Starting phenix.real_space_refine on Thu Nov 14 08:47:02 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/11_2024/8i9q_35280_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/11_2024/8i9q_35280.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.22 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/11_2024/8i9q_35280.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/11_2024/8i9q_35280.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/11_2024/8i9q_35280_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i9q_35280/11_2024/8i9q_35280_neut.cif" } resolution = 4.22 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= 0.003 sd= 0.059 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 29 5.16 5 C 3264 2.51 5 N 897 2.21 5 O 989 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5179 Number of models: 1 Model: "" Number of chains: 2 Chain: "D" Number of atoms: 3832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 3832 Classifications: {'peptide': 508} Link IDs: {'PTRANS': 14, 'TRANS': 493} Chain: "Q" Number of atoms: 1347 Number of conformers: 1 Conformer: "" Number of residues, atoms: 167, 1347 Classifications: {'peptide': 167} Link IDs: {'PTRANS': 8, 'TRANS': 158} Time building chain proxies: 3.78, per 1000 atoms: 0.73 Number of scatterers: 5179 At special positions: 0 Unit cell: (117.52, 118.65, 110.74, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 29 16.00 O 989 8.00 N 897 7.00 C 3264 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: 1.30 Conformation dependent library (CDL) restraints added in 657.0 milliseconds 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1264 Finding SS restraints... Secondary structure from input PDB file: 27 helices and 4 sheets defined 51.4% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.52 Creating SS restraints... Processing helix chain 'D' and resid 27 through 49 removed outlier: 4.035A pdb=" N ILE D 48 " --> pdb=" O VAL D 44 " (cutoff:3.500A) Processing helix chain 'D' and resid 50 through 52 No H-bonds generated for 'chain 'D' and resid 50 through 52' Processing helix chain 'D' and resid 73 through 81 removed outlier: 3.784A pdb=" N ILE D 77 " --> pdb=" O ASP D 73 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N MET D 81 " --> pdb=" O ILE D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 85 through 102 removed outlier: 3.543A pdb=" N LEU D 91 " --> pdb=" O ALA D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 107 through 126 removed outlier: 3.674A pdb=" N ILE D 111 " --> pdb=" O THR D 107 " (cutoff:3.500A) removed outlier: 3.934A pdb=" N LYS D 122 " --> pdb=" O ASP D 118 " (cutoff:3.500A) Processing helix chain 'D' and resid 129 through 152 removed outlier: 3.572A pdb=" N GLU D 146 " --> pdb=" O GLU D 142 " (cutoff:3.500A) Processing helix chain 'D' and resid 159 through 173 Processing helix chain 'D' and resid 188 through 194 Processing helix chain 'D' and resid 204 through 209 removed outlier: 4.009A pdb=" N LYS D 209 " --> pdb=" O ARG D 206 " (cutoff:3.500A) Processing helix chain 'D' and resid 268 through 291 removed outlier: 4.332A pdb=" N MET D 272 " --> pdb=" O ASP D 268 " (cutoff:3.500A) removed outlier: 4.365A pdb=" N ASP D 273 " --> pdb=" O TYR D 269 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ARG D 274 " --> pdb=" O ALA D 270 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N LEU D 276 " --> pdb=" O MET D 272 " (cutoff:3.500A) removed outlier: 4.974A pdb=" N ARG D 277 " --> pdb=" O ASP D 273 " (cutoff:3.500A) removed outlier: 3.768A pdb=" N GLU D 278 " --> pdb=" O ARG D 274 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU D 284 " --> pdb=" O ARG D 280 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LEU D 286 " --> pdb=" O TYR D 282 " (cutoff:3.500A) removed outlier: 5.021A pdb=" N VAL D 287 " --> pdb=" O ILE D 283 " (cutoff:3.500A) Processing helix chain 'D' and resid 311 through 320 Processing helix chain 'D' and resid 329 through 340 removed outlier: 3.888A pdb=" N CYS D 337 " --> pdb=" O ILE D 333 " (cutoff:3.500A) Processing helix chain 'D' and resid 394 through 401 removed outlier: 3.581A pdb=" N ILE D 398 " --> pdb=" O ASN D 394 " (cutoff:3.500A) Processing helix chain 'D' and resid 403 through 419 removed outlier: 3.640A pdb=" N LEU D 415 " --> pdb=" O VAL D 411 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N VAL D 416 " --> pdb=" O ILE D 412 " (cutoff:3.500A) removed outlier: 4.880A pdb=" N LYS D 417 " --> pdb=" O ARG D 413 " (cutoff:3.500A) removed outlier: 3.982A pdb=" N LYS D 418 " --> pdb=" O CYS D 414 " (cutoff:3.500A) Processing helix chain 'D' and resid 426 through 443 Processing helix chain 'D' and resid 445 through 459 removed outlier: 4.454A pdb=" N TYR D 449 " --> pdb=" O GLY D 445 " (cutoff:3.500A) removed outlier: 4.443A pdb=" N CYS D 450 " --> pdb=" O MET D 446 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N GLU D 459 " --> pdb=" O ALA D 455 " (cutoff:3.500A) Processing helix chain 'D' and resid 460 through 470 removed outlier: 3.598A pdb=" N THR D 464 " --> pdb=" O VAL D 460 " (cutoff:3.500A) Processing helix chain 'D' and resid 472 through 487 removed outlier: 3.809A pdb=" N THR D 476 " --> pdb=" O ASN D 472 " (cutoff:3.500A) Processing helix chain 'D' and resid 512 through 532 removed outlier: 4.101A pdb=" N ALA D 518 " --> pdb=" O VAL D 514 " (cutoff:3.500A) Processing helix chain 'Q' and resid 67 through 78 removed outlier: 4.581A pdb=" N TYR Q 74 " --> pdb=" O ALA Q 70 " (cutoff:3.500A) removed outlier: 4.841A pdb=" N ARG Q 75 " --> pdb=" O ILE Q 71 " (cutoff:3.500A) removed outlier: 3.659A pdb=" N ARG Q 76 " --> pdb=" O GLU Q 72 " (cutoff:3.500A) Processing helix chain 'Q' and resid 81 through 85 Processing helix chain 'Q' and resid 104 through 109 Processing helix chain 'Q' and resid 124 through 141 removed outlier: 3.637A pdb=" N ALA Q 128 " --> pdb=" O ILE Q 124 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N LEU Q 129 " --> pdb=" O PRO Q 125 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASN Q 131 " --> pdb=" O CYS Q 127 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N GLN Q 132 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N HIS Q 133 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N SER Q 135 " --> pdb=" O ASN Q 131 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N ARG Q 139 " --> pdb=" O SER Q 135 " (cutoff:3.500A) removed outlier: 3.811A pdb=" N LYS Q 140 " --> pdb=" O GLY Q 136 " (cutoff:3.500A) Processing helix chain 'Q' and resid 181 through 185 Processing helix chain 'Q' and resid 190 through 196 Processing helix chain 'Q' and resid 204 through 208 Processing helix chain 'Q' and resid 220 through 231 removed outlier: 4.348A pdb=" N VAL Q 224 " --> pdb=" O LEU Q 220 " (cutoff:3.500A) removed outlier: 3.931A pdb=" N ARG Q 225 " --> pdb=" O LEU Q 221 " (cutoff:3.500A) removed outlier: 3.657A pdb=" N SER Q 227 " --> pdb=" O SER Q 223 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 59 through 62 removed outlier: 3.606A pdb=" N LYS D 59 " --> pdb=" O THR D 71 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 153 through 154 removed outlier: 3.590A pdb=" N ARG D 153 " --> pdb=" O LEU D 421 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'D' and resid 299 through 301 removed outlier: 7.077A pdb=" N ILE D 300 " --> pdb=" O ILE D 328 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'Q' and resid 95 through 96 removed outlier: 7.682A pdb=" N LEU Q 95 " --> pdb=" O LYS Q 148 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 207 hydrogen bonds defined for protein. 597 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.29 Time building geometry restraints manager: 1.51 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: 1640 1.34 - 1.46: 540 1.46 - 1.57: 3009 1.57 - 1.69: 0 1.69 - 1.81: 47 Bond restraints: 5236 Sorted by residual: bond pdb=" C ILE Q 155 " pdb=" N PRO Q 156 " ideal model delta sigma weight residual 1.335 1.498 -0.162 1.36e-02 5.41e+03 1.43e+02 bond pdb=" C TYR Q 158 " pdb=" N PRO Q 159 " ideal model delta sigma weight residual 1.333 1.497 -0.164 1.44e-02 4.82e+03 1.29e+02 bond pdb=" N ARG Q 161 " pdb=" CA ARG Q 161 " ideal model delta sigma weight residual 1.457 1.518 -0.061 1.33e-02 5.65e+03 2.09e+01 bond pdb=" N CYS Q 154 " pdb=" CA CYS Q 154 " ideal model delta sigma weight residual 1.454 1.495 -0.041 1.17e-02 7.31e+03 1.21e+01 bond pdb=" N ILE Q 155 " pdb=" CA ILE Q 155 " ideal model delta sigma weight residual 1.461 1.501 -0.040 1.23e-02 6.61e+03 1.04e+01 ... (remaining 5231 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.12: 7018 4.12 - 8.25: 38 8.25 - 12.37: 4 12.37 - 16.50: 2 16.50 - 20.62: 2 Bond angle restraints: 7064 Sorted by residual: angle pdb=" C TYR Q 158 " pdb=" N PRO Q 159 " pdb=" CA PRO Q 159 " ideal model delta sigma weight residual 119.47 140.09 -20.62 1.16e+00 7.43e-01 3.16e+02 angle pdb=" C ILE Q 155 " pdb=" N PRO Q 156 " pdb=" CA PRO Q 156 " ideal model delta sigma weight residual 119.05 137.20 -18.15 1.11e+00 8.12e-01 2.67e+02 angle pdb=" C PRO Q 159 " pdb=" CA PRO Q 159 " pdb=" CB PRO Q 159 " ideal model delta sigma weight residual 112.26 102.02 10.24 1.67e+00 3.59e-01 3.76e+01 angle pdb=" N PRO Q 159 " pdb=" CD PRO Q 159 " pdb=" CG PRO Q 159 " ideal model delta sigma weight residual 103.20 94.78 8.42 1.50e+00 4.44e-01 3.15e+01 angle pdb=" N PRO Q 156 " pdb=" CA PRO Q 156 " pdb=" C PRO Q 156 " ideal model delta sigma weight residual 113.53 121.08 -7.55 1.39e+00 5.18e-01 2.95e+01 ... (remaining 7059 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.46: 2925 17.46 - 34.92: 281 34.92 - 52.38: 52 52.38 - 69.84: 11 69.84 - 87.30: 6 Dihedral angle restraints: 3275 sinusoidal: 1328 harmonic: 1947 Sorted by residual: dihedral pdb=" CA CYS D 221 " pdb=" C CYS D 221 " pdb=" N GLU D 222 " pdb=" CA GLU D 222 " ideal model delta harmonic sigma weight residual -180.00 -152.79 -27.21 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ILE Q 216 " pdb=" C ILE Q 216 " pdb=" N GLU Q 217 " pdb=" CA GLU Q 217 " ideal model delta harmonic sigma weight residual 180.00 -156.70 -23.30 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" C PRO Q 159 " pdb=" N PRO Q 159 " pdb=" CA PRO Q 159 " pdb=" CB PRO Q 159 " ideal model delta harmonic sigma weight residual -120.70 -109.29 -11.41 0 2.50e+00 1.60e-01 2.08e+01 ... (remaining 3272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 620 0.048 - 0.095: 173 0.095 - 0.143: 53 0.143 - 0.190: 9 0.190 - 0.238: 6 Chirality restraints: 861 Sorted by residual: chirality pdb=" CA PRO Q 156 " pdb=" N PRO Q 156 " pdb=" C PRO Q 156 " pdb=" CB PRO Q 156 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.41e+00 chirality pdb=" CA ILE Q 155 " pdb=" N ILE Q 155 " pdb=" C ILE Q 155 " pdb=" CB ILE Q 155 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.23e+00 chirality pdb=" CA VAL Q 94 " pdb=" N VAL Q 94 " pdb=" C VAL Q 94 " pdb=" CB VAL Q 94 " both_signs ideal model delta sigma weight residual False 2.44 2.66 -0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 858 not shown) Planarity restraints: 894 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE Q 147 " 0.019 2.00e-02 2.50e+03 3.79e-02 1.43e+01 pdb=" C ILE Q 147 " -0.065 2.00e-02 2.50e+03 pdb=" O ILE Q 147 " 0.025 2.00e-02 2.50e+03 pdb=" N LYS Q 148 " 0.022 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS Q 214 " -0.058 5.00e-02 4.00e+02 8.92e-02 1.27e+01 pdb=" N PRO Q 215 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO Q 215 " -0.048 5.00e-02 4.00e+02 pdb=" CD PRO Q 215 " -0.048 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY D 64 " 0.015 2.00e-02 2.50e+03 3.06e-02 9.35e+00 pdb=" C GLY D 64 " -0.053 2.00e-02 2.50e+03 pdb=" O GLY D 64 " 0.020 2.00e-02 2.50e+03 pdb=" N LYS D 65 " 0.018 2.00e-02 2.50e+03 ... (remaining 891 not shown) Histogram of nonbonded interaction distances: 1.70 - 2.34: 17 2.34 - 2.98: 2777 2.98 - 3.62: 7797 3.62 - 4.26: 10534 4.26 - 4.90: 16543 Nonbonded interactions: 37668 Sorted by model distance: nonbonded pdb=" CE LYS Q 121 " pdb=" O PRO Q 159 " model vdw 1.697 3.440 nonbonded pdb=" CG1 VAL Q 94 " pdb=" NZ LYS Q 148 " model vdw 1.954 3.540 nonbonded pdb=" CE1 TYR Q 158 " pdb=" OD1 ASN Q 162 " model vdw 1.969 3.340 nonbonded pdb=" OG1 THR Q 190 " pdb=" OD1 ASP Q 192 " model vdw 2.153 3.040 nonbonded pdb=" O ASN Q 157 " pdb=" ND2 ASN Q 157 " model vdw 2.161 3.120 ... (remaining 37663 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.220 Check model and map are aligned: 0.030 Set scattering table: 0.060 Process input model: 16.210 Find NCS groups from input model: 0.060 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:2.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.460 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6784 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 : 0.007 0.164 5236 Z= 0.465 Angle : 0.984 20.623 7064 Z= 0.599 Chirality : 0.052 0.238 861 Planarity : 0.005 0.089 894 Dihedral : 14.664 87.297 2011 Min Nonbonded Distance : 1.697 Molprobity Statistics. All-atom Clashscore : 22.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.48 % Favored : 88.52 % Rotamer: Outliers : 0.86 % Allowed : 10.17 % Favored : 88.97 % Cbeta Deviations : 0.16 % 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: -3.94 (0.28), residues: 671 helix: -1.30 (0.28), residues: 275 sheet: -3.77 (0.58), residues: 49 loop : -3.68 (0.27), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 196 HIS 0.003 0.001 HIS D 315 PHE 0.011 0.001 PHE D 335 TYR 0.017 0.002 TYR D 269 ARG 0.009 0.000 ARG D 413 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.608 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7996 (tmm) cc_final: 0.7286 (tmm) REVERT: D 279 GLU cc_start: 0.7575 (pt0) cc_final: 0.6811 (mm-30) REVERT: D 391 ARG cc_start: 0.6703 (ptm-80) cc_final: 0.6404 (ptm-80) REVERT: Q 69 ARG cc_start: 0.9642 (mtm180) cc_final: 0.9107 (ptp90) REVERT: Q 160 ASP cc_start: 0.6489 (OUTLIER) cc_final: 0.6019 (p0) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 0.2775 time to fit residues: 24.8219 Evaluate side-chains 57 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 55 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 55 optimal weight: 1.9990 chunk 50 optimal weight: 6.9990 chunk 27 optimal weight: 0.2980 chunk 17 optimal weight: 0.0670 chunk 33 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 51 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 38 optimal weight: 0.9990 chunk 59 optimal weight: 0.0060 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 98 GLN D 231 GLN D 296 ASN D 318 ASN D 350 GLN D 484 HIS ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6552 moved from start: 0.2438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5236 Z= 0.170 Angle : 0.681 9.018 7064 Z= 0.344 Chirality : 0.046 0.189 861 Planarity : 0.004 0.055 894 Dihedral : 5.514 19.403 718 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.17 % Allowed : 7.41 % Favored : 92.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.62 (0.31), residues: 671 helix: 0.11 (0.32), residues: 286 sheet: -3.06 (0.66), residues: 45 loop : -3.36 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP Q 82 HIS 0.004 0.001 HIS D 484 PHE 0.011 0.001 PHE D 137 TYR 0.011 0.001 TYR Q 169 ARG 0.004 0.000 ARG D 419 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 85 time to evaluate : 0.756 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 272 MET cc_start: 0.7786 (tmm) cc_final: 0.7347 (tmm) REVERT: D 279 GLU cc_start: 0.7497 (pt0) cc_final: 0.6762 (mm-30) REVERT: D 283 ILE cc_start: 0.9041 (mt) cc_final: 0.8673 (tp) REVERT: D 374 LEU cc_start: 0.7630 (pp) cc_final: 0.7397 (tt) REVERT: D 391 ARG cc_start: 0.6268 (ptm-80) cc_final: 0.5949 (ptm-80) REVERT: Q 73 MET cc_start: 0.8872 (mmt) cc_final: 0.8617 (mmt) REVERT: Q 139 ARG cc_start: 0.7745 (mmp-170) cc_final: 0.7518 (mmm160) REVERT: Q 165 THR cc_start: 0.8083 (p) cc_final: 0.7878 (p) outliers start: 1 outliers final: 0 residues processed: 85 average time/residue: 0.2296 time to fit residues: 24.2761 Evaluate side-chains 63 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 63 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 33 optimal weight: 7.9990 chunk 18 optimal weight: 0.7980 chunk 49 optimal weight: 5.9990 chunk 40 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 chunk 60 optimal weight: 0.7980 chunk 64 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 59 optimal weight: 0.9990 chunk 20 optimal weight: 0.9990 chunk 48 optimal weight: 9.9990 overall best weight: 0.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 85 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 494 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6643 moved from start: 0.2868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5236 Z= 0.174 Angle : 0.655 9.068 7064 Z= 0.329 Chirality : 0.044 0.161 861 Planarity : 0.004 0.047 894 Dihedral : 5.333 19.768 718 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.19 (0.32), residues: 671 helix: 0.42 (0.31), residues: 295 sheet: -2.49 (0.73), residues: 45 loop : -3.22 (0.29), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 196 HIS 0.001 0.000 HIS D 129 PHE 0.015 0.001 PHE D 137 TYR 0.016 0.001 TYR Q 169 ARG 0.002 0.000 ARG D 419 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 73 time to evaluate : 0.655 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 GLU cc_start: 0.7533 (pt0) cc_final: 0.6892 (mm-30) REVERT: D 320 MET cc_start: 0.8246 (tpt) cc_final: 0.7991 (tpp) REVERT: D 391 ARG cc_start: 0.6298 (ptm-80) cc_final: 0.6011 (ptm-80) REVERT: Q 69 ARG cc_start: 0.9668 (mtm180) cc_final: 0.9347 (ptp90) REVERT: Q 73 MET cc_start: 0.8910 (mmt) cc_final: 0.8706 (mmt) REVERT: Q 210 GLU cc_start: 0.5811 (mp0) cc_final: 0.5438 (mp0) outliers start: 0 outliers final: 0 residues processed: 73 average time/residue: 0.2239 time to fit residues: 20.6590 Evaluate side-chains 54 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 54 time to evaluate : 0.675 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 59 optimal weight: 0.8980 chunk 45 optimal weight: 6.9990 chunk 31 optimal weight: 0.8980 chunk 6 optimal weight: 9.9990 chunk 28 optimal weight: 0.9990 chunk 40 optimal weight: 10.0000 chunk 60 optimal weight: 2.9990 chunk 63 optimal weight: 1.9990 chunk 57 optimal weight: 0.5980 chunk 17 optimal weight: 0.0370 chunk 53 optimal weight: 0.3980 overall best weight: 0.5658 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 85 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6565 moved from start: 0.3366 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 5236 Z= 0.147 Angle : 0.622 8.835 7064 Z= 0.310 Chirality : 0.043 0.188 861 Planarity : 0.003 0.037 894 Dihedral : 4.944 17.608 718 Min Nonbonded Distance : 2.581 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 2.41 % Favored : 97.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.01 (0.32), residues: 671 helix: 0.52 (0.31), residues: 297 sheet: -2.02 (0.76), residues: 45 loop : -3.16 (0.29), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP Q 196 HIS 0.001 0.000 HIS D 484 PHE 0.013 0.001 PHE Q 91 TYR 0.007 0.001 TYR Q 74 ARG 0.002 0.000 ARG D 274 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.764 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 GLU cc_start: 0.7536 (pt0) cc_final: 0.6826 (mm-30) REVERT: Q 210 GLU cc_start: 0.5759 (mp0) cc_final: 0.5381 (mp0) outliers start: 0 outliers final: 0 residues processed: 71 average time/residue: 0.2538 time to fit residues: 22.7305 Evaluate side-chains 55 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 55 time to evaluate : 0.849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 36 optimal weight: 2.9990 chunk 0 optimal weight: 30.0000 chunk 47 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 44 optimal weight: 4.9990 chunk 32 optimal weight: 0.4980 chunk 57 optimal weight: 0.0670 chunk 16 optimal weight: 0.0770 chunk 21 optimal weight: 9.9990 chunk 12 optimal weight: 0.0570 overall best weight: 0.7396 ------------------------------------------------------------------------------- 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: 0.6611 moved from start: 0.3682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 5236 Z= 0.158 Angle : 0.642 8.638 7064 Z= 0.321 Chirality : 0.044 0.182 861 Planarity : 0.004 0.032 894 Dihedral : 4.938 18.838 718 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 11.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.94 % Favored : 91.06 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.82 (0.32), residues: 671 helix: 0.61 (0.31), residues: 297 sheet: -1.81 (0.70), residues: 51 loop : -3.01 (0.30), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 114 HIS 0.001 0.000 HIS D 129 PHE 0.027 0.002 PHE D 137 TYR 0.007 0.001 TYR Q 74 ARG 0.008 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 279 GLU cc_start: 0.7505 (pt0) cc_final: 0.6830 (mm-30) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2390 time to fit residues: 19.6926 Evaluate side-chains 51 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 51 time to evaluate : 0.829 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 37 optimal weight: 0.9980 chunk 15 optimal weight: 0.0040 chunk 63 optimal weight: 2.9990 chunk 53 optimal weight: 0.0980 chunk 29 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 61 optimal weight: 0.1980 chunk 7 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 overall best weight: 0.3992 ------------------------------------------------------------------------------- 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: 0.6539 moved from start: 0.4064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5236 Z= 0.142 Angle : 0.625 8.481 7064 Z= 0.309 Chirality : 0.044 0.217 861 Planarity : 0.003 0.032 894 Dihedral : 4.707 17.776 718 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.32), residues: 671 helix: 0.70 (0.31), residues: 297 sheet: -1.52 (0.73), residues: 51 loop : -2.75 (0.31), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP Q 196 HIS 0.001 0.000 HIS Q 118 PHE 0.025 0.002 PHE D 137 TYR 0.008 0.001 TYR Q 74 ARG 0.005 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 0.650 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.7935 (tpt) cc_final: 0.7652 (mmm) REVERT: D 279 GLU cc_start: 0.7487 (pt0) cc_final: 0.6846 (mm-30) REVERT: Q 210 GLU cc_start: 0.5627 (mp0) cc_final: 0.5273 (mp0) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.2379 time to fit residues: 20.2510 Evaluate side-chains 57 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 46 optimal weight: 50.0000 chunk 36 optimal weight: 2.9990 chunk 53 optimal weight: 0.8980 chunk 35 optimal weight: 0.0670 chunk 63 optimal weight: 0.0470 chunk 39 optimal weight: 10.0000 chunk 38 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 0.3980 chunk 19 optimal weight: 5.9990 overall best weight: 0.3616 ------------------------------------------------------------------------------- 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: 0.6519 moved from start: 0.4334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5236 Z= 0.142 Angle : 0.637 8.448 7064 Z= 0.309 Chirality : 0.043 0.209 861 Planarity : 0.003 0.036 894 Dihedral : 4.577 18.262 718 Min Nonbonded Distance : 2.571 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.43 (0.32), residues: 671 helix: 0.76 (0.31), residues: 297 sheet: -1.35 (0.72), residues: 51 loop : -2.65 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP Q 196 HIS 0.001 0.000 HIS Q 118 PHE 0.031 0.001 PHE D 137 TYR 0.009 0.001 TYR Q 74 ARG 0.007 0.000 ARG Q 161 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 68 time to evaluate : 1.244 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.7893 (tpt) cc_final: 0.7658 (mmm) REVERT: D 279 GLU cc_start: 0.7516 (pt0) cc_final: 0.6819 (mm-30) REVERT: Q 137 LEU cc_start: 0.8026 (mp) cc_final: 0.7598 (tt) outliers start: 0 outliers final: 0 residues processed: 68 average time/residue: 0.3160 time to fit residues: 27.6351 Evaluate side-chains 56 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 12 optimal weight: 10.0000 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 10.0000 chunk 31 optimal weight: 0.6980 chunk 5 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 60 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 59 optimal weight: 0.0070 chunk 35 optimal weight: 0.0170 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 133 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6529 moved from start: 0.4524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 5236 Z= 0.148 Angle : 0.658 9.457 7064 Z= 0.318 Chirality : 0.044 0.238 861 Planarity : 0.003 0.035 894 Dihedral : 4.593 19.058 718 Min Nonbonded Distance : 2.558 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.60 % Favored : 92.40 % Rotamer: Outliers : 0.00 % Allowed : 1.21 % Favored : 98.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.30 (0.33), residues: 671 helix: 0.77 (0.31), residues: 301 sheet: -1.12 (0.74), residues: 52 loop : -2.56 (0.33), residues: 318 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 196 HIS 0.002 0.000 HIS D 347 PHE 0.026 0.002 PHE D 137 TYR 0.006 0.001 TYR Q 169 ARG 0.006 0.000 ARG Q 161 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.624 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.7875 (tpt) cc_final: 0.7657 (mmm) REVERT: D 279 GLU cc_start: 0.7506 (pt0) cc_final: 0.6840 (mm-30) REVERT: Q 137 LEU cc_start: 0.8076 (mp) cc_final: 0.7650 (tt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2151 time to fit residues: 18.3124 Evaluate side-chains 57 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 57 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 25 optimal weight: 0.5980 chunk 46 optimal weight: 50.0000 chunk 18 optimal weight: 0.5980 chunk 53 optimal weight: 0.0050 chunk 56 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 38 optimal weight: 0.9980 chunk 62 optimal weight: 0.9980 chunk 29 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 65 optimal weight: 0.0770 overall best weight: 0.3952 ------------------------------------------------------------------------------- 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: 0.6511 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 5236 Z= 0.151 Angle : 0.669 9.274 7064 Z= 0.319 Chirality : 0.044 0.226 861 Planarity : 0.003 0.035 894 Dihedral : 4.533 21.802 718 Min Nonbonded Distance : 2.457 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.20 % Favored : 91.80 % Rotamer: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.29 (0.33), residues: 671 helix: 0.64 (0.31), residues: 308 sheet: -1.02 (0.85), residues: 40 loop : -2.43 (0.33), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP Q 196 HIS 0.002 0.000 HIS D 347 PHE 0.014 0.001 PHE Q 91 TYR 0.011 0.001 TYR Q 74 ARG 0.005 0.000 ARG Q 161 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.712 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 81 MET cc_start: 0.7905 (tpt) cc_final: 0.7696 (mmm) REVERT: D 279 GLU cc_start: 0.7499 (pt0) cc_final: 0.6867 (mm-30) REVERT: D 347 HIS cc_start: 0.7299 (m-70) cc_final: 0.6075 (p-80) REVERT: Q 111 GLU cc_start: 0.7700 (tp30) cc_final: 0.7466 (tp30) REVERT: Q 137 LEU cc_start: 0.8065 (mp) cc_final: 0.7629 (tt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2100 time to fit residues: 17.9070 Evaluate side-chains 58 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.778 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 60 optimal weight: 0.0050 chunk 52 optimal weight: 6.9990 chunk 5 optimal weight: 20.0000 chunk 40 optimal weight: 30.0000 chunk 32 optimal weight: 0.8980 chunk 41 optimal weight: 7.9990 chunk 55 optimal weight: 0.4980 chunk 16 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 0.9980 chunk 14 optimal weight: 7.9990 overall best weight: 0.6594 ------------------------------------------------------------------------------- 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: 0.6539 moved from start: 0.4774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 5236 Z= 0.163 Angle : 0.679 9.328 7064 Z= 0.329 Chirality : 0.045 0.230 861 Planarity : 0.003 0.034 894 Dihedral : 4.611 22.416 718 Min Nonbonded Distance : 2.426 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.90 % Favored : 92.10 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.24 (0.33), residues: 671 helix: 0.60 (0.31), residues: 309 sheet: -0.97 (0.86), residues: 40 loop : -2.33 (0.34), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP Q 196 HIS 0.002 0.001 HIS D 347 PHE 0.018 0.001 PHE Q 91 TYR 0.005 0.001 TYR Q 169 ARG 0.006 0.000 ARG Q 69 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1342 Ramachandran restraints generated. 671 Oldfield, 0 Emsley, 671 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 66 time to evaluate : 0.637 Fit side-chains revert: symmetry clash REVERT: D 81 MET cc_start: 0.7888 (tpt) cc_final: 0.7685 (mmm) REVERT: D 279 GLU cc_start: 0.7473 (pt0) cc_final: 0.6814 (mm-30) REVERT: D 347 HIS cc_start: 0.7284 (m-70) cc_final: 0.6083 (p-80) REVERT: Q 73 MET cc_start: 0.9104 (mmt) cc_final: 0.8822 (mmm) REVERT: Q 76 ARG cc_start: 0.8915 (mpt-90) cc_final: 0.8204 (tmt170) REVERT: Q 124 ILE cc_start: 0.8491 (mm) cc_final: 0.8247 (mm) REVERT: Q 137 LEU cc_start: 0.8080 (mp) cc_final: 0.7640 (tt) outliers start: 0 outliers final: 0 residues processed: 66 average time/residue: 0.2105 time to fit residues: 17.8361 Evaluate side-chains 56 residues out of total 580 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 56 time to evaluate : 0.656 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 66 random chunks: chunk 52 optimal weight: 7.9990 chunk 21 optimal weight: 9.9990 chunk 53 optimal weight: 0.2980 chunk 6 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 46 optimal weight: 50.0000 chunk 2 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 60 optimal weight: 1.9990 chunk 35 optimal weight: 0.9980 chunk 44 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: Q 122 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4521 r_free = 0.4521 target = 0.182508 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.4352 r_free = 0.4352 target = 0.169191 restraints weight = 13631.223| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4318 r_free = 0.4318 target = 0.167255 restraints weight = 26382.765| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.4282 r_free = 0.4282 target = 0.164388 restraints weight = 20391.798| |-----------------------------------------------------------------------------| r_work (final): 0.4281 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5953 moved from start: 0.4470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 5236 Z= 0.269 Angle : 0.758 9.959 7064 Z= 0.372 Chirality : 0.046 0.240 861 Planarity : 0.004 0.030 894 Dihedral : 5.169 23.069 718 Min Nonbonded Distance : 2.431 Molprobity Statistics. All-atom Clashscore : 13.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 0.00 % Allowed : 0.34 % Favored : 99.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.33), residues: 671 helix: 0.67 (0.31), residues: 308 sheet: -1.36 (0.75), residues: 52 loop : -2.52 (0.33), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP Q 82 HIS 0.005 0.001 HIS D 347 PHE 0.015 0.002 PHE Q 91 TYR 0.022 0.002 TYR Q 169 ARG 0.006 0.000 ARG D 413 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1560.47 seconds wall clock time: 29 minutes 45.00 seconds (1785.00 seconds total)