Starting phenix.real_space_refine on Wed Nov 13 23:12:18 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwm_35771/11_2024/8iwm_35771.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwm_35771/11_2024/8iwm_35771.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwm_35771/11_2024/8iwm_35771.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwm_35771/11_2024/8iwm_35771.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwm_35771/11_2024/8iwm_35771.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8iwm_35771/11_2024/8iwm_35771.cif" } resolution = 3.17 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= 0.003 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 14 5.16 5 C 1323 2.51 5 N 309 2.21 5 O 334 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 1980 Number of models: 1 Model: "" Number of chains: 2 Chain: "R" Number of atoms: 1971 Number of conformers: 1 Conformer: "" Number of residues, atoms: 271, 1971 Classifications: {'peptide': 271} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 260} Chain breaks: 1 Unresolved non-hydrogen bonds: 206 Unresolved non-hydrogen angles: 269 Unresolved non-hydrogen dihedrals: 186 Unresolved non-hydrogen chiralities: 10 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 4, 'ASN:plan1': 2, 'TRP:plan': 3, 'ASP:plan': 2, 'PHE:plan': 5, 'GLU:plan': 7, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 147 Chain: "R" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 9 Unusual residues: {'PEA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.43, per 1000 atoms: 1.23 Number of scatterers: 1980 At special positions: 0 Unit cell: (60.256, 57.028, 79.624, 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 14 16.00 O 334 8.00 N 309 7.00 C 1323 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 105 " - pdb=" SG CYS R 190 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.53 Conformation dependent library (CDL) restraints added in 279.7 milliseconds 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 516 Finding SS restraints... Secondary structure from input PDB file: 18 helices and 0 sheets defined 88.2% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'R' and resid 37 through 59 removed outlier: 4.501A pdb=" N ASN R 50 " --> pdb=" O ALA R 46 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N LEU R 52 " --> pdb=" O PHE R 48 " (cutoff:3.500A) removed outlier: 4.818A pdb=" N VAL R 53 " --> pdb=" O GLY R 49 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N ILE R 57 " --> pdb=" O VAL R 53 " (cutoff:3.500A) removed outlier: 4.127A pdb=" N LEU R 58 " --> pdb=" O ILE R 54 " (cutoff:3.500A) Processing helix chain 'R' and resid 60 through 64 removed outlier: 3.627A pdb=" N LEU R 63 " --> pdb=" O PHE R 60 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N HIS R 64 " --> pdb=" O LYS R 61 " (cutoff:3.500A) No H-bonds generated for 'chain 'R' and resid 60 through 64' Processing helix chain 'R' and resid 65 through 84 removed outlier: 4.017A pdb=" N LEU R 70 " --> pdb=" O PRO R 66 " (cutoff:3.500A) removed outlier: 3.907A pdb=" N VAL R 71 " --> pdb=" O THR R 67 " (cutoff:3.500A) Processing helix chain 'R' and resid 84 through 96 removed outlier: 4.214A pdb=" N PHE R 88 " --> pdb=" O THR R 84 " (cutoff:3.500A) removed outlier: 3.835A pdb=" N VAL R 91 " --> pdb=" O PRO R 87 " (cutoff:3.500A) removed outlier: 3.519A pdb=" N ARG R 92 " --> pdb=" O PHE R 88 " (cutoff:3.500A) Processing helix chain 'R' and resid 102 through 116 removed outlier: 4.517A pdb=" N CYS R 110 " --> pdb=" O LYS R 106 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N PHE R 111 " --> pdb=" O PHE R 107 " (cutoff:3.500A) removed outlier: 3.521A pdb=" N ASP R 112 " --> pdb=" O HIS R 108 " (cutoff:3.500A) Processing helix chain 'R' and resid 117 through 136 removed outlier: 3.826A pdb=" N PHE R 121 " --> pdb=" O PHE R 117 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS R 122 " --> pdb=" O ALA R 118 " (cutoff:3.500A) Processing helix chain 'R' and resid 139 through 144 Processing helix chain 'R' and resid 145 through 163 removed outlier: 3.696A pdb=" N ILE R 153 " --> pdb=" O SER R 149 " (cutoff:3.500A) removed outlier: 3.557A pdb=" N ALA R 154 " --> pdb=" O GLY R 150 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N SER R 160 " --> pdb=" O SER R 156 " (cutoff:3.500A) removed outlier: 3.863A pdb=" N VAL R 161 " --> pdb=" O TRP R 157 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N TYR R 163 " --> pdb=" O PHE R 159 " (cutoff:3.500A) Processing helix chain 'R' and resid 164 through 169 removed outlier: 3.810A pdb=" N TYR R 169 " --> pdb=" O PHE R 165 " (cutoff:3.500A) Processing helix chain 'R' and resid 177 through 185 removed outlier: 3.788A pdb=" N VAL R 182 " --> pdb=" O GLU R 178 " (cutoff:3.500A) removed outlier: 3.560A pdb=" N ALA R 183 " --> pdb=" O GLU R 179 " (cutoff:3.500A) Processing helix chain 'R' and resid 195 through 232 removed outlier: 3.805A pdb=" N LEU R 200 " --> pdb=" O GLN R 196 " (cutoff:3.500A) removed outlier: 4.615A pdb=" N LEU R 201 " --> pdb=" O ASN R 197 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE R 206 " --> pdb=" O CYS R 202 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N LEU R 208 " --> pdb=" O LEU R 204 " (cutoff:3.500A) Proline residue: R 209 - end of helix removed outlier: 4.176A pdb=" N MET R 213 " --> pdb=" O PRO R 209 " (cutoff:3.500A) removed outlier: 4.021A pdb=" N ILE R 220 " --> pdb=" O LEU R 216 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ALA R 228 " --> pdb=" O ALA R 224 " (cutoff:3.500A) removed outlier: 3.634A pdb=" N ILE R 231 " --> pdb=" O GLN R 227 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N GLU R 232 " --> pdb=" O ALA R 228 " (cutoff:3.500A) Processing helix chain 'R' and resid 254 through 269 removed outlier: 3.714A pdb=" N LYS R 258 " --> pdb=" O ARG R 254 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N PHE R 267 " --> pdb=" O ALA R 263 " (cutoff:3.500A) Processing helix chain 'R' and resid 270 through 280 removed outlier: 4.008A pdb=" N TYR R 274 " --> pdb=" O SER R 270 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ILE R 280 " --> pdb=" O ILE R 276 " (cutoff:3.500A) Processing helix chain 'R' and resid 281 through 283 No H-bonds generated for 'chain 'R' and resid 281 through 283' Processing helix chain 'R' and resid 289 through 292 Processing helix chain 'R' and resid 293 through 311 removed outlier: 4.065A pdb=" N VAL R 300 " --> pdb=" O LEU R 296 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N TYR R 301 " --> pdb=" O VAL R 297 " (cutoff:3.500A) Proline residue: R 308 - end of helix Processing helix chain 'R' and resid 315 through 323 removed outlier: 3.686A pdb=" N ARG R 319 " --> pdb=" O TYR R 315 " (cutoff:3.500A) removed outlier: 3.609A pdb=" N ALA R 321 " --> pdb=" O TRP R 317 " (cutoff:3.500A) Processing helix chain 'R' and resid 324 through 326 No H-bonds generated for 'chain 'R' and resid 324 through 326' 123 hydrogen bonds defined for protein. 366 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: 0.58 Time building geometry restraints manager: 0.62 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: 582 1.34 - 1.46: 518 1.46 - 1.58: 915 1.58 - 1.70: 0 1.70 - 1.81: 17 Bond restraints: 2032 Sorted by residual: bond pdb=" CA ASN R 307 " pdb=" C ASN R 307 " ideal model delta sigma weight residual 1.524 1.545 -0.022 1.26e-02 6.30e+03 2.91e+00 bond pdb=" N PEA R 401 " pdb=" C1 PEA R 401 " ideal model delta sigma weight residual 1.486 1.452 0.034 2.00e-02 2.50e+03 2.89e+00 bond pdb=" CA ASN R 195 " pdb=" C ASN R 195 " ideal model delta sigma weight residual 1.528 1.508 0.019 1.37e-02 5.33e+03 1.95e+00 bond pdb=" CA MET R 284 " pdb=" C MET R 284 " ideal model delta sigma weight residual 1.530 1.517 0.013 1.14e-02 7.69e+03 1.29e+00 bond pdb=" C TYR R 104 " pdb=" O TYR R 104 " ideal model delta sigma weight residual 1.236 1.223 0.013 1.15e-02 7.56e+03 1.24e+00 ... (remaining 2027 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.84: 2687 1.84 - 3.69: 82 3.69 - 5.53: 10 5.53 - 7.37: 4 7.37 - 9.22: 1 Bond angle restraints: 2784 Sorted by residual: angle pdb=" N ASP R 112 " pdb=" CA ASP R 112 " pdb=" C ASP R 112 " ideal model delta sigma weight residual 111.03 105.07 5.96 1.11e+00 8.12e-01 2.88e+01 angle pdb=" N TYR R 301 " pdb=" CA TYR R 301 " pdb=" C TYR R 301 " ideal model delta sigma weight residual 112.23 107.14 5.09 1.26e+00 6.30e-01 1.63e+01 angle pdb=" N ILE R 57 " pdb=" CA ILE R 57 " pdb=" C ILE R 57 " ideal model delta sigma weight residual 111.62 108.60 3.02 7.90e-01 1.60e+00 1.46e+01 angle pdb=" N VAL R 182 " pdb=" CA VAL R 182 " pdb=" C VAL R 182 " ideal model delta sigma weight residual 110.42 113.80 -3.38 9.60e-01 1.09e+00 1.24e+01 angle pdb=" N TYR R 302 " pdb=" CA TYR R 302 " pdb=" C TYR R 302 " ideal model delta sigma weight residual 111.14 107.35 3.79 1.08e+00 8.57e-01 1.23e+01 ... (remaining 2779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.71: 957 11.71 - 23.43: 112 23.43 - 35.14: 62 35.14 - 46.86: 21 46.86 - 58.57: 6 Dihedral angle restraints: 1158 sinusoidal: 360 harmonic: 798 Sorted by residual: dihedral pdb=" CA PHE R 115 " pdb=" C PHE R 115 " pdb=" N CYS R 116 " pdb=" CA CYS R 116 " ideal model delta harmonic sigma weight residual 180.00 157.73 22.27 0 5.00e+00 4.00e-02 1.98e+01 dihedral pdb=" CA LEU R 205 " pdb=" C LEU R 205 " pdb=" N PHE R 206 " pdb=" CA PHE R 206 " ideal model delta harmonic sigma weight residual 180.00 160.28 19.72 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CB CYS R 105 " pdb=" SG CYS R 105 " pdb=" SG CYS R 190 " pdb=" CB CYS R 190 " ideal model delta sinusoidal sigma weight residual 93.00 124.40 -31.40 1 1.00e+01 1.00e-02 1.41e+01 ... (remaining 1155 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 164 0.026 - 0.052: 105 0.052 - 0.077: 49 0.077 - 0.103: 18 0.103 - 0.129: 7 Chirality restraints: 343 Sorted by residual: chirality pdb=" CA PHE R 115 " pdb=" N PHE R 115 " pdb=" C PHE R 115 " pdb=" CB PHE R 115 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.16e-01 chirality pdb=" CA ASP R 112 " pdb=" N ASP R 112 " pdb=" C ASP R 112 " pdb=" CB ASP R 112 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA VAL R 292 " pdb=" N VAL R 292 " pdb=" C VAL R 292 " pdb=" CB VAL R 292 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.81e-01 ... (remaining 340 not shown) Planarity restraints: 338 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN R 307 " 0.032 5.00e-02 4.00e+02 4.77e-02 3.65e+00 pdb=" N PRO R 308 " -0.083 5.00e-02 4.00e+02 pdb=" CA PRO R 308 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO R 308 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 192 " 0.009 2.00e-02 2.50e+03 1.75e-02 3.07e+00 pdb=" C ALA R 192 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA R 192 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO R 193 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR R 140 " 0.008 2.00e-02 2.50e+03 1.72e-02 2.97e+00 pdb=" C TYR R 140 " -0.030 2.00e-02 2.50e+03 pdb=" O TYR R 140 " 0.011 2.00e-02 2.50e+03 pdb=" N PRO R 141 " 0.010 2.00e-02 2.50e+03 ... (remaining 335 not shown) Histogram of nonbonded interaction distances: 2.39 - 2.89: 835 2.89 - 3.39: 1996 3.39 - 3.90: 3109 3.90 - 4.40: 3574 4.40 - 4.90: 5679 Nonbonded interactions: 15193 Sorted by model distance: nonbonded pdb=" N GLU R 232 " pdb=" OE1 GLU R 232 " model vdw 2.390 3.120 nonbonded pdb=" OG SER R 114 " pdb=" N PHE R 115 " model vdw 2.412 3.120 nonbonded pdb=" O MET R 86 " pdb=" OG1 THR R 90 " model vdw 2.424 3.040 nonbonded pdb=" O SER R 166 " pdb=" OG SER R 166 " model vdw 2.462 3.040 nonbonded pdb=" O VAL R 181 " pdb=" OG1 THR R 185 " model vdw 2.464 3.040 ... (remaining 15188 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: 0.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 11.590 Find NCS groups from input model: 0.020 Set up NCS constraints: 0.010 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:3.100 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.210 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7409 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 : 0.004 0.034 2032 Z= 0.276 Angle : 0.760 9.218 2784 Z= 0.457 Chirality : 0.043 0.129 343 Planarity : 0.005 0.048 338 Dihedral : 14.982 58.570 639 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 9.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 5.26 % Allowed : 28.42 % Favored : 66.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.66 (0.49), residues: 267 helix: -1.82 (0.35), residues: 204 sheet: None (None), residues: 0 loop : -0.73 (0.76), residues: 63 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 157 HIS 0.002 0.001 HIS R 122 PHE 0.026 0.002 PHE R 159 TYR 0.006 0.001 TYR R 140 ARG 0.003 0.001 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 57 time to evaluate : 0.359 Fit side-chains REVERT: R 92 ARG cc_start: 0.8321 (tmm-80) cc_final: 0.7891 (ttp-170) REVERT: R 127 SER cc_start: 0.8784 (m) cc_final: 0.8536 (p) REVERT: R 225 LYS cc_start: 0.8281 (tptp) cc_final: 0.7825 (ttpt) REVERT: R 307 ASN cc_start: 0.7756 (t0) cc_final: 0.7547 (t0) outliers start: 10 outliers final: 6 residues processed: 66 average time/residue: 0.1313 time to fit residues: 10.1615 Evaluate side-chains 52 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 46 time to evaluate : 0.223 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 57 ILE Chi-restraints excluded: chain R residue 135 THR Chi-restraints excluded: chain R residue 138 LEU Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 204 LEU Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 11 optimal weight: 2.9990 chunk 6 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 21 optimal weight: 0.7980 chunk 8 optimal weight: 0.7980 chunk 12 optimal weight: 0.7980 chunk 15 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7341 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 2032 Z= 0.190 Angle : 0.592 8.469 2784 Z= 0.300 Chirality : 0.037 0.128 343 Planarity : 0.004 0.034 338 Dihedral : 6.594 52.079 299 Min Nonbonded Distance : 2.587 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 6.84 % Allowed : 30.00 % Favored : 63.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.58 (0.50), residues: 267 helix: -0.72 (0.37), residues: 199 sheet: None (None), residues: 0 loop : -1.58 (0.69), residues: 68 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 298 HIS 0.002 0.001 HIS R 108 PHE 0.017 0.001 PHE R 144 TYR 0.008 0.001 TYR R 302 ARG 0.002 0.001 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 48 time to evaluate : 0.177 Fit side-chains REVERT: R 106 LYS cc_start: 0.8112 (OUTLIER) cc_final: 0.7764 (ttmt) REVERT: R 225 LYS cc_start: 0.8083 (tptp) cc_final: 0.7739 (ttpt) REVERT: R 314 PHE cc_start: 0.7734 (t80) cc_final: 0.7518 (t80) outliers start: 13 outliers final: 8 residues processed: 56 average time/residue: 0.0902 time to fit residues: 6.2971 Evaluate side-chains 55 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 46 time to evaluate : 0.245 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 85 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 161 VAL Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 275 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 13 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 6 optimal weight: 4.9990 chunk 24 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2032 Z= 0.183 Angle : 0.541 5.751 2784 Z= 0.278 Chirality : 0.038 0.128 343 Planarity : 0.004 0.025 338 Dihedral : 5.355 49.694 290 Min Nonbonded Distance : 2.591 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 6.84 % Allowed : 31.05 % Favored : 62.11 % 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: -0.88 (0.53), residues: 267 helix: -0.09 (0.40), residues: 192 sheet: None (None), residues: 0 loop : -1.63 (0.68), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 317 HIS 0.002 0.000 HIS R 108 PHE 0.020 0.001 PHE R 115 TYR 0.010 0.001 TYR R 311 ARG 0.002 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 47 time to evaluate : 0.238 Fit side-chains REVERT: R 106 LYS cc_start: 0.8086 (OUTLIER) cc_final: 0.7786 (ttmt) REVERT: R 225 LYS cc_start: 0.8159 (tptp) cc_final: 0.7788 (ttpt) outliers start: 13 outliers final: 8 residues processed: 54 average time/residue: 0.0939 time to fit residues: 6.3173 Evaluate side-chains 52 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 43 time to evaluate : 0.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 23 optimal weight: 0.0050 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 0.6994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 2032 Z= 0.166 Angle : 0.512 5.265 2784 Z= 0.260 Chirality : 0.037 0.126 343 Planarity : 0.003 0.023 338 Dihedral : 5.064 49.342 290 Min Nonbonded Distance : 2.597 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer: Outliers : 5.79 % Allowed : 33.68 % Favored : 60.53 % 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: -0.63 (0.53), residues: 267 helix: 0.13 (0.40), residues: 192 sheet: None (None), residues: 0 loop : -1.63 (0.69), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 317 HIS 0.002 0.000 HIS R 108 PHE 0.019 0.001 PHE R 115 TYR 0.008 0.001 TYR R 274 ARG 0.001 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 46 time to evaluate : 0.182 Fit side-chains REVERT: R 106 LYS cc_start: 0.8048 (OUTLIER) cc_final: 0.7761 (ttmt) REVERT: R 225 LYS cc_start: 0.8149 (tptp) cc_final: 0.7681 (ttpt) outliers start: 11 outliers final: 9 residues processed: 51 average time/residue: 0.0707 time to fit residues: 4.6044 Evaluate side-chains 52 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 42 time to evaluate : 0.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 19 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 22 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 0 optimal weight: 8.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.0782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7403 moved from start: 0.3419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 2032 Z= 0.211 Angle : 0.543 7.071 2784 Z= 0.275 Chirality : 0.038 0.131 343 Planarity : 0.003 0.025 338 Dihedral : 5.154 49.088 290 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 8.42 % Allowed : 29.47 % Favored : 62.11 % 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: -0.59 (0.53), residues: 267 helix: 0.07 (0.39), residues: 198 sheet: None (None), residues: 0 loop : -1.47 (0.72), residues: 69 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP R 317 HIS 0.001 0.000 HIS R 108 PHE 0.021 0.001 PHE R 115 TYR 0.007 0.001 TYR R 274 ARG 0.001 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 42 time to evaluate : 0.229 Fit side-chains REVERT: R 106 LYS cc_start: 0.8036 (OUTLIER) cc_final: 0.7776 (ttmt) REVERT: R 225 LYS cc_start: 0.8164 (tptp) cc_final: 0.7685 (ttpt) outliers start: 16 outliers final: 12 residues processed: 52 average time/residue: 0.0856 time to fit residues: 5.6074 Evaluate side-chains 53 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 40 time to evaluate : 0.178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 106 LYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 6 optimal weight: 5.9990 chunk 26 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 12 optimal weight: 6.9990 chunk 2 optimal weight: 1.9990 chunk 8 optimal weight: 0.2980 chunk 13 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 14 optimal weight: 0.0060 chunk 19 optimal weight: 4.9990 chunk 16 optimal weight: 0.7980 overall best weight: 1.0200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.3601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 2032 Z= 0.200 Angle : 0.542 6.244 2784 Z= 0.274 Chirality : 0.038 0.127 343 Planarity : 0.003 0.026 338 Dihedral : 5.112 48.863 290 Min Nonbonded Distance : 2.605 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 6.32 % Allowed : 32.63 % Favored : 61.05 % 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: -0.39 (0.53), residues: 267 helix: 0.33 (0.40), residues: 192 sheet: None (None), residues: 0 loop : -1.64 (0.70), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP R 317 HIS 0.002 0.000 HIS R 108 PHE 0.022 0.001 PHE R 115 TYR 0.007 0.001 TYR R 274 ARG 0.001 0.000 ARG R 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 39 time to evaluate : 0.220 Fit side-chains REVERT: R 225 LYS cc_start: 0.8147 (tptp) cc_final: 0.7677 (ttpt) outliers start: 12 outliers final: 10 residues processed: 47 average time/residue: 0.0879 time to fit residues: 5.2379 Evaluate side-chains 48 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 38 time to evaluate : 0.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 91 VAL Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 127 SER Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 15 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 7 optimal weight: 0.9990 chunk 5 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 2 optimal weight: 0.1980 chunk 20 optimal weight: 0.9980 chunk 23 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7367 moved from start: 0.3833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2032 Z= 0.159 Angle : 0.522 5.917 2784 Z= 0.261 Chirality : 0.037 0.121 343 Planarity : 0.003 0.027 338 Dihedral : 4.888 48.148 290 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.12 % Favored : 98.88 % Rotamer: Outliers : 4.74 % Allowed : 32.11 % Favored : 63.16 % 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: -0.18 (0.54), residues: 267 helix: 0.50 (0.40), residues: 193 sheet: None (None), residues: 0 loop : -1.64 (0.70), residues: 74 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 317 HIS 0.002 0.000 HIS R 108 PHE 0.021 0.001 PHE R 115 TYR 0.006 0.001 TYR R 274 ARG 0.001 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 42 time to evaluate : 0.211 Fit side-chains REVERT: R 225 LYS cc_start: 0.8144 (tptp) cc_final: 0.7703 (ttpt) outliers start: 9 outliers final: 8 residues processed: 47 average time/residue: 0.0945 time to fit residues: 5.5635 Evaluate side-chains 48 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 40 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 142 THR Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 10.0000 chunk 10 optimal weight: 0.2980 chunk 19 optimal weight: 2.9990 chunk 7 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 15 optimal weight: 0.0770 chunk 25 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7345 moved from start: 0.3986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2032 Z= 0.150 Angle : 0.516 5.588 2784 Z= 0.254 Chirality : 0.037 0.117 343 Planarity : 0.003 0.027 338 Dihedral : 4.751 47.543 290 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 5.26 % Allowed : 33.68 % Favored : 61.05 % 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: 0.10 (0.54), residues: 267 helix: 0.76 (0.40), residues: 192 sheet: None (None), residues: 0 loop : -1.65 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 317 HIS 0.002 0.000 HIS R 108 PHE 0.020 0.001 PHE R 115 TYR 0.006 0.001 TYR R 274 ARG 0.001 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 43 time to evaluate : 0.241 Fit side-chains REVERT: R 225 LYS cc_start: 0.8134 (tptp) cc_final: 0.7704 (ttpt) outliers start: 10 outliers final: 10 residues processed: 49 average time/residue: 0.0978 time to fit residues: 6.0108 Evaluate side-chains 50 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 40 time to evaluate : 0.230 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 107 PHE Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 306 MET Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 26 optimal weight: 0.7980 chunk 24 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 2 optimal weight: 1.9990 chunk 16 optimal weight: 0.0870 chunk 13 optimal weight: 0.1980 chunk 17 optimal weight: 0.7980 chunk 22 optimal weight: 2.9990 chunk 6 optimal weight: 7.9990 chunk 19 optimal weight: 3.9990 chunk 3 optimal weight: 0.2980 overall best weight: 0.4358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7323 moved from start: 0.4113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2032 Z= 0.141 Angle : 0.513 6.006 2784 Z= 0.249 Chirality : 0.036 0.111 343 Planarity : 0.003 0.028 338 Dihedral : 4.673 46.886 290 Min Nonbonded Distance : 2.609 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 3.68 % Allowed : 36.32 % Favored : 60.00 % 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: 0.21 (0.54), residues: 267 helix: 0.89 (0.40), residues: 192 sheet: None (None), residues: 0 loop : -1.76 (0.71), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.002 0.000 HIS R 108 PHE 0.018 0.001 PHE R 115 TYR 0.005 0.001 TYR R 163 ARG 0.001 0.000 ARG R 219 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 41 time to evaluate : 0.233 Fit side-chains REVERT: R 129 ASP cc_start: 0.8892 (OUTLIER) cc_final: 0.8592 (t0) REVERT: R 225 LYS cc_start: 0.8116 (tptp) cc_final: 0.7693 (ttpt) outliers start: 7 outliers final: 6 residues processed: 45 average time/residue: 0.0947 time to fit residues: 5.3475 Evaluate side-chains 47 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 40 time to evaluate : 0.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 306 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 5 optimal weight: 0.8980 chunk 21 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 22 optimal weight: 0.9980 chunk 2 optimal weight: 2.9990 chunk 3 optimal weight: 1.9990 chunk 18 optimal weight: 0.7980 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 14 optimal weight: 7.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 moved from start: 0.4006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2032 Z= 0.187 Angle : 0.542 6.249 2784 Z= 0.266 Chirality : 0.038 0.121 343 Planarity : 0.004 0.029 338 Dihedral : 4.867 47.580 290 Min Nonbonded Distance : 2.608 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 4.21 % Allowed : 36.32 % Favored : 59.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.54), residues: 267 helix: 0.90 (0.40), residues: 192 sheet: None (None), residues: 0 loop : -1.58 (0.73), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.002 0.001 HIS R 108 PHE 0.021 0.001 PHE R 115 TYR 0.006 0.001 TYR R 274 ARG 0.001 0.000 ARG R 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 534 Ramachandran restraints generated. 267 Oldfield, 0 Emsley, 267 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.236 Fit side-chains REVERT: R 129 ASP cc_start: 0.8938 (OUTLIER) cc_final: 0.8620 (t0) REVERT: R 225 LYS cc_start: 0.8172 (tptp) cc_final: 0.7735 (ttpt) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.0928 time to fit residues: 5.5941 Evaluate side-chains 50 residues out of total 233 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 42 time to evaluate : 0.224 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 67 THR Chi-restraints excluded: chain R residue 105 CYS Chi-restraints excluded: chain R residue 115 PHE Chi-restraints excluded: chain R residue 124 CYS Chi-restraints excluded: chain R residue 129 ASP Chi-restraints excluded: chain R residue 163 TYR Chi-restraints excluded: chain R residue 170 THR Chi-restraints excluded: chain R residue 325 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 27 random chunks: chunk 18 optimal weight: 0.5980 chunk 0 optimal weight: 8.9990 chunk 17 optimal weight: 0.0030 chunk 16 optimal weight: 0.7980 chunk 15 optimal weight: 3.9990 chunk 10 optimal weight: 0.0020 chunk 9 optimal weight: 0.7980 chunk 26 optimal weight: 0.5980 chunk 25 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 overall best weight: 0.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 307 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 = 0.3888 r_free = 0.3888 target = 0.139484 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3708 r_free = 0.3708 target = 0.125164 restraints weight = 3178.002| |-----------------------------------------------------------------------------| r_work (start): 0.3698 rms_B_bonded: 1.99 r_work: 0.3602 rms_B_bonded: 2.60 restraints_weight: 0.5000 r_work: 0.3494 rms_B_bonded: 4.55 restraints_weight: 0.2500 r_work (final): 0.3494 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7552 moved from start: 0.4209 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 2032 Z= 0.141 Angle : 0.550 8.832 2784 Z= 0.254 Chirality : 0.036 0.111 343 Planarity : 0.003 0.029 338 Dihedral : 4.656 46.596 290 Min Nonbonded Distance : 2.616 Molprobity Statistics. All-atom Clashscore : 8.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.75 % Favored : 99.25 % Rotamer: Outliers : 4.74 % Allowed : 36.32 % Favored : 58.95 % 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: 0.40 (0.55), residues: 267 helix: 1.04 (0.40), residues: 192 sheet: None (None), residues: 0 loop : -1.75 (0.73), residues: 75 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 317 HIS 0.002 0.000 HIS R 108 PHE 0.020 0.001 PHE R 115 TYR 0.005 0.001 TYR R 315 ARG 0.001 0.000 ARG R 219 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 966.34 seconds wall clock time: 22 minutes 53.33 seconds (1373.33 seconds total)