Starting phenix.real_space_refine on Thu Mar 6 05:51:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7lrs_23498/03_2025/7lrs_23498.cif Found real_map, /net/cci-nas-00/data/ceres_data/7lrs_23498/03_2025/7lrs_23498.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.89 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7lrs_23498/03_2025/7lrs_23498.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7lrs_23498/03_2025/7lrs_23498.map" model { file = "/net/cci-nas-00/data/ceres_data/7lrs_23498/03_2025/7lrs_23498.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7lrs_23498/03_2025/7lrs_23498.cif" } resolution = 3.89 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= -0.001 sd= 0.006 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 22 5.16 5 C 3100 2.51 5 N 812 2.21 5 O 978 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 13 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 4912 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 1551 Number of conformers: 1 Conformer: "" Number of residues, atoms: 196, 1551 Classifications: {'peptide': 196} Link IDs: {'PTRANS': 11, 'TRANS': 184} Chain: "D" Number of atoms: 1625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 216, 1625 Classifications: {'peptide': 216} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 12, 'TRANS': 203} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "E" Number of atoms: 1636 Number of conformers: 1 Conformer: "" Number of residues, atoms: 213, 1636 Classifications: {'peptide': 213} Link IDs: {'PCIS': 1, 'PTRANS': 11, 'TRANS': 200} Chain: "A" Number of atoms: 61 Number of conformers: 1 Conformer: "" Number of residues, atoms: 5, 61 Unusual residues: {'BMA': 1, 'MAN': 2, 'NAG': 2} Classifications: {'undetermined': 5} Link IDs: {None: 4} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 5 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 6.15, per 1000 atoms: 1.25 Number of scatterers: 4912 At special positions: 0 Unit cell: (79.515, 66.69, 140.22, 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 22 16.00 O 978 8.00 N 812 7.00 C 3100 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=9, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 391 " - pdb=" SG CYS C 525 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 22 " - pdb=" SG CYS D 92 " distance=2.03 Simple disulfide: pdb=" SG CYS D 97 " - pdb=" SG CYS D 100B" distance=2.03 Simple disulfide: pdb=" SG CYS D 140 " - pdb=" SG CYS D 196 " distance=2.04 Simple disulfide: pdb=" SG CYS E 23 " - pdb=" SG CYS E 88 " distance=2.03 Simple disulfide: pdb=" SG CYS E 134 " - pdb=" SG CYS E 194 " distance=2.04 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 Links applied ALPHA1-3 " BMA A 3 " - " MAN A 4 " ALPHA1-6 " BMA A 3 " - " MAN A 5 " BETA1-4 " NAG A 1 " - " NAG A 2 " " NAG A 2 " - " BMA A 3 " " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " NAG-ASN " NAG A 1 " - " ASN C 343 " " NAG B 1 " - " ASN D 96 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 589.9 milliseconds 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1160 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 16 sheets defined 3.7% alpha, 22.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'C' and resid 337 through 343 Processing helix chain 'C' and resid 366 through 371 removed outlier: 4.186A pdb=" N SER C 371 " --> pdb=" O VAL C 367 " (cutoff:3.500A) Processing helix chain 'D' and resid 83 through 87 removed outlier: 3.795A pdb=" N THR D 87 " --> pdb=" O SER D 84 " (cutoff:3.500A) Processing helix chain 'E' and resid 198 through 202 removed outlier: 3.664A pdb=" N LEU E 201 " --> pdb=" O HIS E 198 " (cutoff:3.500A) removed outlier: 4.212A pdb=" N SER E 202 " --> pdb=" O GLN E 199 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 198 through 202' Processing sheet with id=AA1, first strand: chain 'C' and resid 357 through 358 removed outlier: 3.768A pdb=" N ILE C 402 " --> pdb=" O TYR C 508 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'D' and resid 3 through 6 removed outlier: 3.749A pdb=" N GLN D 3 " --> pdb=" O SER D 25 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N SER D 25 " --> pdb=" O GLN D 3 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N VAL D 5 " --> pdb=" O LYS D 23 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'D' and resid 10 through 12 removed outlier: 3.736A pdb=" N THR D 110 " --> pdb=" O GLU D 10 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N LYS D 12 " --> pdb=" O THR D 110 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 33 through 36 removed outlier: 3.786A pdb=" N GLY D 49 " --> pdb=" O TRP D 36 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'D' and resid 38 through 39 Processing sheet with id=AA7, first strand: chain 'D' and resid 93 through 94 removed outlier: 3.505A pdb=" N ILE D 102 " --> pdb=" O ALA D 94 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'D' and resid 97 through 98 removed outlier: 3.631A pdb=" N VAL D 100A" --> pdb=" O SER D 98 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.515A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 180 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'D' and resid 120 through 124 removed outlier: 3.515A pdb=" N GLY D 139 " --> pdb=" O LEU D 124 " (cutoff:3.500A) removed outlier: 3.859A pdb=" N SER D 180 " --> pdb=" O CYS D 140 " (cutoff:3.500A) removed outlier: 6.431A pdb=" N TYR D 176 " --> pdb=" O ASP D 144 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'D' and resid 151 through 152 removed outlier: 4.133A pdb=" N THR D 151 " --> pdb=" O ASN D 199 " (cutoff:3.500A) removed outlier: 3.930A pdb=" N ASN D 199 " --> pdb=" O THR D 151 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'E' and resid 10 through 12 Processing sheet with id=AB4, first strand: chain 'E' and resid 20 through 22 Processing sheet with id=AB5, first strand: chain 'E' and resid 45 through 49 removed outlier: 6.681A pdb=" N TRP E 35 " --> pdb=" O LEU E 47 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR E 49 " --> pdb=" O LEU E 33 " (cutoff:3.500A) removed outlier: 6.595A pdb=" N LEU E 33 " --> pdb=" O TYR E 49 " (cutoff:3.500A) removed outlier: 3.535A pdb=" N VAL E 85 " --> pdb=" O GLN E 38 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'E' and resid 114 through 118 removed outlier: 3.594A pdb=" N PHE E 116 " --> pdb=" O LEU E 135 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL E 133 " --> pdb=" O PHE E 118 " (cutoff:3.500A) removed outlier: 3.933A pdb=" N VAL E 132 " --> pdb=" O LEU E 179 " (cutoff:3.500A) removed outlier: 6.178A pdb=" N TYR E 173 " --> pdb=" O ASN E 138 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'E' and resid 145 through 148 removed outlier: 4.106A pdb=" N LYS E 145 " --> pdb=" O THR E 197 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N THR E 197 " --> pdb=" O LYS E 145 " (cutoff:3.500A) 86 hydrogen bonds defined for protein. 225 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: 1.18 Time building geometry restraints manager: 1.67 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: 1550 1.34 - 1.46: 1294 1.46 - 1.58: 2160 1.58 - 1.70: 0 1.70 - 1.82: 26 Bond restraints: 5030 Sorted by residual: bond pdb=" C1 MAN A 4 " pdb=" C2 MAN A 4 " ideal model delta sigma weight residual 1.526 1.580 -0.054 2.00e-02 2.50e+03 7.27e+00 bond pdb=" C1 MAN A 5 " pdb=" C2 MAN A 5 " ideal model delta sigma weight residual 1.526 1.567 -0.041 2.00e-02 2.50e+03 4.18e+00 bond pdb=" C1 MAN A 4 " pdb=" O5 MAN A 4 " ideal model delta sigma weight residual 1.399 1.437 -0.038 2.00e-02 2.50e+03 3.61e+00 bond pdb=" C5 MAN A 5 " pdb=" O5 MAN A 5 " ideal model delta sigma weight residual 1.418 1.455 -0.037 2.00e-02 2.50e+03 3.46e+00 bond pdb=" C1 BMA A 3 " pdb=" C2 BMA A 3 " ideal model delta sigma weight residual 1.519 1.556 -0.037 2.00e-02 2.50e+03 3.40e+00 ... (remaining 5025 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.66: 6592 1.66 - 3.31: 200 3.31 - 4.97: 43 4.97 - 6.63: 10 6.63 - 8.28: 2 Bond angle restraints: 6847 Sorted by residual: angle pdb=" CA GLY C 502 " pdb=" C GLY C 502 " pdb=" N VAL C 503 " ideal model delta sigma weight residual 114.23 116.84 -2.61 8.80e-01 1.29e+00 8.77e+00 angle pdb=" C PHE C 486 " pdb=" N ASN C 487 " pdb=" CA ASN C 487 " ideal model delta sigma weight residual 122.08 126.25 -4.17 1.47e+00 4.63e-01 8.06e+00 angle pdb=" C THR E 109 " pdb=" N VAL E 110 " pdb=" CA VAL E 110 " ideal model delta sigma weight residual 121.97 126.69 -4.72 1.80e+00 3.09e-01 6.87e+00 angle pdb=" N LYS D 201 " pdb=" CA LYS D 201 " pdb=" C LYS D 201 " ideal model delta sigma weight residual 109.81 115.60 -5.79 2.21e+00 2.05e-01 6.87e+00 angle pdb=" CA ASP E 185 " pdb=" C ASP E 185 " pdb=" N TYR E 186 " ideal model delta sigma weight residual 119.71 116.70 3.01 1.17e+00 7.31e-01 6.64e+00 ... (remaining 6842 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 22.68: 2866 22.68 - 45.36: 190 45.36 - 68.03: 15 68.03 - 90.71: 23 90.71 - 113.39: 10 Dihedral angle restraints: 3104 sinusoidal: 1291 harmonic: 1813 Sorted by residual: dihedral pdb=" CB CYS E 23 " pdb=" SG CYS E 23 " pdb=" SG CYS E 88 " pdb=" CB CYS E 88 " ideal model delta sinusoidal sigma weight residual 93.00 163.08 -70.08 1 1.00e+01 1.00e-02 6.33e+01 dihedral pdb=" CB CYS D 22 " pdb=" SG CYS D 22 " pdb=" SG CYS D 92 " pdb=" CB CYS D 92 " ideal model delta sinusoidal sigma weight residual 93.00 143.13 -50.13 1 1.00e+01 1.00e-02 3.45e+01 dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual -86.00 -133.21 47.21 1 1.00e+01 1.00e-02 3.08e+01 ... (remaining 3101 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.055: 638 0.055 - 0.110: 121 0.110 - 0.165: 22 0.165 - 0.220: 2 0.220 - 0.276: 3 Chirality restraints: 786 Sorted by residual: chirality pdb=" C5 BMA B 3 " pdb=" C4 BMA B 3 " pdb=" C6 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.55 0.28 2.00e-01 2.50e+01 1.90e+00 chirality pdb=" CB ILE C 468 " pdb=" CA ILE C 468 " pdb=" CG1 ILE C 468 " pdb=" CG2 ILE C 468 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.27 2.00e-01 2.50e+01 1.79e+00 chirality pdb=" C5 BMA A 3 " pdb=" C4 BMA A 3 " pdb=" C6 BMA A 3 " pdb=" O5 BMA A 3 " both_signs ideal model delta sigma weight residual False -2.27 -2.54 0.26 2.00e-01 2.50e+01 1.75e+00 ... (remaining 783 not shown) Planarity restraints: 871 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE D 146 " -0.028 5.00e-02 4.00e+02 4.28e-02 2.93e+00 pdb=" N PRO D 147 " 0.074 5.00e-02 4.00e+02 pdb=" CA PRO D 147 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO D 147 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU E 79 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.10e+00 pdb=" N PRO E 80 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO E 80 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO E 80 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA C 520 " -0.023 5.00e-02 4.00e+02 3.52e-02 1.98e+00 pdb=" N PRO C 521 " 0.061 5.00e-02 4.00e+02 pdb=" CA PRO C 521 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO C 521 " -0.020 5.00e-02 4.00e+02 ... (remaining 868 not shown) Histogram of nonbonded interaction distances: 2.18 - 2.72: 297 2.72 - 3.27: 4858 3.27 - 3.81: 7198 3.81 - 4.36: 8340 4.36 - 4.90: 14373 Nonbonded interactions: 35066 Sorted by model distance: nonbonded pdb=" OD2 ASP E 82 " pdb=" OH TYR E 86 " model vdw 2.181 3.040 nonbonded pdb=" O SER E 171 " pdb=" OG SER E 171 " model vdw 2.240 3.040 nonbonded pdb=" OG SER E 182 " pdb=" NZ LYS E 188 " model vdw 2.245 3.120 nonbonded pdb=" O4 MAN A 5 " pdb=" O6 MAN A 5 " model vdw 2.266 3.040 nonbonded pdb=" OE2 GLU E 105 " pdb=" NE2 GLN E 166 " model vdw 2.302 3.120 ... (remaining 35061 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: 8.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 0.200 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.690 Find NCS groups from input model: 0.080 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:3.010 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7903 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5030 Z= 0.229 Angle : 0.719 8.282 6847 Z= 0.350 Chirality : 0.048 0.276 786 Planarity : 0.005 0.043 869 Dihedral : 16.973 113.391 1917 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.70 % Favored : 88.65 % Rotamer: Outliers : 0.19 % Allowed : 0.37 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.85 (0.33), residues: 617 helix: -4.54 (0.94), residues: 13 sheet: -1.37 (0.38), residues: 207 loop : -2.18 (0.30), residues: 397 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP C 353 HIS 0.003 0.001 HIS D 200 PHE 0.013 0.001 PHE E 118 TYR 0.011 0.001 TYR D 145 ARG 0.004 0.001 ARG D 44 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 103 time to evaluate : 0.567 Fit side-chains REVERT: D 82 LEU cc_start: 0.8695 (mt) cc_final: 0.8347 (mm) REVERT: D 90 TYR cc_start: 0.8121 (m-10) cc_final: 0.7531 (m-80) REVERT: D 155 ASN cc_start: 0.8474 (OUTLIER) cc_final: 0.8181 (t0) REVERT: D 201 LYS cc_start: 0.8906 (pptt) cc_final: 0.8632 (pptt) REVERT: E 82 ASP cc_start: 0.8046 (t70) cc_final: 0.7829 (t0) REVERT: E 123 GLU cc_start: 0.8605 (tp30) cc_final: 0.8375 (tp30) outliers start: 1 outliers final: 0 residues processed: 103 average time/residue: 0.2414 time to fit residues: 32.0003 Evaluate side-chains 82 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 81 time to evaluate : 0.994 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 46 optimal weight: 0.4980 chunk 25 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 1.9990 chunk 35 optimal weight: 0.0570 chunk 55 optimal weight: 4.9990 overall best weight: 0.5898 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 388 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 58 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.066698 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.057726 restraints weight = 19281.463| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3132 r_free = 0.3132 target = 0.059545 restraints weight = 10543.530| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.060794 restraints weight = 6610.291| |-----------------------------------------------------------------------------| r_work (final): 0.3158 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8163 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 5030 Z= 0.233 Angle : 0.733 10.502 6847 Z= 0.355 Chirality : 0.046 0.172 786 Planarity : 0.005 0.044 869 Dihedral : 13.559 90.379 839 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.37 % Favored : 88.82 % Rotamer: Outliers : 0.93 % Allowed : 10.02 % Favored : 89.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.77 (0.33), residues: 617 helix: -4.06 (1.12), residues: 13 sheet: -0.94 (0.40), residues: 189 loop : -2.35 (0.28), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.003 0.001 HIS C 519 PHE 0.015 0.001 PHE E 118 TYR 0.010 0.001 TYR C 380 ARG 0.006 0.001 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 90 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: C 389 ASP cc_start: 0.8442 (p0) cc_final: 0.8183 (p0) REVERT: D 155 ASN cc_start: 0.8621 (OUTLIER) cc_final: 0.8332 (t0) REVERT: D 176 TYR cc_start: 0.8048 (m-10) cc_final: 0.7743 (m-10) REVERT: D 194 TYR cc_start: 0.3671 (m-80) cc_final: 0.3436 (m-10) REVERT: E 123 GLU cc_start: 0.8752 (tp30) cc_final: 0.8466 (tp30) REVERT: E 167 ASP cc_start: 0.8347 (t70) cc_final: 0.8128 (m-30) outliers start: 5 outliers final: 2 residues processed: 92 average time/residue: 0.2295 time to fit residues: 26.9347 Evaluate side-chains 84 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 81 time to evaluate : 0.610 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 50 optimal weight: 0.9980 chunk 60 optimal weight: 4.9990 chunk 18 optimal weight: 2.9990 chunk 11 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 58 optimal weight: 0.0970 chunk 27 optimal weight: 0.7980 chunk 51 optimal weight: 3.9990 chunk 10 optimal weight: 0.9990 chunk 16 optimal weight: 0.6980 chunk 25 optimal weight: 0.5980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 = 0.3284 r_free = 0.3284 target = 0.065628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.056444 restraints weight = 19534.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.058358 restraints weight = 10410.617| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.059661 restraints weight = 6428.330| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.1915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5030 Z= 0.223 Angle : 0.703 11.003 6847 Z= 0.339 Chirality : 0.046 0.156 786 Planarity : 0.005 0.047 869 Dihedral : 11.931 82.997 839 Min Nonbonded Distance : 2.389 Molprobity Statistics. All-atom Clashscore : 9.64 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.86 % Favored : 88.33 % Rotamer: Outliers : 1.30 % Allowed : 13.91 % Favored : 84.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.69 (0.33), residues: 617 helix: -2.19 (2.15), residues: 7 sheet: -0.94 (0.39), residues: 189 loop : -2.34 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 436 HIS 0.004 0.002 HIS C 519 PHE 0.009 0.001 PHE D 146 TYR 0.020 0.001 TYR C 380 ARG 0.007 0.001 ARG C 454 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 86 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 155 ASN cc_start: 0.8575 (OUTLIER) cc_final: 0.8299 (t0) REVERT: D 176 TYR cc_start: 0.8058 (m-10) cc_final: 0.7665 (m-10) REVERT: E 82 ASP cc_start: 0.8862 (t0) cc_final: 0.8632 (t0) REVERT: E 123 GLU cc_start: 0.8717 (tp30) cc_final: 0.8491 (tp30) REVERT: E 167 ASP cc_start: 0.8326 (t70) cc_final: 0.8080 (m-30) outliers start: 7 outliers final: 2 residues processed: 88 average time/residue: 0.3512 time to fit residues: 41.6925 Evaluate side-chains 83 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 80 time to evaluate : 0.564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 55 optimal weight: 0.0070 chunk 27 optimal weight: 2.9990 chunk 30 optimal weight: 0.9990 chunk 3 optimal weight: 0.8980 chunk 5 optimal weight: 0.0970 chunk 33 optimal weight: 0.8980 chunk 13 optimal weight: 1.9990 chunk 8 optimal weight: 0.0980 chunk 35 optimal weight: 0.2980 overall best weight: 0.2596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 388 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.067036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.058025 restraints weight = 19711.171| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059869 restraints weight = 10740.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3171 r_free = 0.3171 target = 0.061102 restraints weight = 6708.730| |-----------------------------------------------------------------------------| r_work (final): 0.3167 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8152 moved from start: 0.2177 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5030 Z= 0.175 Angle : 0.667 10.727 6847 Z= 0.321 Chirality : 0.046 0.152 786 Planarity : 0.005 0.044 869 Dihedral : 10.110 71.146 839 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.49 % Allowed : 9.40 % Favored : 90.11 % Rotamer: Outliers : 1.86 % Allowed : 14.84 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.64 (0.33), residues: 617 helix: -2.12 (2.14), residues: 7 sheet: -0.95 (0.38), residues: 200 loop : -2.31 (0.29), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 PHE 0.005 0.001 PHE E 118 TYR 0.026 0.001 TYR C 380 ARG 0.006 0.001 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 86 time to evaluate : 0.503 Fit side-chains REVERT: C 380 TYR cc_start: 0.6409 (m-10) cc_final: 0.6190 (m-10) REVERT: D 155 ASN cc_start: 0.8550 (OUTLIER) cc_final: 0.8253 (t0) REVERT: D 176 TYR cc_start: 0.8040 (m-10) cc_final: 0.7724 (m-10) REVERT: E 82 ASP cc_start: 0.8788 (t0) cc_final: 0.8471 (t0) REVERT: E 123 GLU cc_start: 0.8623 (tp30) cc_final: 0.8373 (tp30) REVERT: E 167 ASP cc_start: 0.8298 (t70) cc_final: 0.8072 (m-30) outliers start: 10 outliers final: 5 residues processed: 91 average time/residue: 0.2299 time to fit residues: 26.7201 Evaluate side-chains 85 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 79 time to evaluate : 0.527 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 2 optimal weight: 0.9990 chunk 47 optimal weight: 3.9990 chunk 25 optimal weight: 0.7980 chunk 11 optimal weight: 4.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.7980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.064822 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3046 r_free = 0.3046 target = 0.055971 restraints weight = 20001.086| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.057778 restraints weight = 10802.858| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.058964 restraints weight = 6718.284| |-----------------------------------------------------------------------------| r_work (final): 0.3112 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5030 Z= 0.255 Angle : 0.709 11.537 6847 Z= 0.346 Chirality : 0.046 0.168 786 Planarity : 0.006 0.053 869 Dihedral : 9.721 68.900 839 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.65 % Allowed : 11.35 % Favored : 88.01 % Rotamer: Outliers : 2.41 % Allowed : 16.51 % Favored : 81.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.65 (0.33), residues: 617 helix: -1.84 (2.25), residues: 7 sheet: -0.90 (0.40), residues: 189 loop : -2.33 (0.28), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.001 HIS C 519 PHE 0.015 0.001 PHE D 146 TYR 0.018 0.001 TYR C 380 ARG 0.013 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 84 time to evaluate : 0.573 Fit side-chains revert: symmetry clash REVERT: C 498 GLN cc_start: 0.8869 (mm110) cc_final: 0.8572 (mm110) REVERT: D 10 GLU cc_start: 0.8403 (mp0) cc_final: 0.8149 (mp0) REVERT: D 155 ASN cc_start: 0.8517 (OUTLIER) cc_final: 0.8246 (t0) REVERT: D 176 TYR cc_start: 0.8127 (m-10) cc_final: 0.7682 (m-10) REVERT: E 82 ASP cc_start: 0.8848 (t0) cc_final: 0.8480 (t0) REVERT: E 123 GLU cc_start: 0.8689 (tp30) cc_final: 0.8459 (tp30) REVERT: E 167 ASP cc_start: 0.8386 (t70) cc_final: 0.8080 (m-30) outliers start: 13 outliers final: 9 residues processed: 90 average time/residue: 0.2086 time to fit residues: 23.9357 Evaluate side-chains 90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 15 optimal weight: 1.9990 chunk 20 optimal weight: 0.2980 chunk 38 optimal weight: 0.3980 chunk 55 optimal weight: 4.9990 chunk 23 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 16 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.063949 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3017 r_free = 0.3017 target = 0.054913 restraints weight = 19802.024| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056774 restraints weight = 10646.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057995 restraints weight = 6610.248| |-----------------------------------------------------------------------------| r_work (final): 0.3090 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8245 moved from start: 0.2520 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 5030 Z= 0.271 Angle : 0.723 11.909 6847 Z= 0.354 Chirality : 0.046 0.177 786 Planarity : 0.006 0.083 869 Dihedral : 9.516 67.214 839 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.37 % Favored : 88.82 % Rotamer: Outliers : 2.23 % Allowed : 18.55 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.76 (0.32), residues: 617 helix: -4.11 (0.91), residues: 19 sheet: -0.95 (0.40), residues: 187 loop : -2.29 (0.28), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 436 HIS 0.013 0.003 HIS C 519 PHE 0.009 0.001 PHE E 118 TYR 0.020 0.001 TYR C 380 ARG 0.018 0.001 ARG D 71 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 81 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: C 498 GLN cc_start: 0.8866 (mm110) cc_final: 0.8595 (mm-40) REVERT: D 155 ASN cc_start: 0.8500 (OUTLIER) cc_final: 0.8279 (t0) REVERT: E 82 ASP cc_start: 0.8912 (t0) cc_final: 0.8443 (t0) REVERT: E 123 GLU cc_start: 0.8673 (tp30) cc_final: 0.8448 (tp30) REVERT: E 167 ASP cc_start: 0.8413 (t70) cc_final: 0.8068 (m-30) outliers start: 12 outliers final: 8 residues processed: 86 average time/residue: 0.2910 time to fit residues: 32.5393 Evaluate side-chains 87 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 78 time to evaluate : 1.927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 198 VAL Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 21 optimal weight: 0.6980 chunk 58 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 1 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 59 optimal weight: 0.9990 chunk 32 optimal weight: 0.0070 chunk 18 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.055142 restraints weight = 19358.252| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.057057 restraints weight = 10405.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3106 r_free = 0.3106 target = 0.058341 restraints weight = 6437.439| |-----------------------------------------------------------------------------| r_work (final): 0.3100 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.2602 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 5030 Z= 0.239 Angle : 0.718 11.919 6847 Z= 0.351 Chirality : 0.046 0.190 786 Planarity : 0.005 0.047 869 Dihedral : 8.978 63.163 839 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.70 % Favored : 88.65 % Rotamer: Outliers : 2.23 % Allowed : 18.00 % Favored : 79.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.77 (0.32), residues: 617 helix: -3.54 (1.25), residues: 13 sheet: -0.97 (0.39), residues: 187 loop : -2.35 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.004 0.001 HIS C 519 PHE 0.011 0.001 PHE E 118 TYR 0.016 0.001 TYR C 380 ARG 0.005 0.000 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.513 Fit side-chains revert: symmetry clash REVERT: C 388 ASN cc_start: 0.7852 (m-40) cc_final: 0.7549 (m-40) REVERT: C 498 GLN cc_start: 0.8908 (mm110) cc_final: 0.8622 (mm-40) REVERT: D 72 ASP cc_start: 0.8718 (t0) cc_final: 0.8475 (t0) REVERT: D 155 ASN cc_start: 0.8430 (OUTLIER) cc_final: 0.8230 (t0) REVERT: D 176 TYR cc_start: 0.8134 (m-10) cc_final: 0.7827 (m-10) REVERT: E 82 ASP cc_start: 0.8976 (t0) cc_final: 0.8558 (t0) REVERT: E 123 GLU cc_start: 0.8618 (tp30) cc_final: 0.8391 (tp30) REVERT: E 167 ASP cc_start: 0.8438 (t70) cc_final: 0.8101 (m-30) outliers start: 12 outliers final: 9 residues processed: 85 average time/residue: 0.1712 time to fit residues: 18.5935 Evaluate side-chains 89 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 79 time to evaluate : 0.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 155 ASN Chi-restraints excluded: chain D residue 189 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 19 optimal weight: 0.6980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 58 optimal weight: 0.4980 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 35 optimal weight: 0.0970 chunk 54 optimal weight: 0.4980 chunk 45 optimal weight: 0.5980 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3265 r_free = 0.3265 target = 0.064728 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.055737 restraints weight = 19684.040| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3087 r_free = 0.3087 target = 0.057595 restraints weight = 10638.754| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3118 r_free = 0.3118 target = 0.058831 restraints weight = 6618.003| |-----------------------------------------------------------------------------| r_work (final): 0.3110 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.2752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.054 5030 Z= 0.209 Angle : 0.707 11.798 6847 Z= 0.343 Chirality : 0.046 0.205 786 Planarity : 0.005 0.046 869 Dihedral : 8.500 59.750 839 Min Nonbonded Distance : 2.387 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.49 % Allowed : 10.70 % Favored : 88.82 % Rotamer: Outliers : 1.67 % Allowed : 19.11 % Favored : 79.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.76 (0.32), residues: 617 helix: -3.57 (1.23), residues: 13 sheet: -0.99 (0.39), residues: 187 loop : -2.32 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.005 0.002 HIS C 519 PHE 0.014 0.001 PHE E 62 TYR 0.012 0.001 TYR C 380 ARG 0.009 0.001 ARG D 41 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.510 Fit side-chains revert: symmetry clash REVERT: C 388 ASN cc_start: 0.7798 (m-40) cc_final: 0.7516 (m-40) REVERT: C 465 GLU cc_start: 0.8752 (tp30) cc_final: 0.8438 (tp30) REVERT: C 498 GLN cc_start: 0.8844 (mm110) cc_final: 0.8546 (mm-40) REVERT: D 176 TYR cc_start: 0.8088 (m-10) cc_final: 0.7813 (m-10) REVERT: E 82 ASP cc_start: 0.8928 (t0) cc_final: 0.8500 (t0) REVERT: E 123 GLU cc_start: 0.8585 (tp30) cc_final: 0.8382 (tp30) REVERT: E 167 ASP cc_start: 0.8380 (t70) cc_final: 0.8047 (m-30) outliers start: 9 outliers final: 9 residues processed: 84 average time/residue: 0.2039 time to fit residues: 22.1217 Evaluate side-chains 90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.547 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain C residue 519 HIS Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 46 optimal weight: 3.9990 chunk 35 optimal weight: 0.0970 chunk 25 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 37 optimal weight: 5.9990 chunk 33 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 9 optimal weight: 0.5980 chunk 53 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 519 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.064620 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3048 r_free = 0.3048 target = 0.055652 restraints weight = 19308.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.057466 restraints weight = 10487.646| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.058685 restraints weight = 6573.321| |-----------------------------------------------------------------------------| r_work (final): 0.3113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5030 Z= 0.240 Angle : 0.734 11.952 6847 Z= 0.359 Chirality : 0.046 0.222 786 Planarity : 0.005 0.046 869 Dihedral : 8.306 58.793 837 Min Nonbonded Distance : 2.386 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.49 % Allowed : 11.18 % Favored : 88.33 % Rotamer: Outliers : 2.23 % Allowed : 18.92 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.79 (0.32), residues: 617 helix: -3.54 (1.24), residues: 13 sheet: -1.06 (0.39), residues: 187 loop : -2.32 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.008 0.002 HIS C 519 PHE 0.014 0.001 PHE E 62 TYR 0.019 0.001 TYR C 380 ARG 0.004 0.001 ARG E 54 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 79 time to evaluate : 0.637 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 388 ASN cc_start: 0.7814 (m-40) cc_final: 0.7537 (m-40) REVERT: C 465 GLU cc_start: 0.8791 (tp30) cc_final: 0.8466 (tp30) REVERT: C 498 GLN cc_start: 0.8884 (mm110) cc_final: 0.8566 (mm-40) REVERT: D 176 TYR cc_start: 0.8079 (m-10) cc_final: 0.7769 (m-10) REVERT: E 82 ASP cc_start: 0.8980 (t0) cc_final: 0.8566 (t0) REVERT: E 123 GLU cc_start: 0.8595 (tp30) cc_final: 0.8390 (tp30) REVERT: E 167 ASP cc_start: 0.8439 (t70) cc_final: 0.8112 (m-30) outliers start: 12 outliers final: 8 residues processed: 85 average time/residue: 0.2073 time to fit residues: 22.8653 Evaluate side-chains 88 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 80 time to evaluate : 0.578 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 24 optimal weight: 0.9980 chunk 45 optimal weight: 0.1980 chunk 49 optimal weight: 0.8980 chunk 54 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.9980 chunk 6 optimal weight: 2.9990 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.064036 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.055047 restraints weight = 19501.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3077 r_free = 0.3077 target = 0.056870 restraints weight = 10644.000| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.058042 restraints weight = 6652.866| |-----------------------------------------------------------------------------| r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8247 moved from start: 0.2930 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 5030 Z= 0.256 Angle : 0.743 12.364 6847 Z= 0.365 Chirality : 0.046 0.224 786 Planarity : 0.005 0.046 869 Dihedral : 8.197 58.758 837 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 10.26 Ramachandran Plot: Outliers : 0.81 % Allowed : 10.86 % Favored : 88.33 % Rotamer: Outliers : 2.04 % Allowed : 19.11 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.82 (0.32), residues: 617 helix: -3.50 (1.26), residues: 13 sheet: -1.15 (0.39), residues: 187 loop : -2.31 (0.28), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 436 HIS 0.004 0.001 HIS D 200 PHE 0.012 0.001 PHE E 62 TYR 0.020 0.001 TYR C 380 ARG 0.010 0.001 ARG D 41 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1234 Ramachandran restraints generated. 617 Oldfield, 0 Emsley, 617 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 83 time to evaluate : 1.259 Fit side-chains revert: symmetry clash REVERT: C 388 ASN cc_start: 0.7759 (m-40) cc_final: 0.7507 (m-40) REVERT: C 465 GLU cc_start: 0.8794 (tp30) cc_final: 0.8503 (tp30) REVERT: C 498 GLN cc_start: 0.8890 (mm110) cc_final: 0.8593 (mm-40) REVERT: D 175 LEU cc_start: 0.8127 (OUTLIER) cc_final: 0.7831 (pp) REVERT: D 176 TYR cc_start: 0.8156 (m-10) cc_final: 0.7804 (m-10) REVERT: E 82 ASP cc_start: 0.8977 (t0) cc_final: 0.8583 (t0) REVERT: E 167 ASP cc_start: 0.8453 (t70) cc_final: 0.8121 (m-30) outliers start: 11 outliers final: 8 residues processed: 89 average time/residue: 0.2557 time to fit residues: 29.6399 Evaluate side-chains 90 residues out of total 540 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 81 time to evaluate : 0.541 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 512 VAL Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 56 ASN Chi-restraints excluded: chain D residue 138 LEU Chi-restraints excluded: chain D residue 175 LEU Chi-restraints excluded: chain E residue 178 THR Chi-restraints excluded: chain E residue 189 HIS Chi-restraints excluded: chain E residue 194 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 1 optimal weight: 0.7980 chunk 33 optimal weight: 1.9990 chunk 56 optimal weight: 0.5980 chunk 45 optimal weight: 0.0980 chunk 40 optimal weight: 0.0270 chunk 17 optimal weight: 2.9990 chunk 54 optimal weight: 1.9990 chunk 38 optimal weight: 0.9990 chunk 10 optimal weight: 0.3980 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 0.8980 overall best weight: 0.3838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 448 ASN ** D 39 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 197 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3285 r_free = 0.3285 target = 0.065280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 24)----------------| | r_work = 0.3062 r_free = 0.3062 target = 0.056206 restraints weight = 19421.810| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 22)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.058068 restraints weight = 10481.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3137 r_free = 0.3137 target = 0.059301 restraints weight = 6515.181| |-----------------------------------------------------------------------------| r_work (final): 0.3130 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8204 moved from start: 0.2962 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 5030 Z= 0.202 Angle : 0.730 11.939 6847 Z= 0.360 Chirality : 0.046 0.221 786 Planarity : 0.005 0.045 869 Dihedral : 7.683 59.805 837 Min Nonbonded Distance : 2.388 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.65 % Allowed : 10.05 % Favored : 89.30 % Rotamer: Outliers : 1.67 % Allowed : 19.48 % Favored : 78.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.86 % 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: -2.77 (0.32), residues: 617 helix: -3.62 (1.19), residues: 13 sheet: -1.17 (0.39), residues: 187 loop : -2.23 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 436 HIS 0.003 0.001 HIS D 200 PHE 0.007 0.001 PHE E 118 TYR 0.018 0.001 TYR C 380 ARG 0.004 0.000 ARG E 142 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3139.61 seconds wall clock time: 57 minutes 49.20 seconds (3469.20 seconds total)