Starting phenix.real_space_refine on Mon Sep 23 13:08:39 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/09_2024/7ypq_34011.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/09_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_34011/09_2024/7ypq_34011.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/09_2024/7ypq_34011.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/09_2024/7ypq_34011.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypq_34011/09_2024/7ypq_34011.cif" } resolution = 3.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 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. Time to flip 27 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/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: 2.35, per 1000 atoms: 0.81 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 - 3.00 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: 0.69 Conformation dependent library (CDL) restraints added in 472.5 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: 1.16 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: 0.83 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: 0.00 - 1.32: 3893 1.32 - 2.65: 154 2.65 - 3.97: 27 3.97 - 5.29: 5 5.29 - 6.62: 2 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 3.040 nonbonded pdb=" OD1 ASN A 98 " pdb=" NE2 GLN A 243 " model vdw 2.360 3.120 nonbonded pdb=" OG SER A 292 " pdb=" OP1 DA Q 9 " model vdw 2.402 3.040 nonbonded pdb=" NH2 ARG A 223 " pdb=" O ASN A 241 " model vdw 2.413 3.120 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 Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.850 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: 0.120 Check model and map are aligned: 0.020 Set scattering table: 0.040 Process input model: 13.420 Find NCS groups from input model: 0.030 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:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.220 ------------------------------------------------------------------------------- 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 : 0.302 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: 0.1703 time to fit residues: 11.1651 Evaluate side-chains 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 50 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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: 0.8980 chunk 25 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 19 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 24 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 106 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.0942 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2990 Z= 0.257 Angle : 0.583 8.302 4081 Z= 0.321 Chirality : 0.045 0.136 459 Planarity : 0.003 0.022 481 Dihedral : 17.027 70.211 510 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 0.65 % Allowed : 4.52 % Favored : 94.84 % 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: -0.30 (0.47), residues: 323 helix: 0.68 (0.70), residues: 62 sheet: -0.04 (0.46), residues: 123 loop : -0.63 (0.52), residues: 138 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 0.009 0.001 TYR A 351 ARG 0.004 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 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.327 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8125 (m110) cc_final: 0.7398 (t0) REVERT: A 130 CYS cc_start: 0.8026 (m) cc_final: 0.7762 (m) REVERT: A 213 LYS cc_start: 0.8353 (mttm) cc_final: 0.8043 (mptt) REVERT: A 262 TYR cc_start: 0.8959 (p90) cc_final: 0.8580 (p90) outliers start: 2 outliers final: 2 residues processed: 48 average time/residue: 0.1741 time to fit residues: 10.0173 Evaluate side-chains 45 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 113 LEU Chi-restraints excluded: chain A residue 160 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 20 optimal weight: 0.4980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 32 optimal weight: 1.9990 chunk 26 optimal weight: 0.7980 chunk 29 optimal weight: 1.9990 chunk 10 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 chunk 22 optimal weight: 0.4980 chunk 15 optimal weight: 1.9990 chunk 3 optimal weight: 5.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- 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: 0.7521 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.025 2990 Z= 0.228 Angle : 0.523 6.250 4081 Z= 0.293 Chirality : 0.043 0.136 459 Planarity : 0.002 0.019 481 Dihedral : 17.723 70.731 510 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 0.97 % Allowed : 7.10 % Favored : 91.94 % 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 (0.47), residues: 323 helix: 0.96 (0.69), residues: 62 sheet: 0.05 (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 0.007 0.001 PHE A 189 TYR 0.009 0.001 TYR A 299 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 : 0.323 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8041 (m110) cc_final: 0.7337 (t0) REVERT: A 130 CYS cc_start: 0.7981 (m) cc_final: 0.7756 (m) REVERT: A 213 LYS cc_start: 0.8349 (mttm) cc_final: 0.7992 (mptt) REVERT: A 262 TYR cc_start: 0.8941 (p90) cc_final: 0.8547 (p90) outliers start: 3 outliers final: 3 residues processed: 51 average time/residue: 0.1661 time to fit residues: 10.2236 Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 160 SER Chi-restraints excluded: chain A residue 352 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 14 optimal weight: 0.2980 chunk 20 optimal weight: 5.9990 chunk 30 optimal weight: 1.9990 chunk 31 optimal weight: 0.9980 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 8 optimal weight: 0.7980 chunk 26 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 0.5980 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: 0.7517 moved from start: 0.1484 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= 0.210 Angle : 0.502 5.345 4081 Z= 0.283 Chirality : 0.042 0.137 459 Planarity : 0.002 0.019 481 Dihedral : 17.634 71.900 510 Min Nonbonded Distance : 2.575 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 1.29 % Allowed : 9.35 % Favored : 89.35 % 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: 0.03 (0.47), residues: 323 helix: 1.23 (0.71), residues: 62 sheet: 0.13 (0.46), residues: 120 loop : -0.52 (0.53), residues: 141 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 0.015 0.001 TYR A 260 ARG 0.003 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 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 46 time to evaluate : 0.319 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.8044 (m110) cc_final: 0.7345 (t0) REVERT: A 130 CYS cc_start: 0.7917 (m) cc_final: 0.7711 (m) REVERT: A 213 LYS cc_start: 0.8372 (mttm) cc_final: 0.8030 (mptt) REVERT: A 262 TYR cc_start: 0.8935 (p90) cc_final: 0.8669 (p90) outliers start: 4 outliers final: 4 residues processed: 48 average time/residue: 0.1634 time to fit residues: 9.5457 Evaluate side-chains 46 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.321 ------------------------------------------------------------------------------- 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 308 THR 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: 2.9990 chunk 0 optimal weight: 10.0000 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 10 optimal weight: 0.8980 chunk 6 optimal weight: 6.9990 chunk 18 optimal weight: 0.8980 chunk 7 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7541 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2990 Z= 0.278 Angle : 0.528 4.874 4081 Z= 0.296 Chirality : 0.043 0.141 459 Planarity : 0.002 0.020 481 Dihedral : 17.646 73.565 510 Min Nonbonded Distance : 2.586 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.58 % Allowed : 9.35 % Favored : 88.06 % 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: 0.05 (0.47), residues: 323 helix: 1.24 (0.71), residues: 62 sheet: 0.15 (0.46), residues: 120 loop : -0.53 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.002 0.001 HIS A 276 PHE 0.009 0.001 PHE A 189 TYR 0.015 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 53 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.328 Fit side-chains revert: symmetry clash REVERT: A 80 ASN cc_start: 0.7989 (m110) cc_final: 0.7288 (t0) REVERT: A 113 LEU cc_start: 0.7911 (OUTLIER) cc_final: 0.7313 (mp) REVERT: A 130 CYS cc_start: 0.7970 (m) cc_final: 0.7754 (m) REVERT: A 213 LYS cc_start: 0.8389 (mttm) cc_final: 0.8056 (mptt) REVERT: A 262 TYR cc_start: 0.8958 (p90) cc_final: 0.8571 (p90) outliers start: 8 outliers final: 7 residues processed: 48 average time/residue: 0.1639 time to fit residues: 9.4906 Evaluate side-chains 52 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.300 ------------------------------------------------------------------------------- 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 143 ILE 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 352 LEU Chi-restraints excluded: chain A residue 372 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 33 random chunks: chunk 31 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 14 optimal weight: 1.9990 chunk 2 optimal weight: 4.9990 chunk 10 optimal weight: 0.9980 chunk 16 optimal weight: 0.7980 chunk 30 optimal weight: 0.0070 chunk 3 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 17 optimal weight: 0.6980 overall best weight: 0.5176 ------------------------------------------------------------------------------- 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: 0.7506 moved from start: 0.1669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2990 Z= 0.189 Angle : 0.494 5.030 4081 Z= 0.279 Chirality : 0.042 0.135 459 Planarity : 0.002 0.018 481 Dihedral : 17.588 75.726 510 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 1.94 % Allowed : 10.97 % 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: 0.14 (0.47), residues: 323 helix: 1.36 (0.71), residues: 62 sheet: 0.20 (0.46), residues: 120 loop : -0.49 (0.53), residues: 141 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 228 PHE 0.007 0.001 PHE A 258 TYR 0.011 0.001 TYR A 260 ARG 0.003 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 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 45 time to evaluate : 0.353 Fit side-chains REVERT: A 80 ASN cc_start: 0.7967 (m110) cc_final: 0.7282 (t0) REVERT: A 99 LYS cc_start: 0.7109 (mmtt) cc_final: 0.6540 (mmmt) REVERT: A 113 LEU cc_start: 0.7880 (OUTLIER) cc_final: 0.7291 (mp) REVERT: A 213 LYS cc_start: 0.8366 (mttm) cc_final: 0.8061 (mptt) REVERT: A 262 TYR cc_start: 0.8924 (p90) cc_final: 0.8639 (p90) outliers start: 6 outliers final: 5 residues processed: 48 average time/residue: 0.1759 time to fit residues: 10.1262 Evaluate side-chains 48 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.320 ------------------------------------------------------------------------------- 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 308 THR 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: 1.9990 chunk 19 optimal weight: 3.9990 chunk 14 optimal weight: 0.7980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.9990 chunk 9 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 21 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 2 optimal weight: 3.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.7531 moved from start: 0.1613 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 2990 Z= 0.260 Angle : 0.517 4.124 4081 Z= 0.290 Chirality : 0.043 0.141 459 Planarity : 0.002 0.019 481 Dihedral : 17.631 76.721 510 Min Nonbonded Distance : 2.560 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.58 % Allowed : 11.61 % 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: 0.18 (0.47), residues: 323 helix: 1.34 (0.71), residues: 62 sheet: 0.34 (0.47), residues: 118 loop : -0.54 (0.52), residues: 143 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 0.011 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 53 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 45 time to evaluate : 0.326 Fit side-chains REVERT: A 80 ASN cc_start: 0.7994 (m110) cc_final: 0.7293 (t0) REVERT: A 99 LYS cc_start: 0.7044 (mmtt) cc_final: 0.6502 (mmmt) REVERT: A 113 LEU cc_start: 0.7896 (OUTLIER) cc_final: 0.7304 (mp) REVERT: A 213 LYS cc_start: 0.8391 (mttm) cc_final: 0.8100 (mptt) REVERT: A 262 TYR cc_start: 0.8952 (p90) cc_final: 0.8679 (p90) outliers start: 8 outliers final: 6 residues processed: 49 average time/residue: 0.1665 time to fit residues: 9.8548 Evaluate side-chains 51 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 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 143 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR 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: 0.6980 chunk 28 optimal weight: 0.9990 chunk 30 optimal weight: 0.8980 chunk 27 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 0.9980 chunk 12 optimal weight: 5.9990 chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7530 moved from start: 0.1692 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.026 2990 Z= 0.252 Angle : 0.534 7.935 4081 Z= 0.294 Chirality : 0.043 0.139 459 Planarity : 0.002 0.018 481 Dihedral : 17.631 77.626 510 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % 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: 0.16 (0.47), residues: 323 helix: 1.37 (0.71), residues: 62 sheet: 0.31 (0.47), residues: 118 loop : -0.56 (0.52), residues: 143 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 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.352 Fit side-chains REVERT: A 80 ASN cc_start: 0.7993 (m110) cc_final: 0.7293 (t0) REVERT: A 99 LYS cc_start: 0.7045 (mmtt) cc_final: 0.6505 (mmmt) REVERT: A 113 LEU cc_start: 0.7899 (OUTLIER) cc_final: 0.7311 (mp) REVERT: A 213 LYS cc_start: 0.8391 (mttm) cc_final: 0.8112 (mptt) REVERT: A 262 TYR cc_start: 0.8950 (p90) cc_final: 0.8677 (p90) outliers start: 7 outliers final: 6 residues processed: 46 average time/residue: 0.1743 time to fit residues: 9.6938 Evaluate side-chains 49 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 42 time to evaluate : 0.314 ------------------------------------------------------------------------------- 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 143 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR 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: 3.9990 chunk 14 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 32 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 26 optimal weight: 0.9980 chunk 2 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 27 optimal weight: 0.6980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.7535 moved from start: 0.1639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 2990 Z= 0.273 Angle : 0.539 7.119 4081 Z= 0.298 Chirality : 0.043 0.140 459 Planarity : 0.002 0.020 481 Dihedral : 17.645 78.637 510 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 7.05 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: 0.14 (0.47), residues: 323 helix: 1.35 (0.71), residues: 62 sheet: 0.29 (0.47), residues: 118 loop : -0.58 (0.52), residues: 143 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS A 276 PHE 0.009 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 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 42 time to evaluate : 0.330 Fit side-chains REVERT: A 80 ASN cc_start: 0.7997 (m110) cc_final: 0.7292 (t0) REVERT: A 99 LYS cc_start: 0.7046 (mmtt) cc_final: 0.6507 (mmmt) REVERT: A 113 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7323 (mp) REVERT: A 213 LYS cc_start: 0.8395 (mttm) cc_final: 0.8107 (mptt) REVERT: A 262 TYR cc_start: 0.8957 (p90) cc_final: 0.8684 (p90) outliers start: 8 outliers final: 6 residues processed: 46 average time/residue: 0.1700 time to fit residues: 9.4871 Evaluate side-chains 50 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 43 time to evaluate : 0.372 ------------------------------------------------------------------------------- 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 143 ILE Chi-restraints excluded: chain A residue 183 VAL Chi-restraints excluded: chain A residue 308 THR 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: 0.5980 chunk 24 optimal weight: 0.5980 chunk 3 optimal weight: 0.3980 chunk 7 optimal weight: 7.9990 chunk 26 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.7514 moved from start: 0.1711 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= 0.195 Angle : 0.523 7.059 4081 Z= 0.291 Chirality : 0.042 0.133 459 Planarity : 0.002 0.018 481 Dihedral : 17.617 79.456 510 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 13.23 % Favored : 84.84 % 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 (0.48), residues: 323 helix: 1.45 (0.71), residues: 62 sheet: 0.31 (0.46), residues: 120 loop : -0.54 (0.53), residues: 141 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 260 ARG 0.003 0.000 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 48 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.340 Fit side-chains REVERT: A 80 ASN cc_start: 0.7978 (m110) cc_final: 0.7287 (t0) REVERT: A 99 LYS cc_start: 0.7037 (mmtt) cc_final: 0.6501 (mmmt) REVERT: A 113 LEU cc_start: 0.7902 (OUTLIER) cc_final: 0.7319 (mp) REVERT: A 213 LYS cc_start: 0.8386 (mttm) cc_final: 0.8111 (mptt) REVERT: A 262 TYR cc_start: 0.8934 (p90) cc_final: 0.8650 (p90) outliers start: 6 outliers final: 5 residues processed: 45 average time/residue: 0.1669 time to fit residues: 9.1166 Evaluate side-chains 47 residues out of total 310 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 41 time to evaluate : 0.308 ------------------------------------------------------------------------------- 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 183 VAL Chi-restraints excluded: chain A residue 308 THR 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: 0.7980 chunk 22 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 4.9990 chunk 32 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 31 optimal weight: 0.5980 chunk 6 optimal weight: 3.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.1984 ------------------------------------------------------------------------------- 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 = 0.3763 r_free = 0.3763 target = 0.166109 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.119203 restraints weight = 2956.146| |-----------------------------------------------------------------------------| r_work (start): 0.3259 rms_B_bonded: 2.17 r_work: 0.3087 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.034 2990 Z= 0.339 Angle : 0.573 6.904 4081 Z= 0.315 Chirality : 0.044 0.142 459 Planarity : 0.003 0.021 481 Dihedral : 17.702 81.018 510 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 7.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.17 % Favored : 97.83 % Rotamer: Outliers : 1.94 % Allowed : 13.23 % Favored : 84.84 % 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: 0.11 (0.48), residues: 323 helix: 1.30 (0.71), residues: 62 sheet: 0.27 (0.47), residues: 120 loop : -0.58 (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 0.011 0.002 TYR A 351 ARG 0.005 0.001 ARG A 286 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1104.21 seconds wall clock time: 20 minutes 9.23 seconds (1209.23 seconds total)