Starting phenix.real_space_refine on Sun Mar 10 15:23:13 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/03_2024/7ypq_34011.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/03_2024/7ypq_34011.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/7ypq_34011/03_2024/7ypq_34011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/03_2024/7ypq_34011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/03_2024/7ypq_34011.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/03_2024/7ypq_34011.pdb" } 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= 0.002 sd= 0.137 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: 5 Type Number sf(0) Gaussians P 11 5.49 5 S 12 5.16 5 C 1811 2.51 5 N 493 2.21 5 O 588 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 76": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 137": "OE1" <-> "OE2" Residue "A GLU 142": "OE1" <-> "OE2" Residue "A PHE 150": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 157": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 184": "OE1" <-> "OE2" Residue "A PHE 189": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 196": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 216": "OE1" <-> "OE2" Residue "A PHE 219": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 257": "OE1" <-> "OE2" Residue "A PHE 258": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 293": "OD1" <-> "OD2" Residue "A GLU 304": "OE1" <-> "OE2" Residue "A TYR 311": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 318": "OE1" <-> "OE2" Residue "A ASP 322": "OD1" <-> "OD2" Residue "A ASP 349": "OD1" <-> "OD2" Residue "A TYR 351": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 355": "OD1" <-> "OD2" Residue "A GLU 377": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2915 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2684 Number of conformers: 1 Conformer: "" Number of residues, atoms: 327, 2684 Classifications: {'peptide': 327} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 324} Chain breaks: 1 Chain: "Q" Number of atoms: 231 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 231 Classifications: {'DNA': 11} Link IDs: {'rna3p': 10} Time building chain proxies: 2.06, per 1000 atoms: 0.71 Number of scatterers: 2915 At special positions: 0 Unit cell: (65.55, 79.8, 75.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 12 16.00 P 11 15.00 O 588 8.00 N 493 7.00 C 1811 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 1.16 Conformation dependent library (CDL) restraints added in 480.8 milliseconds 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 634 Finding SS restraints... Secondary structure from input PDB file: 6 helices and 4 sheets defined 18.7% alpha, 48.6% beta 0 base pairs and 8 stacking pairs defined. Time for finding SS restraints: 1.07 Creating SS restraints... Processing helix chain 'A' and resid 88 through 95 Processing helix chain 'A' and resid 135 through 140 Processing helix chain 'A' and resid 188 through 196 removed outlier: 3.742A pdb=" N PHE A 196 " --> pdb=" O LEU A 192 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 214 Processing helix chain 'A' and resid 319 through 336 Processing helix chain 'A' and resid 336 through 343 Processing sheet with id=AA1, first strand: chain 'A' and resid 51 through 66 removed outlier: 6.671A pdb=" N LYS A 75 " --> pdb=" O LEU A 59 " (cutoff:3.500A) removed outlier: 4.578A pdb=" N LYS A 61 " --> pdb=" O LEU A 73 " (cutoff:3.500A) removed outlier: 6.693A pdb=" N LEU A 73 " --> pdb=" O LYS A 61 " (cutoff:3.500A) removed outlier: 4.330A pdb=" N THR A 63 " --> pdb=" O TYR A 71 " (cutoff:3.500A) removed outlier: 6.439A pdb=" N TYR A 71 " --> pdb=" O THR A 63 " (cutoff:3.500A) removed outlier: 4.446A pdb=" N SER A 65 " --> pdb=" O GLU A 69 " (cutoff:3.500A) removed outlier: 6.082A pdb=" N GLU A 69 " --> pdb=" O SER A 65 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N TYR A 72 " --> pdb=" O GLY A 87 " (cutoff:3.500A) removed outlier: 12.776A pdb=" N LEU A 112 " --> pdb=" O SER A 82 " (cutoff:3.500A) removed outlier: 8.260A pdb=" N ASP A 84 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 8.456A pdb=" N ILE A 114 " --> pdb=" O ASP A 84 " (cutoff:3.500A) removed outlier: 7.168A pdb=" N TYR A 86 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 8.500A pdb=" N SER A 116 " --> pdb=" O TYR A 86 " (cutoff:3.500A) removed outlier: 4.911A pdb=" N LEU A 112 " --> pdb=" O SER A 108 " (cutoff:3.500A) removed outlier: 6.435A pdb=" N SER A 108 " --> pdb=" O LEU A 112 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N ILE A 114 " --> pdb=" O GLN A 106 " (cutoff:3.500A) removed outlier: 6.362A pdb=" N GLN A 106 " --> pdb=" O ILE A 114 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N SER A 116 " --> pdb=" O VAL A 104 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 133 through 134 removed outlier: 8.221A pdb=" N LEU A 236 " --> pdb=" O GLN A 182 " (cutoff:3.500A) removed outlier: 6.333A pdb=" N GLU A 184 " --> pdb=" O LEU A 236 " (cutoff:3.500A) removed outlier: 8.090A pdb=" N LEU A 238 " --> pdb=" O GLU A 184 " (cutoff:3.500A) removed outlier: 8.210A pdb=" N MET A 186 " --> pdb=" O LEU A 238 " (cutoff:3.500A) removed outlier: 10.171A pdb=" N SER A 240 " --> pdb=" O MET A 186 " (cutoff:3.500A) removed outlier: 10.998A pdb=" N SER A 239 " --> pdb=" O CYS A 226 " (cutoff:3.500A) removed outlier: 11.082A pdb=" N CYS A 226 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 9.684A pdb=" N ASN A 241 " --> pdb=" O ILE A 224 " (cutoff:3.500A) removed outlier: 6.762A pdb=" N ILE A 224 " --> pdb=" O ASN A 241 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N LYS A 217 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 5.648A pdb=" N LYS A 144 " --> pdb=" O ARG A 223 " (cutoff:3.500A) removed outlier: 14.863A pdb=" N LEU A 146 " --> pdb=" O GLU A 172 " (cutoff:3.500A) removed outlier: 13.885A pdb=" N GLU A 172 " --> pdb=" O LEU A 146 " (cutoff:3.500A) removed outlier: 9.017A pdb=" N ALA A 148 " --> pdb=" O LEU A 170 " (cutoff:3.500A) removed outlier: 8.543A pdb=" N LEU A 170 " --> pdb=" O ALA A 148 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N PHE A 150 " --> pdb=" O VAL A 168 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N VAL A 168 " --> pdb=" O PHE A 150 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N TYR A 152 " --> pdb=" O VAL A 166 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 272 through 278 removed outlier: 4.579A pdb=" N VAL A 348 " --> pdb=" O VAL A 278 " (cutoff:3.500A) removed outlier: 6.294A pdb=" N GLN A 347 " --> pdb=" O LYS A 369 " (cutoff:3.500A) removed outlier: 4.555A pdb=" N LYS A 369 " --> pdb=" O GLN A 347 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N ASP A 349 " --> pdb=" O ILE A 367 " (cutoff:3.500A) removed outlier: 4.449A pdb=" N ILE A 367 " --> pdb=" O ASP A 349 " (cutoff:3.500A) removed outlier: 6.629A pdb=" N TYR A 351 " --> pdb=" O ALA A 365 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 283 through 288 102 hydrogen bonds defined for protein. 291 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 8 stacking parallelities Total time for adding SS restraints: 0.84 Time building geometry restraints manager: 1.29 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: 919 1.34 - 1.46: 637 1.46 - 1.57: 1394 1.57 - 1.69: 21 1.69 - 1.81: 19 Bond restraints: 2990 Sorted by residual: bond pdb=" C LEU A 165 " pdb=" N VAL A 166 " ideal model delta sigma weight residual 1.330 1.302 0.028 1.26e-02 6.30e+03 4.94e+00 bond pdb=" CG LEU A 379 " pdb=" CD1 LEU A 379 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.52e+00 bond pdb=" CB VAL A 183 " pdb=" CG2 VAL A 183 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.50e-01 bond pdb=" CG LEU A 352 " pdb=" CD1 LEU A 352 " ideal model delta sigma weight residual 1.521 1.490 0.031 3.30e-02 9.18e+02 8.74e-01 bond pdb=" CB VAL A 166 " pdb=" CG1 VAL A 166 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.50e-01 ... (remaining 2985 not shown) Histogram of bond angle deviations from ideal: 99.84 - 106.35: 98 106.35 - 112.86: 1587 112.86 - 119.37: 815 119.37 - 125.89: 1510 125.89 - 132.40: 71 Bond angle restraints: 4081 Sorted by residual: angle pdb=" CA GLU A 216 " pdb=" CB GLU A 216 " pdb=" CG GLU A 216 " ideal model delta sigma weight residual 114.10 119.08 -4.98 2.00e+00 2.50e-01 6.21e+00 angle pdb=" C MET A 253 " pdb=" CA MET A 253 " pdb=" CB MET A 253 " ideal model delta sigma weight residual 111.41 115.04 -3.63 1.70e+00 3.46e-01 4.55e+00 angle pdb=" C ASP A 293 " pdb=" N ARG A 294 " pdb=" CA ARG A 294 " ideal model delta sigma weight residual 122.62 119.34 3.28 1.56e+00 4.11e-01 4.43e+00 angle pdb=" CG1 VAL A 359 " pdb=" CB VAL A 359 " pdb=" CG2 VAL A 359 " ideal model delta sigma weight residual 110.80 106.25 4.55 2.20e+00 2.07e-01 4.28e+00 angle pdb=" N ASN A 161 " pdb=" CA ASN A 161 " pdb=" C ASN A 161 " ideal model delta sigma weight residual 110.80 115.15 -4.35 2.13e+00 2.20e-01 4.16e+00 ... (remaining 4076 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.98: 1553 17.98 - 35.96: 180 35.96 - 53.94: 56 53.94 - 71.92: 12 71.92 - 89.90: 4 Dihedral angle restraints: 1805 sinusoidal: 823 harmonic: 982 Sorted by residual: dihedral pdb=" CA TYR A 351 " pdb=" C TYR A 351 " pdb=" N LEU A 352 " pdb=" CA LEU A 352 " ideal model delta harmonic sigma weight residual -180.00 -156.65 -23.35 0 5.00e+00 4.00e-02 2.18e+01 dihedral pdb=" CA PHE A 219 " pdb=" C PHE A 219 " pdb=" N ASN A 220 " pdb=" CA ASN A 220 " ideal model delta harmonic sigma weight residual 180.00 160.39 19.61 0 5.00e+00 4.00e-02 1.54e+01 dihedral pdb=" CA GLU A 304 " pdb=" C GLU A 304 " pdb=" N LYS A 305 " pdb=" CA LYS A 305 " ideal model delta harmonic sigma weight residual 180.00 162.02 17.98 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 1802 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 260 0.031 - 0.062: 131 0.062 - 0.092: 35 0.092 - 0.123: 28 0.123 - 0.154: 5 Chirality restraints: 459 Sorted by residual: chirality pdb=" CA ILE A 310 " pdb=" N ILE A 310 " pdb=" C ILE A 310 " pdb=" CB ILE A 310 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.91e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.78e-01 chirality pdb=" CA ILE A 370 " pdb=" N ILE A 370 " pdb=" C ILE A 370 " pdb=" CB ILE A 370 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.71e-01 ... (remaining 456 not shown) Planarity restraints: 481 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 377 " -0.019 5.00e-02 4.00e+02 2.86e-02 1.31e+00 pdb=" N PRO A 378 " 0.049 5.00e-02 4.00e+02 pdb=" CA PRO A 378 " -0.015 5.00e-02 4.00e+02 pdb=" CD PRO A 378 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 216 " 0.004 2.00e-02 2.50e+03 7.45e-03 5.55e-01 pdb=" C GLU A 216 " -0.013 2.00e-02 2.50e+03 pdb=" O GLU A 216 " 0.005 2.00e-02 2.50e+03 pdb=" N LYS A 217 " 0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 297 " 0.004 2.00e-02 2.50e+03 7.39e-03 5.46e-01 pdb=" C ILE A 297 " -0.013 2.00e-02 2.50e+03 pdb=" O ILE A 297 " 0.005 2.00e-02 2.50e+03 pdb=" N SER A 298 " 0.004 2.00e-02 2.50e+03 ... (remaining 478 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 611 2.79 - 3.32: 2563 3.32 - 3.84: 4682 3.84 - 4.37: 5819 4.37 - 4.90: 9706 Nonbonded interactions: 23381 Sorted by model distance: nonbonded pdb=" O CYS A 210 " pdb=" OG SER A 214 " model vdw 2.261 2.440 nonbonded pdb=" OD1 ASN A 98 " pdb=" NE2 GLN A 243 " model vdw 2.360 2.520 nonbonded pdb=" OG SER A 292 " pdb=" OP1 DA Q 9 " model vdw 2.402 2.440 nonbonded pdb=" NH2 ARG A 223 " pdb=" O ASN A 241 " model vdw 2.413 2.520 nonbonded pdb=" O ASN A 358 " pdb=" OD1 ASN A 358 " model vdw 2.421 3.040 ... (remaining 23376 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: 0.010 Normalize map: mean=0, sd=1: 0.570 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.050 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.860 Find NCS groups from input model: 0.070 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:2.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.370 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7543 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 2990 Z= 0.314 Angle : 0.632 6.618 4081 Z= 0.360 Chirality : 0.046 0.154 459 Planarity : 0.002 0.029 481 Dihedral : 17.794 89.903 1171 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.00 % Allowed : 0.32 % Favored : 99.68 % 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: -0.66 (0.46), residues: 323 helix: 0.04 (0.66), residues: 62 sheet: -0.22 (0.45), residues: 125 loop : -0.73 (0.53), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.010 0.001 TYR A 299 ARG 0.004 0.001 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 55 time to evaluate : 0.321 Fit side-chains REVERT: A 80 ASN cc_start: 0.8098 (m110) cc_final: 0.7333 (t0) REVERT: A 130 CYS cc_start: 0.8140 (m) cc_final: 0.7935 (m) REVERT: A 206 ASP cc_start: 0.7749 (m-30) cc_final: 0.7522 (m-30) REVERT: A 262 TYR cc_start: 0.8966 (p90) cc_final: 0.8652 (p90) outliers start: 0 outliers final: 0 residues processed: 55 average time/residue: 0.1695 time to fit residues: 11.1903 Evaluate side-chains 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 27 optimal weight: 0.5980 chunk 25 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.7980 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.3980 chunk 15 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN A 175 ASN ** A 227 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7514 moved from start: 0.1116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2990 Z= 0.217 Angle : 0.535 7.349 4081 Z= 0.298 Chirality : 0.043 0.139 459 Planarity : 0.002 0.021 481 Dihedral : 17.616 68.389 510 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.97 % Allowed : 3.55 % Favored : 95.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.46), residues: 323 helix: 0.80 (0.70), residues: 62 sheet: -0.02 (0.45), residues: 123 loop : -0.70 (0.52), residues: 138 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.010 0.001 TYR A 299 ARG 0.003 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.321 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8110 (m110) cc_final: 0.7368 (t0) REVERT: A 262 TYR cc_start: 0.8947 (p90) cc_final: 0.8687 (p90) outliers start: 3 outliers final: 3 residues processed: 50 average time/residue: 0.1645 time to fit residues: 9.9478 Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.0370 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 22 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.1280 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2990 Z= 0.193 Angle : 0.496 5.927 4081 Z= 0.277 Chirality : 0.042 0.136 459 Planarity : 0.002 0.018 481 Dihedral : 17.617 70.739 510 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.97 % Allowed : 8.06 % Favored : 90.97 % 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: -0.01 (0.47), residues: 323 helix: 1.15 (0.71), residues: 62 sheet: 0.11 (0.45), residues: 122 loop : -0.55 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.007 0.001 PHE A 189 TYR 0.010 0.001 TYR A 351 ARG 0.003 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 49 time to evaluate : 0.314 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8012 (m110) cc_final: 0.7322 (t0) REVERT: A 213 LYS cc_start: 0.8390 (mttm) cc_final: 0.8027 (mmtm) REVERT: A 262 TYR cc_start: 0.8926 (p90) cc_final: 0.8646 (p90) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.1624 time to fit residues: 9.9666 Evaluate side-chains 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.258 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 2.9990 chunk 20 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.0980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 8 optimal weight: 0.6980 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.7980 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7542 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2990 Z= 0.275 Angle : 0.522 4.936 4081 Z= 0.292 Chirality : 0.043 0.140 459 Planarity : 0.002 0.019 481 Dihedral : 17.605 73.836 510 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.94 % Allowed : 9.35 % Favored : 88.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.07 (0.47), residues: 323 helix: 1.26 (0.71), residues: 62 sheet: 0.19 (0.46), residues: 120 loop : -0.54 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 276 PHE 0.009 0.001 PHE A 189 TYR 0.016 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.320 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.7970 (m110) cc_final: 0.7287 (t0) REVERT: A 113 LEU cc_start: 0.7905 (OUTLIER) cc_final: 0.7344 (mp) REVERT: A 213 LYS cc_start: 0.8420 (mttm) cc_final: 0.8066 (mptt) REVERT: A 262 TYR cc_start: 0.8950 (p90) cc_final: 0.8566 (p90) outliers start: 6 outliers final: 5 residues processed: 52 average time/residue: 0.1630 time to fit residues: 10.2490 Evaluate side-chains 52 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 1.9990 chunk 28 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 6 optimal weight: 0.8980 chunk 18 optimal weight: 0.9990 chunk 7 optimal weight: 0.0970 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7520 moved from start: 0.1460 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2990 Z= 0.211 Angle : 0.498 4.601 4081 Z= 0.280 Chirality : 0.042 0.137 459 Planarity : 0.002 0.018 481 Dihedral : 17.576 75.545 510 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 8.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.26 % Allowed : 10.00 % Favored : 87.74 % 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: 0.14 (0.47), residues: 323 helix: 1.34 (0.71), residues: 62 sheet: 0.26 (0.46), residues: 120 loop : -0.53 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.008 0.001 PHE A 189 TYR 0.013 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 50 time to evaluate : 0.307 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8045 (m110) cc_final: 0.7349 (t0) REVERT: A 113 LEU cc_start: 0.7881 (OUTLIER) cc_final: 0.7317 (mp) REVERT: A 213 LYS cc_start: 0.8407 (mttm) cc_final: 0.8072 (mptt) REVERT: A 262 TYR cc_start: 0.8931 (p90) cc_final: 0.8668 (p90) outliers start: 7 outliers final: 6 residues processed: 54 average time/residue: 0.1631 time to fit residues: 10.6243 Evaluate side-chains 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 47 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.5980 chunk 26 optimal weight: 0.0010 chunk 14 optimal weight: 2.9990 chunk 2 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 0.6188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7517 moved from start: 0.1580 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 2990 Z= 0.207 Angle : 0.504 6.345 4081 Z= 0.280 Chirality : 0.042 0.145 459 Planarity : 0.002 0.019 481 Dihedral : 17.571 76.365 510 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 7.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.58 % Allowed : 10.32 % Favored : 87.10 % 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: 0.19 (0.47), residues: 323 helix: 1.40 (0.71), residues: 62 sheet: 0.31 (0.46), residues: 120 loop : -0.53 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 276 PHE 0.007 0.001 PHE A 189 TYR 0.011 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 48 time to evaluate : 0.326 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8028 (m110) cc_final: 0.7327 (t0) REVERT: A 102 GLU cc_start: 0.7192 (mm-30) cc_final: 0.6897 (mm-30) REVERT: A 113 LEU cc_start: 0.7853 (OUTLIER) cc_final: 0.7293 (mp) REVERT: A 213 LYS cc_start: 0.8396 (mttm) cc_final: 0.8067 (mptt) REVERT: A 262 TYR cc_start: 0.8934 (p90) cc_final: 0.8666 (p90) outliers start: 8 outliers final: 7 residues processed: 53 average time/residue: 0.1656 time to fit residues: 10.6706 Evaluate side-chains 52 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 2.9990 chunk 19 optimal weight: 2.9990 chunk 14 optimal weight: 0.6980 chunk 12 optimal weight: 5.9990 chunk 18 optimal weight: 0.6980 chunk 9 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 20 optimal weight: 3.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 2 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7515 moved from start: 0.1558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2990 Z= 0.206 Angle : 0.497 5.879 4081 Z= 0.278 Chirality : 0.042 0.136 459 Planarity : 0.002 0.019 481 Dihedral : 17.572 77.404 510 Min Nonbonded Distance : 2.243 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.58 % Allowed : 10.65 % Favored : 86.77 % 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 (0.47), residues: 323 helix: 1.45 (0.71), residues: 62 sheet: 0.32 (0.46), residues: 120 loop : -0.53 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 276 PHE 0.007 0.001 PHE A 189 TYR 0.010 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.300 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8022 (m110) cc_final: 0.7323 (t0) REVERT: A 102 GLU cc_start: 0.7190 (mm-30) cc_final: 0.6905 (mm-30) REVERT: A 113 LEU cc_start: 0.7843 (OUTLIER) cc_final: 0.7253 (mp) REVERT: A 213 LYS cc_start: 0.8392 (mttm) cc_final: 0.8080 (mptt) REVERT: A 262 TYR cc_start: 0.8929 (p90) cc_final: 0.8650 (p90) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.1673 time to fit residues: 10.3004 Evaluate side-chains 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 25 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 30 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.1980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7526 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 2990 Z= 0.244 Angle : 0.512 5.653 4081 Z= 0.285 Chirality : 0.042 0.139 459 Planarity : 0.002 0.019 481 Dihedral : 17.601 78.698 510 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 2.90 % Allowed : 10.65 % Favored : 86.45 % 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 (0.47), residues: 323 helix: 1.44 (0.71), residues: 62 sheet: 0.30 (0.46), residues: 120 loop : -0.51 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 276 PHE 0.008 0.001 PHE A 189 TYR 0.010 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 46 time to evaluate : 0.324 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.7937 (m110) cc_final: 0.7270 (t0) REVERT: A 102 GLU cc_start: 0.7154 (mm-30) cc_final: 0.6861 (mm-30) REVERT: A 113 LEU cc_start: 0.7798 (OUTLIER) cc_final: 0.7205 (mp) REVERT: A 213 LYS cc_start: 0.8390 (mttm) cc_final: 0.8092 (mptt) REVERT: A 262 TYR cc_start: 0.8934 (p90) cc_final: 0.8657 (p90) outliers start: 9 outliers final: 7 residues processed: 52 average time/residue: 0.1666 time to fit residues: 10.5591 Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 43 time to evaluate : 0.340 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 1.9990 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 26 optimal weight: 0.0050 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 16 optimal weight: 0.5980 chunk 27 optimal weight: 0.8980 overall best weight: 0.6394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 2990 Z= 0.215 Angle : 0.511 5.504 4081 Z= 0.286 Chirality : 0.042 0.136 459 Planarity : 0.002 0.019 481 Dihedral : 17.596 79.387 510 Min Nonbonded Distance : 2.246 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.58 % Allowed : 11.94 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.16 (0.47), residues: 323 helix: 1.49 (0.70), residues: 62 sheet: 0.21 (0.46), residues: 122 loop : -0.54 (0.53), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 276 PHE 0.007 0.001 PHE A 189 TYR 0.010 0.001 TYR A 260 ARG 0.004 0.000 ARG A 286 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8016 (m110) cc_final: 0.7340 (t0) REVERT: A 113 LEU cc_start: 0.7792 (OUTLIER) cc_final: 0.7198 (mp) REVERT: A 213 LYS cc_start: 0.8387 (mttm) cc_final: 0.8088 (mptt) REVERT: A 262 TYR cc_start: 0.8925 (p90) cc_final: 0.8646 (p90) outliers start: 8 outliers final: 7 residues processed: 45 average time/residue: 0.1801 time to fit residues: 10.1196 Evaluate side-chains 48 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 8 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 3 optimal weight: 3.9990 chunk 7 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 1 optimal weight: 3.9990 chunk 18 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7585 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.040 2990 Z= 0.422 Angle : 0.607 6.234 4081 Z= 0.333 Chirality : 0.046 0.147 459 Planarity : 0.003 0.020 481 Dihedral : 17.735 83.025 510 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.58 % Allowed : 11.94 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.47), residues: 323 helix: 1.14 (0.69), residues: 62 sheet: 0.19 (0.47), residues: 122 loop : -0.51 (0.54), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 276 PHE 0.012 0.002 PHE A 189 TYR 0.013 0.002 TYR A 222 ARG 0.005 0.001 ARG A 286 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 646 Ramachandran restraints generated. 323 Oldfield, 0 Emsley, 323 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 54 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 46 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8012 (m110) cc_final: 0.7288 (t0) REVERT: A 113 LEU cc_start: 0.8038 (OUTLIER) cc_final: 0.7515 (mp) REVERT: A 213 LYS cc_start: 0.8383 (mttm) cc_final: 0.8026 (mptt) outliers start: 8 outliers final: 7 residues processed: 51 average time/residue: 0.1657 time to fit residues: 10.3030 Evaluate side-chains 48 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 40 time to evaluate : 0.325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 52 LEU Chi-restraints excluded: chain A residue 73 LEU Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR Chi-restraints excluded: chain A residue 335 SER Chi-restraints excluded: chain A residue 352 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 17 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.0010 chunk 19 optimal weight: 0.8980 chunk 12 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 0.0770 overall best weight: 0.5344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3791 r_free = 0.3791 target = 0.168606 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.121990 restraints weight = 2960.594| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.17 r_work: 0.3118 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2990 Z= 0.205 Angle : 0.526 7.698 4081 Z= 0.292 Chirality : 0.042 0.140 459 Planarity : 0.002 0.023 481 Dihedral : 17.642 87.820 510 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.55 % Favored : 98.45 % Rotamer: Outliers : 2.26 % Allowed : 11.94 % Favored : 85.81 % 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: 0.08 (0.47), residues: 323 helix: 1.38 (0.70), residues: 62 sheet: 0.24 (0.47), residues: 121 loop : -0.64 (0.52), residues: 140 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.001 HIS A 276 PHE 0.008 0.001 PHE A 189 TYR 0.010 0.001 TYR A 351 ARG 0.004 0.000 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1145.36 seconds wall clock time: 21 minutes 21.35 seconds (1281.35 seconds total)