Starting phenix.real_space_refine on Fri Aug 2 22:26:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/08_2024/8u4r_41892.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/08_2024/8u4r_41892.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/08_2024/8u4r_41892.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/08_2024/8u4r_41892.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/08_2024/8u4r_41892.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u4r_41892/08_2024/8u4r_41892.cif" } resolution = 3.1 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= 0.049 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 2008 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: 4 Type Number sf(0) Gaussians S 23 5.16 5 C 2680 2.51 5 N 676 2.21 5 O 728 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 121": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4107 Number of models: 1 Model: "" Number of chains: 4 Chain: "L" Number of atoms: 864 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 864 Classifications: {'peptide': 111} Link IDs: {'PCIS': 2, 'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 976 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 976 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 2, 'TRANS': 122} Chain: "R" Number of atoms: 2239 Number of conformers: 1 Conformer: "" Number of residues, atoms: 277, 2239 Classifications: {'peptide': 277} Link IDs: {'PTRANS': 10, 'TRANS': 266} Chain breaks: 2 Chain: "R" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 28 Unusual residues: {'CLR': 1} Classifications: {'undetermined': 1} Time building chain proxies: 3.26, per 1000 atoms: 0.79 Number of scatterers: 4107 At special positions: 0 Unit cell: (55.25, 65.45, 110.5, 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 23 16.00 O 728 8.00 N 676 7.00 C 2680 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 93 " distance=2.04 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS R 28 " - pdb=" SG CYS R 274 " distance=2.03 Simple disulfide: pdb=" SG CYS R 109 " - pdb=" SG CYS R 186 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 690.0 milliseconds 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 954 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 7 sheets defined 46.0% alpha, 26.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'H' and resid 28 through 30 No H-bonds generated for 'chain 'H' and resid 28 through 30' Processing helix chain 'H' and resid 87 through 91 removed outlier: 3.539A pdb=" N THR H 91 " --> pdb=" O SER H 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 36 through 65 Proline residue: R 42 - end of helix Processing helix chain 'R' and resid 71 through 100 removed outlier: 3.709A pdb=" N LYS R 75 " --> pdb=" O SER R 71 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LEU R 86 " --> pdb=" O VAL R 82 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N PHE R 87 " --> pdb=" O ALA R 83 " (cutoff:3.500A) Proline residue: R 92 - end of helix Processing helix chain 'R' and resid 106 through 140 removed outlier: 4.133A pdb=" N SER R 123 " --> pdb=" O SER R 119 " (cutoff:3.500A) removed outlier: 4.608A pdb=" N VAL R 124 " --> pdb=" O LEU R 120 " (cutoff:3.500A) removed outlier: 4.182A pdb=" N LEU R 125 " --> pdb=" O TYR R 121 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N ILE R 126 " --> pdb=" O SER R 122 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS R 140 " --> pdb=" O LEU R 136 " (cutoff:3.500A) Processing helix chain 'R' and resid 144 through 160 removed outlier: 3.880A pdb=" N VAL R 156 " --> pdb=" O ALA R 152 " (cutoff:3.500A) removed outlier: 4.617A pdb=" N TYR R 157 " --> pdb=" O GLU R 153 " (cutoff:3.500A) removed outlier: 3.965A pdb=" N VAL R 158 " --> pdb=" O LYS R 154 " (cutoff:3.500A) Processing helix chain 'R' and resid 160 through 167 Processing helix chain 'R' and resid 168 through 174 Processing helix chain 'R' and resid 192 through 209 removed outlier: 4.494A pdb=" N VAL R 196 " --> pdb=" O ASN R 192 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N VAL R 197 " --> pdb=" O ASP R 193 " (cutoff:3.500A) Processing helix chain 'R' and resid 209 through 226 Processing helix chain 'R' and resid 235 through 252 removed outlier: 3.819A pdb=" N THR R 240 " --> pdb=" O LYS R 236 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N TRP R 252 " --> pdb=" O PHE R 248 " (cutoff:3.500A) Processing helix chain 'R' and resid 252 through 267 Processing helix chain 'R' and resid 274 through 292 Processing helix chain 'R' and resid 293 through 295 No H-bonds generated for 'chain 'R' and resid 293 through 295' Processing helix chain 'R' and resid 296 through 304 Processing sheet with id=AA1, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.624A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 6.535A pdb=" N LEU L 38 " --> pdb=" O TYR L 54 " (cutoff:3.500A) removed outlier: 5.011A pdb=" N TYR L 54 " --> pdb=" O LEU L 38 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP L 40 " --> pdb=" O LEU L 52 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'L' and resid 10 through 12 removed outlier: 3.624A pdb=" N GLY L 89 " --> pdb=" O VAL L 109 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N THR L 102 " --> pdb=" O GLN L 95 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 3 through 6 removed outlier: 3.506A pdb=" N THR H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 12 removed outlier: 8.327A pdb=" N TYR H 32 " --> pdb=" O SER H 52 " (cutoff:3.500A) removed outlier: 6.018A pdb=" N SER H 52 " --> pdb=" O TYR H 32 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ILE H 34 " --> pdb=" O TRP H 50 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N TRP H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.543A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'H' and resid 10 through 12 removed outlier: 6.944A pdb=" N CYS H 96 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 6.969A pdb=" N VAL H 115 " --> pdb=" O CYS H 96 " (cutoff:3.500A) removed outlier: 6.213A pdb=" N ARG H 98 " --> pdb=" O MET H 113 " (cutoff:3.500A) removed outlier: 6.033A pdb=" N TYR H 111 " --> pdb=" O GLY H 100 " (cutoff:3.500A) removed outlier: 9.413A pdb=" N THR H 102 " --> pdb=" O TYR H 109 " (cutoff:3.500A) removed outlier: 10.182A pdb=" N TYR H 109 " --> pdb=" O THR H 102 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'R' and resid 175 through 180 243 hydrogen bonds defined for protein. 678 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: 1.14 Time building geometry restraints manager: 1.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1254 1.34 - 1.46: 1017 1.46 - 1.58: 1910 1.58 - 1.70: 1 1.70 - 1.82: 33 Bond restraints: 4215 Sorted by residual: bond pdb=" C6 CLR R 701 " pdb=" C7 CLR R 701 " ideal model delta sigma weight residual 1.492 1.542 -0.050 2.00e-02 2.50e+03 6.17e+00 bond pdb=" C14 CLR R 701 " pdb=" C15 CLR R 701 " ideal model delta sigma weight residual 1.523 1.565 -0.042 2.00e-02 2.50e+03 4.40e+00 bond pdb=" C13 CLR R 701 " pdb=" C14 CLR R 701 " ideal model delta sigma weight residual 1.537 1.578 -0.041 2.00e-02 2.50e+03 4.23e+00 bond pdb=" C20 CLR R 701 " pdb=" C22 CLR R 701 " ideal model delta sigma weight residual 1.535 1.575 -0.040 2.00e-02 2.50e+03 4.01e+00 bond pdb=" C15 CLR R 701 " pdb=" C16 CLR R 701 " ideal model delta sigma weight residual 1.541 1.581 -0.040 2.00e-02 2.50e+03 3.97e+00 ... (remaining 4210 not shown) Histogram of bond angle deviations from ideal: 99.15 - 106.16: 92 106.16 - 113.17: 2269 113.17 - 120.18: 1536 120.18 - 127.18: 1788 127.18 - 134.19: 52 Bond angle restraints: 5737 Sorted by residual: angle pdb=" CA TRP H 116 " pdb=" CB TRP H 116 " pdb=" CG TRP H 116 " ideal model delta sigma weight residual 113.60 119.67 -6.07 1.90e+00 2.77e-01 1.02e+01 angle pdb=" C TYR H 111 " pdb=" N GLY H 112 " pdb=" CA GLY H 112 " ideal model delta sigma weight residual 123.46 116.30 7.16 2.42e+00 1.71e-01 8.74e+00 angle pdb=" C ASP R 181 " pdb=" CA ASP R 181 " pdb=" CB ASP R 181 " ideal model delta sigma weight residual 110.42 116.07 -5.65 1.99e+00 2.53e-01 8.07e+00 angle pdb=" N LEU L 52 " pdb=" CA LEU L 52 " pdb=" C LEU L 52 " ideal model delta sigma weight residual 112.12 108.44 3.68 1.34e+00 5.57e-01 7.53e+00 angle pdb=" C GLY H 112 " pdb=" N MET H 113 " pdb=" CA MET H 113 " ideal model delta sigma weight residual 123.93 128.07 -4.14 1.54e+00 4.22e-01 7.24e+00 ... (remaining 5732 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.92: 2254 17.92 - 35.83: 205 35.83 - 53.75: 35 53.75 - 71.67: 4 71.67 - 89.58: 5 Dihedral angle restraints: 2503 sinusoidal: 1011 harmonic: 1492 Sorted by residual: dihedral pdb=" CB CYS R 28 " pdb=" SG CYS R 28 " pdb=" SG CYS R 274 " pdb=" CB CYS R 274 " ideal model delta sinusoidal sigma weight residual -86.00 -161.73 75.73 1 1.00e+01 1.00e-02 7.23e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 93 " pdb=" CB CYS L 93 " ideal model delta sinusoidal sigma weight residual 93.00 135.21 -42.21 1 1.00e+01 1.00e-02 2.49e+01 dihedral pdb=" CB GLU L 86 " pdb=" CG GLU L 86 " pdb=" CD GLU L 86 " pdb=" OE1 GLU L 86 " ideal model delta sinusoidal sigma weight residual 0.00 89.58 -89.58 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 2500 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.074: 588 0.074 - 0.148: 55 0.148 - 0.222: 3 0.222 - 0.296: 2 0.296 - 0.371: 2 Chirality restraints: 650 Sorted by residual: chirality pdb=" C17 CLR R 701 " pdb=" C13 CLR R 701 " pdb=" C16 CLR R 701 " pdb=" C20 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.55 2.92 -0.37 2.00e-01 2.50e+01 3.43e+00 chirality pdb=" C20 CLR R 701 " pdb=" C17 CLR R 701 " pdb=" C21 CLR R 701 " pdb=" C22 CLR R 701 " both_signs ideal model delta sigma weight residual False 2.59 2.90 -0.31 2.00e-01 2.50e+01 2.42e+00 chirality pdb=" C13 CLR R 701 " pdb=" C12 CLR R 701 " pdb=" C14 CLR R 701 " pdb=" C17 CLR R 701 " both_signs ideal model delta sigma weight residual False -2.93 -3.22 0.29 2.00e-01 2.50e+01 2.11e+00 ... (remaining 647 not shown) Planarity restraints: 704 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 216 " -0.014 2.00e-02 2.50e+03 2.79e-02 7.81e+00 pdb=" C LEU R 216 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU R 216 " -0.018 2.00e-02 2.50e+03 pdb=" N SER R 217 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C TYR R 190 " -0.042 5.00e-02 4.00e+02 6.31e-02 6.38e+00 pdb=" N PRO R 191 " 0.109 5.00e-02 4.00e+02 pdb=" CA PRO R 191 " -0.032 5.00e-02 4.00e+02 pdb=" CD PRO R 191 " -0.035 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU R 91 " 0.041 5.00e-02 4.00e+02 6.15e-02 6.05e+00 pdb=" N PRO R 92 " -0.106 5.00e-02 4.00e+02 pdb=" CA PRO R 92 " 0.031 5.00e-02 4.00e+02 pdb=" CD PRO R 92 " 0.034 5.00e-02 4.00e+02 ... (remaining 701 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.71: 103 2.71 - 3.26: 3861 3.26 - 3.81: 6317 3.81 - 4.35: 7782 4.35 - 4.90: 14107 Nonbonded interactions: 32170 Sorted by model distance: nonbonded pdb=" OG1 THR R 117 " pdb=" OD2 ASP R 171 " model vdw 2.165 3.040 nonbonded pdb=" NH1 ARG L 51 " pdb=" OD1 ASP H 114 " model vdw 2.221 3.120 nonbonded pdb=" OE1 GLN R 200 " pdb=" OG SER R 263 " model vdw 2.313 3.040 nonbonded pdb=" O ALA R 83 " pdb=" OG SER R 119 " model vdw 2.334 3.040 nonbonded pdb=" NH2 ARG H 105 " pdb=" OE1 GLU R 288 " model vdw 2.404 3.120 ... (remaining 32165 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.040 Construct map_model_manager: 0.010 Extract box with map and model: 0.160 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 16.100 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.830 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 4215 Z= 0.205 Angle : 0.672 7.746 5737 Z= 0.345 Chirality : 0.050 0.371 650 Planarity : 0.006 0.063 704 Dihedral : 14.014 89.582 1537 Min Nonbonded Distance : 2.165 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.00 % Allowed : 0.22 % Favored : 99.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.38 (0.40), residues: 503 helix: 1.07 (0.38), residues: 218 sheet: 0.04 (0.46), residues: 133 loop : -0.55 (0.55), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.002 TRP H 116 HIS 0.004 0.001 HIS R 294 PHE 0.012 0.001 PHE R 293 TYR 0.010 0.001 TYR H 107 ARG 0.004 0.001 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 67 time to evaluate : 0.404 Fit side-chains REVERT: R 24 MET cc_start: 0.6356 (tmm) cc_final: 0.6053 (tmm) REVERT: R 301 LEU cc_start: 0.8430 (mp) cc_final: 0.8173 (mp) outliers start: 0 outliers final: 0 residues processed: 67 average time/residue: 0.2019 time to fit residues: 16.3996 Evaluate side-chains 59 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 59 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 42 optimal weight: 2.9990 chunk 37 optimal weight: 0.1980 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 39 optimal weight: 0.7980 chunk 15 optimal weight: 0.0980 chunk 23 optimal weight: 2.9990 chunk 29 optimal weight: 0.6980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.1048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4215 Z= 0.187 Angle : 0.554 5.319 5737 Z= 0.290 Chirality : 0.042 0.138 650 Planarity : 0.005 0.056 704 Dihedral : 4.414 21.670 627 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 0.45 % Allowed : 5.16 % Favored : 94.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.39), residues: 503 helix: 1.36 (0.37), residues: 214 sheet: 0.23 (0.47), residues: 133 loop : -0.68 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS R 203 PHE 0.007 0.001 PHE L 41 TYR 0.007 0.001 TYR H 54 ARG 0.003 0.000 ARG R 235 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.444 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 58 average time/residue: 0.2019 time to fit residues: 14.4638 Evaluate side-chains 56 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.0670 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.2980 chunk 45 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 15 optimal weight: 0.0050 chunk 36 optimal weight: 0.9980 chunk 44 optimal weight: 0.9980 overall best weight: 0.4732 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8208 moved from start: 0.1292 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4215 Z= 0.178 Angle : 0.520 5.261 5737 Z= 0.273 Chirality : 0.041 0.136 650 Planarity : 0.005 0.057 704 Dihedral : 4.293 20.398 627 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 3.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.58 % Favored : 96.42 % Rotamer: Outliers : 0.67 % Allowed : 7.85 % Favored : 91.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.81 (0.39), residues: 503 helix: 1.63 (0.36), residues: 214 sheet: 0.29 (0.46), residues: 134 loop : -0.69 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.004 0.001 HIS R 203 PHE 0.006 0.001 PHE L 41 TYR 0.008 0.001 TYR H 54 ARG 0.002 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 56 time to evaluate : 0.452 Fit side-chains REVERT: L 94 MET cc_start: 0.9026 (ttt) cc_final: 0.8710 (ttp) REVERT: H 113 MET cc_start: 0.8490 (mmm) cc_final: 0.8014 (mmt) REVERT: R 28 CYS cc_start: 0.6237 (m) cc_final: 0.5854 (m) REVERT: R 154 LYS cc_start: 0.7538 (mptt) cc_final: 0.6568 (tttm) outliers start: 3 outliers final: 2 residues processed: 57 average time/residue: 0.2270 time to fit residues: 15.5842 Evaluate side-chains 55 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 53 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 34 optimal weight: 0.0970 chunk 23 optimal weight: 3.9990 chunk 5 optimal weight: 0.0980 chunk 21 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 45 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 43 optimal weight: 0.3980 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.7980 chunk 27 optimal weight: 5.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8214 moved from start: 0.1485 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4215 Z= 0.178 Angle : 0.514 5.295 5737 Z= 0.267 Chirality : 0.041 0.136 650 Planarity : 0.004 0.057 704 Dihedral : 4.212 19.721 627 Min Nonbonded Distance : 2.602 Molprobity Statistics. All-atom Clashscore : 2.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 0.45 % Allowed : 10.76 % Favored : 88.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.96 (0.39), residues: 503 helix: 1.82 (0.37), residues: 214 sheet: 0.32 (0.46), residues: 134 loop : -0.68 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.003 0.001 HIS R 203 PHE 0.006 0.001 PHE L 41 TYR 0.008 0.001 TYR H 54 ARG 0.002 0.000 ARG H 105 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.414 Fit side-chains REVERT: R 28 CYS cc_start: 0.6299 (m) cc_final: 0.5959 (m) REVERT: R 53 ILE cc_start: 0.8266 (tt) cc_final: 0.8033 (tt) REVERT: R 132 LEU cc_start: 0.7042 (mt) cc_final: 0.6626 (tp) REVERT: R 154 LYS cc_start: 0.7703 (mptt) cc_final: 0.6677 (tttm) outliers start: 2 outliers final: 2 residues processed: 59 average time/residue: 0.2067 time to fit residues: 14.8117 Evaluate side-chains 60 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 0.411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 0 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 33 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 43 optimal weight: 8.9990 chunk 12 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 9 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.1940 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.067 4215 Z= 0.413 Angle : 0.664 6.192 5737 Z= 0.345 Chirality : 0.047 0.157 650 Planarity : 0.005 0.062 704 Dihedral : 4.856 20.240 627 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.79 % Allowed : 10.76 % Favored : 87.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.39), residues: 503 helix: 1.43 (0.37), residues: 213 sheet: 0.17 (0.46), residues: 133 loop : -0.98 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 47 HIS 0.004 0.001 HIS H 110 PHE 0.011 0.001 PHE R 199 TYR 0.019 0.002 TYR H 54 ARG 0.005 0.001 ARG L 51 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.417 Fit side-chains REVERT: L 39 ASN cc_start: 0.8723 (OUTLIER) cc_final: 0.8124 (p0) REVERT: R 53 ILE cc_start: 0.8384 (tt) cc_final: 0.8152 (tt) REVERT: R 154 LYS cc_start: 0.8002 (mptt) cc_final: 0.6900 (tttm) REVERT: R 293 PHE cc_start: 0.8129 (OUTLIER) cc_final: 0.7460 (t80) outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.2375 time to fit residues: 17.3586 Evaluate side-chains 62 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 57 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain R residue 293 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 11 optimal weight: 0.9990 chunk 48 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 chunk 5 optimal weight: 0.0980 chunk 27 optimal weight: 0.6980 chunk 35 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8271 moved from start: 0.1892 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 4215 Z= 0.199 Angle : 0.541 5.505 5737 Z= 0.283 Chirality : 0.042 0.139 650 Planarity : 0.005 0.062 704 Dihedral : 4.514 18.865 627 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 1.57 % Allowed : 13.00 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.70 (0.39), residues: 503 helix: 1.67 (0.37), residues: 213 sheet: 0.19 (0.47), residues: 133 loop : -0.91 (0.51), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.002 0.001 HIS R 294 PHE 0.006 0.001 PHE L 41 TYR 0.008 0.001 TYR H 54 ARG 0.007 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 58 time to evaluate : 0.484 Fit side-chains revert: symmetry clash REVERT: R 53 ILE cc_start: 0.8312 (tt) cc_final: 0.8080 (tt) REVERT: R 154 LYS cc_start: 0.8000 (mptt) cc_final: 0.6911 (tttm) REVERT: R 171 ASP cc_start: 0.7008 (m-30) cc_final: 0.6692 (m-30) REVERT: R 293 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7418 (t80) outliers start: 7 outliers final: 4 residues processed: 60 average time/residue: 0.2304 time to fit residues: 16.6210 Evaluate side-chains 61 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 56 time to evaluate : 0.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 293 PHE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 27 optimal weight: 5.9990 chunk 40 optimal weight: 0.9980 chunk 48 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 29 optimal weight: 0.7980 chunk 22 optimal weight: 0.8980 chunk 19 optimal weight: 2.9990 chunk 28 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 9 optimal weight: 0.3980 chunk 32 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 113 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8281 moved from start: 0.1965 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 4215 Z= 0.235 Angle : 0.558 5.949 5737 Z= 0.290 Chirality : 0.042 0.141 650 Planarity : 0.005 0.062 704 Dihedral : 4.469 18.314 627 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 2.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 1.79 % Allowed : 13.68 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.71 (0.39), residues: 503 helix: 1.71 (0.37), residues: 213 sheet: 0.12 (0.47), residues: 133 loop : -0.87 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP H 47 HIS 0.002 0.001 HIS H 110 PHE 0.006 0.001 PHE L 41 TYR 0.012 0.001 TYR H 54 ARG 0.007 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.456 Fit side-chains REVERT: R 53 ILE cc_start: 0.8309 (tt) cc_final: 0.8072 (tt) REVERT: R 154 LYS cc_start: 0.8114 (mptt) cc_final: 0.6918 (tttm) outliers start: 8 outliers final: 6 residues processed: 60 average time/residue: 0.2271 time to fit residues: 16.3670 Evaluate side-chains 64 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 58 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 23 optimal weight: 3.9990 chunk 4 optimal weight: 0.9990 chunk 37 optimal weight: 0.7980 chunk 43 optimal weight: 10.0000 chunk 46 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 44 optimal weight: 0.5980 chunk 27 optimal weight: 5.9990 chunk 19 optimal weight: 3.9990 chunk 35 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8277 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4215 Z= 0.229 Angle : 0.554 5.689 5737 Z= 0.288 Chirality : 0.042 0.140 650 Planarity : 0.005 0.062 704 Dihedral : 4.425 17.836 627 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 1.79 % Allowed : 14.13 % Favored : 84.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.68 (0.39), residues: 503 helix: 1.71 (0.37), residues: 213 sheet: 0.08 (0.46), residues: 134 loop : -0.90 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP H 47 HIS 0.002 0.001 HIS H 110 PHE 0.006 0.001 PHE L 41 TYR 0.011 0.001 TYR H 54 ARG 0.008 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 58 time to evaluate : 0.468 Fit side-chains revert: symmetry clash REVERT: R 53 ILE cc_start: 0.8299 (tt) cc_final: 0.8059 (tt) REVERT: R 154 LYS cc_start: 0.8073 (mptt) cc_final: 0.6941 (tttm) REVERT: R 171 ASP cc_start: 0.7029 (m-30) cc_final: 0.6707 (m-30) outliers start: 8 outliers final: 7 residues processed: 62 average time/residue: 0.2168 time to fit residues: 16.2203 Evaluate side-chains 64 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 57 time to evaluate : 0.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 39 ASN Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 18 VAL Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 132 LEU Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.0980 chunk 42 optimal weight: 0.7980 chunk 44 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 47 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 49 optimal weight: 1.9990 chunk 45 optimal weight: 0.3980 chunk 39 optimal weight: 0.6980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** R 203 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8244 moved from start: 0.2035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 4215 Z= 0.180 Angle : 0.525 5.461 5737 Z= 0.274 Chirality : 0.041 0.135 650 Planarity : 0.005 0.062 704 Dihedral : 4.240 16.819 627 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 3.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.35 % Allowed : 14.35 % Favored : 84.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.84 (0.39), residues: 503 helix: 1.85 (0.36), residues: 213 sheet: 0.16 (0.47), residues: 134 loop : -0.85 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP H 47 HIS 0.002 0.001 HIS R 203 PHE 0.006 0.001 PHE L 41 TYR 0.008 0.001 TYR H 54 ARG 0.009 0.000 ARG L 82 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 59 time to evaluate : 0.457 Fit side-chains revert: symmetry clash REVERT: R 53 ILE cc_start: 0.8265 (tt) cc_final: 0.8018 (tt) REVERT: R 154 LYS cc_start: 0.8045 (mptt) cc_final: 0.6936 (tttm) REVERT: R 171 ASP cc_start: 0.6991 (m-30) cc_final: 0.6674 (m-30) REVERT: R 293 PHE cc_start: 0.8049 (OUTLIER) cc_final: 0.7394 (t80) outliers start: 6 outliers final: 4 residues processed: 61 average time/residue: 0.2259 time to fit residues: 16.5590 Evaluate side-chains 63 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 293 PHE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 4 optimal weight: 0.8980 chunk 30 optimal weight: 0.6980 chunk 24 optimal weight: 0.0470 chunk 31 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.0980 chunk 11 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.5278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4215 Z= 0.189 Angle : 0.529 5.561 5737 Z= 0.276 Chirality : 0.041 0.136 650 Planarity : 0.005 0.061 704 Dihedral : 4.204 16.392 627 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.35 % Allowed : 14.13 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.86 (0.39), residues: 503 helix: 1.90 (0.36), residues: 213 sheet: 0.16 (0.47), residues: 134 loop : -0.87 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP H 47 HIS 0.002 0.001 HIS R 203 PHE 0.006 0.001 PHE L 41 TYR 0.009 0.001 TYR H 54 ARG 0.009 0.000 ARG L 82 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1006 Ramachandran restraints generated. 503 Oldfield, 0 Emsley, 503 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.443 Fit side-chains revert: symmetry clash REVERT: R 53 ILE cc_start: 0.8278 (tt) cc_final: 0.8020 (tt) REVERT: R 154 LYS cc_start: 0.8087 (mptt) cc_final: 0.6943 (tttm) REVERT: R 171 ASP cc_start: 0.6962 (m-30) cc_final: 0.6649 (m-30) REVERT: R 293 PHE cc_start: 0.8043 (OUTLIER) cc_final: 0.7397 (t80) outliers start: 6 outliers final: 5 residues processed: 58 average time/residue: 0.2314 time to fit residues: 16.0858 Evaluate side-chains 63 residues out of total 446 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 57 time to evaluate : 0.476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 72 SER Chi-restraints excluded: chain L residue 75 ASP Chi-restraints excluded: chain H residue 120 THR Chi-restraints excluded: chain R residue 185 ILE Chi-restraints excluded: chain R residue 293 PHE Chi-restraints excluded: chain R residue 304 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 50 random chunks: chunk 40 optimal weight: 0.9980 chunk 5 optimal weight: 0.4980 chunk 7 optimal weight: 0.6980 chunk 34 optimal weight: 0.0980 chunk 2 optimal weight: 0.7980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 26 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.141768 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3429 r_free = 0.3429 target = 0.122021 restraints weight = 4680.576| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.69 r_work: 0.3299 rms_B_bonded: 2.42 restraints_weight: 0.5000 r_work: 0.3153 rms_B_bonded: 4.18 restraints_weight: 0.2500 r_work (final): 0.3153 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 4215 Z= 0.185 Angle : 0.524 5.468 5737 Z= 0.273 Chirality : 0.041 0.135 650 Planarity : 0.005 0.061 704 Dihedral : 4.173 16.136 627 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 3.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 1.57 % Allowed : 13.90 % Favored : 84.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.90 (0.39), residues: 503 helix: 1.94 (0.36), residues: 213 sheet: 0.16 (0.47), residues: 134 loop : -0.84 (0.52), residues: 156 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 47 HIS 0.002 0.001 HIS R 203 PHE 0.006 0.001 PHE L 41 TYR 0.009 0.001 TYR H 54 ARG 0.009 0.000 ARG L 82 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1290.95 seconds wall clock time: 23 minutes 38.03 seconds (1418.03 seconds total)