.020 0.002 TYR H 54 ARG 0.008 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 286 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 246 time to evaluate : 0.663 Fit side-chains revert: symmetry clash REVERT: H 62 GLU cc_start: 0.7166 (pp20) cc_final: 0.6875 (pp20) REVERT: H 100 TYR cc_start: 0.8625 (t80) cc_final: 0.8363 (t80) REVERT: H 130 TYR cc_start: 0.7900 (m-80) cc_final: 0.7528 (m-80) REVERT: H 159 THR cc_start: 0.9157 (OUTLIER) cc_final: 0.8861 (p) REVERT: L 44 GLN cc_start: 0.8949 (OUTLIER) cc_final: 0.8697 (tt0) outliers start: 40 outliers final: 28 residues processed: 263 average time/residue: 0.1421 time to fit residues: 51.4322 Evaluate side-chains 269 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 239 time to evaluate : 0.671 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 187 VAL Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 34 THR Chi-restraints excluded: chain L residue 44 GLN Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 40 optimal weight: 1.9990 chunk 1 optimal weight: 0.4980 chunk 52 optimal weight: 0.0060 chunk 29 optimal weight: 6.9990 chunk 60 optimal weight: 3.9990 chunk 48 optimal weight: 6.9990 chunk 0 optimal weight: 3.9990 chunk 36 optimal weight: 0.2980 chunk 63 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 overall best weight: 0.7598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 129 GLN L 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.3846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 5835 Z= 0.197 Angle : 0.646 9.005 7929 Z= 0.312 Chirality : 0.043 0.160 918 Planarity : 0.004 0.052 980 Dihedral : 4.125 16.663 794 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 12.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 5.88 % Allowed : 26.01 % Favored : 68.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.58 (0.32), residues: 737 helix: 1.90 (0.33), residues: 251 sheet: 0.63 (0.40), residues: 179 loop : -1.08 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.003 0.001 HIS L 194 PHE 0.016 0.001 PHE A 231 TYR 0.018 0.001 TYR L 98 ARG 0.006 0.001 ARG L 160 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 292 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 254 time to evaluate : 0.692 Fit side-chains revert: symmetry clash REVERT: A 251 ARG cc_start: 0.8074 (ttm110) cc_final: 0.7677 (ttp-110) REVERT: H 62 GLU cc_start: 0.7107 (pp20) cc_final: 0.6862 (pp20) REVERT: H 100 TYR cc_start: 0.8608 (t80) cc_final: 0.8348 (t80) REVERT: H 130 TYR cc_start: 0.7845 (m-80) cc_final: 0.7521 (m-80) REVERT: L 123 PHE cc_start: 0.8809 (m-80) cc_final: 0.8588 (m-80) outliers start: 38 outliers final: 31 residues processed: 269 average time/residue: 0.1319 time to fit residues: 48.5847 Evaluate side-chains 278 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 247 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 205 LEU Chi-restraints excluded: chain A residue 258 THR Chi-restraints excluded: chain A residue 278 VAL Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 137 VAL Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 63 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 41 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 32 optimal weight: 0.8980 chunk 5 optimal weight: 0.7980 chunk 23 optimal weight: 3.9990 chunk 37 optimal weight: 0.8980 chunk 68 optimal weight: 1.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 44 GLN L 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7983 moved from start: 0.4067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5835 Z= 0.215 Angle : 0.673 8.883 7929 Z= 0.324 Chirality : 0.043 0.157 918 Planarity : 0.004 0.051 980 Dihedral : 4.169 16.386 794 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.19 % Favored : 92.81 % Rotamer: Outliers : 6.66 % Allowed : 27.71 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.59 (0.32), residues: 737 helix: 1.96 (0.33), residues: 251 sheet: 0.59 (0.40), residues: 179 loop : -1.09 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 56 HIS 0.003 0.001 HIS L 194 PHE 0.016 0.001 PHE A 231 TYR 0.018 0.002 TYR L 98 ARG 0.005 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 246 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 251 ARG cc_start: 0.8136 (ttm110) cc_final: 0.7438 (ttp-110) REVERT: H 62 GLU cc_start: 0.7133 (pp20) cc_final: 0.6907 (pp20) REVERT: H 100 TYR cc_start: 0.8629 (t80) cc_final: 0.8361 (t80) REVERT: H 130 TYR cc_start: 0.7937 (m-80) cc_final: 0.7596 (m-80) REVERT: L 123 PHE cc_start: 0.8845 (m-80) cc_final: 0.8505 (m-80) REVERT: L 160 ARG cc_start: 0.8164 (ptm-80) cc_final: 0.7939 (ptm-80) outliers start: 43 outliers final: 39 residues processed: 260 average time/residue: 0.1334 time to fit residues: 47.3588 Evaluate side-chains 281 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 242 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 31 LEU Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 7 optimal weight: 2.9990 chunk 40 optimal weight: 0.6980 chunk 51 optimal weight: 3.9990 chunk 39 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 70 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 32 optimal weight: 0.6980 chunk 43 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.0382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 87 ASN A 106 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 129 GLN L 194 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8017 moved from start: 0.4373 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 5835 Z= 0.240 Angle : 0.675 8.757 7929 Z= 0.328 Chirality : 0.043 0.157 918 Planarity : 0.004 0.050 980 Dihedral : 4.328 18.220 794 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.46 % Favored : 92.54 % Rotamer: Outliers : 7.28 % Allowed : 27.24 % Favored : 65.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.31), residues: 737 helix: 1.89 (0.33), residues: 245 sheet: 0.49 (0.39), residues: 182 loop : -1.14 (0.34), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP L 56 HIS 0.003 0.001 HIS L 194 PHE 0.017 0.001 PHE A 231 TYR 0.020 0.002 TYR L 98 ARG 0.007 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 289 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 242 time to evaluate : 0.647 Fit side-chains revert: symmetry clash REVERT: A 133 MET cc_start: 0.7486 (ppp) cc_final: 0.7188 (ppp) REVERT: A 251 ARG cc_start: 0.8009 (ttm110) cc_final: 0.7329 (ttp-110) REVERT: A 256 MET cc_start: 0.6649 (mtm) cc_final: 0.6369 (mtp) REVERT: H 89 GLU cc_start: 0.8337 (pp20) cc_final: 0.7932 (pp20) REVERT: H 159 THR cc_start: 0.9161 (OUTLIER) cc_final: 0.8921 (p) REVERT: L 4 MET cc_start: 0.8734 (mmm) cc_final: 0.7167 (mmm) REVERT: L 123 PHE cc_start: 0.8814 (m-80) cc_final: 0.8360 (m-80) outliers start: 47 outliers final: 42 residues processed: 264 average time/residue: 0.1345 time to fit residues: 48.4467 Evaluate side-chains 281 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 238 time to evaluate : 0.692 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 37 PHE Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 129 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 167 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 187 SER Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 201 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 19 VAL Chi-restraints excluded: chain L residue 58 SER Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 42 optimal weight: 10.0000 chunk 21 optimal weight: 0.1980 chunk 13 optimal weight: 0.9980 chunk 44 optimal weight: 3.9990 chunk 47 optimal weight: 0.8980 chunk 34 optimal weight: 0.3980 chunk 6 optimal weight: 0.2980 chunk 55 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 67 optimal weight: 0.0060 chunk 61 optimal weight: 0.9980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN A 247 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 39 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7968 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5835 Z= 0.176 Angle : 0.686 9.025 7929 Z= 0.326 Chirality : 0.043 0.151 918 Planarity : 0.004 0.049 980 Dihedral : 4.275 18.795 794 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 5.57 % Allowed : 29.10 % Favored : 65.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.31), residues: 737 helix: 1.84 (0.33), residues: 249 sheet: 0.50 (0.40), residues: 178 loop : -1.19 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 305 HIS 0.003 0.001 HIS L 194 PHE 0.016 0.001 PHE A 108 TYR 0.020 0.001 TYR L 98 ARG 0.009 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 279 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 243 time to evaluate : 0.650 Fit side-chains revert: symmetry clash REVERT: A 21 ARG cc_start: 0.8048 (ttp-110) cc_final: 0.7333 (mtp180) REVERT: A 241 SER cc_start: 0.8483 (p) cc_final: 0.8172 (t) REVERT: H 130 TYR cc_start: 0.8080 (m-80) cc_final: 0.7637 (m-80) REVERT: H 159 THR cc_start: 0.9138 (OUTLIER) cc_final: 0.8911 (p) REVERT: L 4 MET cc_start: 0.8771 (mmm) cc_final: 0.7166 (mmm) REVERT: L 123 PHE cc_start: 0.8807 (m-80) cc_final: 0.8309 (m-80) outliers start: 36 outliers final: 30 residues processed: 259 average time/residue: 0.1306 time to fit residues: 46.2921 Evaluate side-chains 271 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 240 time to evaluate : 0.659 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 117 ASN Chi-restraints excluded: chain A residue 125 CYS Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 145 ILE Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 267 SER Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain H residue 212 THR Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 65 optimal weight: 2.9990 chunk 67 optimal weight: 8.9990 chunk 39 optimal weight: 2.9990 chunk 28 optimal weight: 0.5980 chunk 51 optimal weight: 10.0000 chunk 20 optimal weight: 6.9990 chunk 59 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 69 optimal weight: 4.9990 chunk 42 optimal weight: 5.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN A 247 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS ** L 203 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.5165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 5835 Z= 0.443 Angle : 0.814 8.625 7929 Z= 0.404 Chirality : 0.048 0.176 918 Planarity : 0.005 0.049 980 Dihedral : 4.926 19.270 794 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.41 % Favored : 91.59 % Rotamer: Outliers : 6.81 % Allowed : 28.17 % Favored : 65.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.31), residues: 737 helix: 1.55 (0.33), residues: 245 sheet: 0.18 (0.39), residues: 172 loop : -1.46 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 56 HIS 0.004 0.001 HIS L 194 PHE 0.023 0.002 PHE A 108 TYR 0.020 0.003 TYR L 98 ARG 0.009 0.001 ARG A 21 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 297 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 253 time to evaluate : 0.670 Fit side-chains revert: symmetry clash REVERT: A 59 LYS cc_start: 0.7543 (tttt) cc_final: 0.7283 (mttm) REVERT: A 184 MET cc_start: 0.7518 (pmm) cc_final: 0.6646 (pmm) REVERT: A 271 ASN cc_start: 0.8546 (m110) cc_final: 0.8324 (m110) REVERT: H 89 GLU cc_start: 0.8486 (pp20) cc_final: 0.8191 (pp20) REVERT: L 4 MET cc_start: 0.8629 (mmm) cc_final: 0.7368 (mmm) REVERT: L 55 TYR cc_start: 0.9047 (p90) cc_final: 0.8841 (p90) REVERT: L 121 SER cc_start: 0.8550 (t) cc_final: 0.7877 (t) REVERT: L 123 PHE cc_start: 0.8845 (m-80) cc_final: 0.8390 (m-80) REVERT: L 172 ASP cc_start: 0.8294 (p0) cc_final: 0.7386 (p0) outliers start: 44 outliers final: 35 residues processed: 269 average time/residue: 0.1428 time to fit residues: 51.7801 Evaluate side-chains 278 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 243 time to evaluate : 0.607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 13 THR Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 46 MET Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 115 ASP Chi-restraints excluded: chain A residue 123 THR Chi-restraints excluded: chain A residue 127 THR Chi-restraints excluded: chain A residue 136 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 165 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 5 THR Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 211 VAL Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 32 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 72 optimal weight: 7.9990 chunk 66 optimal weight: 0.8980 chunk 57 optimal weight: 0.9980 chunk 6 optimal weight: 0.8980 chunk 44 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 61 optimal weight: 0.9980 chunk 17 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN A 247 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 6 GLN ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8075 moved from start: 0.5161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5835 Z= 0.241 Angle : 0.755 8.937 7929 Z= 0.367 Chirality : 0.045 0.167 918 Planarity : 0.004 0.050 980 Dihedral : 4.687 18.304 794 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 14.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.33 % Favored : 92.67 % Rotamer: Outliers : 5.42 % Allowed : 29.88 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.31), residues: 737 helix: 1.58 (0.33), residues: 249 sheet: 0.18 (0.39), residues: 174 loop : -1.40 (0.33), residues: 314 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 305 HIS 0.003 0.001 HIS H 35 PHE 0.016 0.001 PHE A 108 TYR 0.026 0.002 TYR H 54 ARG 0.009 0.001 ARG A 21 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1474 Ramachandran restraints generated. 737 Oldfield, 0 Emsley, 737 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 276 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 241 time to evaluate : 0.588 Fit side-chains REVERT: A 21 ARG cc_start: 0.7904 (ttm110) cc_final: 0.7703 (mtm-85) REVERT: A 271 ASN cc_start: 0.8379 (m110) cc_final: 0.8163 (m110) REVERT: H 89 GLU cc_start: 0.8405 (pp20) cc_final: 0.8105 (pp20) REVERT: H 159 THR cc_start: 0.9256 (OUTLIER) cc_final: 0.9017 (p) REVERT: L 4 MET cc_start: 0.8568 (mmm) cc_final: 0.7292 (mmm) REVERT: L 55 TYR cc_start: 0.9017 (p90) cc_final: 0.8767 (p90) REVERT: L 123 PHE cc_start: 0.8796 (m-80) cc_final: 0.8402 (m-80) REVERT: L 160 ARG cc_start: 0.8393 (ptm-80) cc_final: 0.8100 (ptm-80) REVERT: L 170 ASP cc_start: 0.7939 (t0) cc_final: 0.7406 (t0) REVERT: L 172 ASP cc_start: 0.8187 (p0) cc_final: 0.7272 (p0) outliers start: 35 outliers final: 28 residues processed: 256 average time/residue: 0.1389 time to fit residues: 48.5409 Evaluate side-chains 266 residues out of total 646 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 237 time to evaluate : 0.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 33 PHE Chi-restraints excluded: chain A residue 38 ILE Chi-restraints excluded: chain A residue 42 LEU Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 61 LEU Chi-restraints excluded: chain A residue 137 LEU Chi-restraints excluded: chain A residue 171 THR Chi-restraints excluded: chain A residue 176 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 246 LEU Chi-restraints excluded: chain A residue 253 THR Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 301 ILE Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 125 THR Chi-restraints excluded: chain H residue 144 VAL Chi-restraints excluded: chain H residue 159 THR Chi-restraints excluded: chain H residue 191 VAL Chi-restraints excluded: chain H residue 205 VAL Chi-restraints excluded: chain L residue 3 VAL Chi-restraints excluded: chain L residue 64 VAL Chi-restraints excluded: chain L residue 66 ASP Chi-restraints excluded: chain L residue 136 SER Chi-restraints excluded: chain L residue 141 LEU Chi-restraints excluded: chain L residue 186 LEU Chi-restraints excluded: chain L residue 211 VAL Chi-restraints excluded: chain L residue 214 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 73 random chunks: chunk 53 optimal weight: 0.8980 chunk 8 optimal weight: 0.5980 chunk 16 optimal weight: 0.0970 chunk 58 optimal weight: 0.0370 chunk 24 optimal weight: 4.9990 chunk 59 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 50 optimal weight: 0.0170 chunk 3 optimal weight: 0.9980 chunk 41 optimal weight: 0.7980 overall best weight: 0.2894 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN A 87 ASN A 106 ASN A 247 ASN ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 37 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 194 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3808 r_free = 0.3808 target = 0.142024 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3434 r_free = 0.3434 target = 0.115421 restraints weight = 10759.451| |-----------------------------------------------------------------------------| r_work (start): 0.3393 rms_B_bonded: 3.47 r_work: 0.3259 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.4980 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5835 Z= 0.177 Angle : 0.729 8.593 7929 Z= 0.347 Chirality : 0.044 0.168 918 Planarity : 0.004 0.051 980 Dihedral : 4.429 17.501 794 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 12.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.87 % Favored : 92.13 % Rotamer: Outliers : 4.33 % Allowed : 30.80 % Favored : 64.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.31), residues: 737 helix: 1.65 (0.33), residues: 244 sheet: 0.35 (0.41), residues: 167 loop : -1.37 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP H 36 HIS 0.003 0.001 HIS H 35 PHE 0.014 0.001 PHE H 154 TYR 0.022 0.002 TYR L 98 ARG 0.008 0.001 ARG A 21 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1822.69 seconds wall clock time: 33 minutes 36.70 seconds (2016.70 seconds total)