Starting phenix.real_space_refine on Mon Sep 23 20:34:48 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/09_2024/7r1d_14239.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/09_2024/7r1d_14239.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/09_2024/7r1d_14239.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/09_2024/7r1d_14239.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/09_2024/7r1d_14239.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r1d_14239/09_2024/7r1d_14239.cif" } resolution = 3.5 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 19 5.16 5 C 3279 2.51 5 N 904 2.21 5 O 981 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 38 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 5183 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1549 Number of conformers: 1 Conformer: "" Number of residues, atoms: 192, 1549 Classifications: {'peptide': 192} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 11, 'TRANS': 180} Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASP:plan': 1} Unresolved non-hydrogen planarities: 3 Chain: "A" Number of atoms: 3206 Number of conformers: 1 Conformer: "" Number of residues, atoms: 405, 3206 Classifications: {'peptide': 405} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 22, 'TRANS': 382} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 26 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'PHE:plan': 1, 'GLU:plan': 1, 'ASP:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 428 Number of conformers: 1 Conformer: "" Number of residues, atoms: 56, 428 Classifications: {'peptide': 56} Incomplete info: {'backbone_only': 2, 'truncation_to_alanine': 4} Link IDs: {'PTRANS': 7, 'TRANS': 48} Chain breaks: 1 Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 1, 'ASN:plan1': 1} Unresolved non-hydrogen planarities: 12 Time building chain proxies: 3.63, per 1000 atoms: 0.70 Number of scatterers: 5183 At special positions: 0 Unit cell: (68.04, 85.05, 99.792, 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 19 16.00 O 981 8.00 N 904 7.00 C 3279 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: 1.28 Conformation dependent library (CDL) restraints added in 576.9 milliseconds 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1234 Finding SS restraints... Secondary structure from input PDB file: 14 helices and 12 sheets defined 21.4% alpha, 24.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.65 Creating SS restraints... Processing helix chain 'C' and resid 96 through 114 Processing helix chain 'C' and resid 115 through 127 removed outlier: 3.608A pdb=" N TRP C 126 " --> pdb=" O CYS C 122 " (cutoff:3.500A) Processing helix chain 'C' and resid 132 through 137 Processing helix chain 'C' and resid 140 through 150 Processing helix chain 'C' and resid 159 through 169 removed outlier: 3.717A pdb=" N LYS C 165 " --> pdb=" O VAL C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 177 through 199 Processing helix chain 'C' and resid 281 through 286 removed outlier: 3.548A pdb=" N PHE C 285 " --> pdb=" O PRO C 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 9 through 27 Processing helix chain 'A' and resid 27 through 31 removed outlier: 4.253A pdb=" N LEU A 31 " --> pdb=" O ASN A 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 27 through 31' Processing helix chain 'A' and resid 348 through 350 No H-bonds generated for 'chain 'A' and resid 348 through 350' Processing helix chain 'A' and resid 356 through 360 removed outlier: 3.892A pdb=" N ALA A 359 " --> pdb=" O PRO A 356 " (cutoff:3.500A) Processing helix chain 'A' and resid 406 through 409 Processing helix chain 'B' and resid 107 through 109 No H-bonds generated for 'chain 'B' and resid 107 through 109' Processing helix chain 'B' and resid 114 through 125 removed outlier: 4.116A pdb=" N ILE B 118 " --> pdb=" O PRO B 114 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'C' and resid 157 through 158 removed outlier: 3.856A pdb=" N PHE A 93 " --> pdb=" O LEU C 158 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 216 through 217 removed outlier: 3.769A pdb=" N MET C 280 " --> pdb=" O ILE C 216 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 263 through 267 removed outlier: 6.958A pdb=" N THR C 251 " --> pdb=" O VAL C 245 " (cutoff:3.500A) removed outlier: 5.222A pdb=" N VAL C 245 " --> pdb=" O THR C 251 " (cutoff:3.500A) removed outlier: 6.631A pdb=" N ARG C 253 " --> pdb=" O ASP C 243 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 32 through 39 removed outlier: 3.982A pdb=" N ILE A 398 " --> pdb=" O SER A 394 " (cutoff:3.500A) removed outlier: 3.697A pdb=" N ASP A 379 " --> pdb=" O VAL A 393 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 48 through 49 removed outlier: 3.660A pdb=" N GLN A 48 " --> pdb=" O VAL A 67 " (cutoff:3.500A) removed outlier: 4.097A pdb=" N ASN A 77 " --> pdb=" O HIS A 123 " (cutoff:3.500A) removed outlier: 4.026A pdb=" N HIS A 123 " --> pdb=" O ASN A 77 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 119 " --> pdb=" O ILE A 81 " (cutoff:3.500A) removed outlier: 6.128A pdb=" N SER A 83 " --> pdb=" O ILE A 117 " (cutoff:3.500A) removed outlier: 5.744A pdb=" N ILE A 117 " --> pdb=" O SER A 83 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 61 through 63 Processing sheet with id=AA7, first strand: chain 'A' and resid 130 through 133 removed outlier: 5.561A pdb=" N ILE A 139 " --> pdb=" O MET A 133 " (cutoff:3.500A) removed outlier: 6.452A pdb=" N ARG A 172 " --> pdb=" O VAL A 217 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 183 through 185 Processing sheet with id=AA9, first strand: chain 'A' and resid 230 through 235 removed outlier: 3.737A pdb=" N ALA A 247 " --> pdb=" O LYS A 251 " (cutoff:3.500A) removed outlier: 4.373A pdb=" N LYS A 251 " --> pdb=" O ALA A 247 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 276 through 281 removed outlier: 3.608A pdb=" N CYS A 278 " --> pdb=" O GLY A 292 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N HIS A 311 " --> pdb=" O LEU A 300 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 322 through 325 removed outlier: 6.664A pdb=" N ASP A 346 " --> pdb=" O LEU A 366 " (cutoff:3.500A) removed outlier: 5.764A pdb=" N LEU A 366 " --> pdb=" O ASP A 346 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 96 through 99 removed outlier: 3.792A pdb=" N ILE B 97 " --> pdb=" O VAL B 104 " (cutoff:3.500A) removed outlier: 4.059A pdb=" N VAL B 104 " --> pdb=" O ILE B 97 " (cutoff:3.500A) 180 hydrogen bonds defined for protein. 495 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: 1.43 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: 1664 1.34 - 1.45: 788 1.45 - 1.57: 2838 1.57 - 1.69: 0 1.69 - 1.81: 27 Bond restraints: 5317 Sorted by residual: bond pdb=" CA GLU A 286 " pdb=" C GLU A 286 " ideal model delta sigma weight residual 1.523 1.497 0.027 1.80e-02 3.09e+03 2.20e+00 bond pdb=" CB PRO C 173 " pdb=" CG PRO C 173 " ideal model delta sigma weight residual 1.492 1.565 -0.073 5.00e-02 4.00e+02 2.13e+00 bond pdb=" CD1 TYR A 98 " pdb=" CE1 TYR A 98 " ideal model delta sigma weight residual 1.382 1.342 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CB TYR A 98 " pdb=" CG TYR A 98 " ideal model delta sigma weight residual 1.512 1.485 0.027 2.20e-02 2.07e+03 1.49e+00 bond pdb=" CA ILE A 81 " pdb=" C ILE A 81 " ideal model delta sigma weight residual 1.527 1.518 0.009 8.50e-03 1.38e+04 1.11e+00 ... (remaining 5312 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.40: 7080 2.40 - 4.81: 121 4.81 - 7.21: 17 7.21 - 9.61: 2 9.61 - 12.02: 2 Bond angle restraints: 7222 Sorted by residual: angle pdb=" C HIS A 97 " pdb=" N TYR A 98 " pdb=" CA TYR A 98 " ideal model delta sigma weight residual 121.54 111.77 9.77 1.91e+00 2.74e-01 2.62e+01 angle pdb=" C LEU C 198 " pdb=" N GLN C 199 " pdb=" CA GLN C 199 " ideal model delta sigma weight residual 122.56 114.04 8.52 1.72e+00 3.38e-01 2.45e+01 angle pdb=" C GLY A 107 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta sigma weight residual 122.41 131.60 -9.19 2.09e+00 2.29e-01 1.93e+01 angle pdb=" CA PRO C 173 " pdb=" N PRO C 173 " pdb=" CD PRO C 173 " ideal model delta sigma weight residual 112.00 106.57 5.43 1.40e+00 5.10e-01 1.51e+01 angle pdb=" CA LEU C 212 " pdb=" CB LEU C 212 " pdb=" CG LEU C 212 " ideal model delta sigma weight residual 116.30 128.32 -12.02 3.50e+00 8.16e-02 1.18e+01 ... (remaining 7217 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.09: 2844 16.09 - 32.18: 270 32.18 - 48.26: 50 48.26 - 64.35: 18 64.35 - 80.44: 3 Dihedral angle restraints: 3185 sinusoidal: 1288 harmonic: 1897 Sorted by residual: dihedral pdb=" CA GLY A 107 " pdb=" C GLY A 107 " pdb=" N PHE A 108 " pdb=" CA PHE A 108 " ideal model delta harmonic sigma weight residual 180.00 152.22 27.78 0 5.00e+00 4.00e-02 3.09e+01 dihedral pdb=" CA SER A 315 " pdb=" C SER A 315 " pdb=" N HIS A 316 " pdb=" CA HIS A 316 " ideal model delta harmonic sigma weight residual 180.00 157.42 22.58 0 5.00e+00 4.00e-02 2.04e+01 dihedral pdb=" CA HIS A 78 " pdb=" C HIS A 78 " pdb=" N LEU A 79 " pdb=" CA LEU A 79 " ideal model delta harmonic sigma weight residual 180.00 158.10 21.90 0 5.00e+00 4.00e-02 1.92e+01 ... (remaining 3182 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.033: 449 0.033 - 0.067: 194 0.067 - 0.100: 93 0.100 - 0.133: 44 0.133 - 0.167: 3 Chirality restraints: 783 Sorted by residual: chirality pdb=" CA GLN C 199 " pdb=" N GLN C 199 " pdb=" C GLN C 199 " pdb=" CB GLN C 199 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.95e-01 chirality pdb=" CA THR A 28 " pdb=" N THR A 28 " pdb=" C THR A 28 " pdb=" CB THR A 28 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CG LEU C 212 " pdb=" CB LEU C 212 " pdb=" CD1 LEU C 212 " pdb=" CD2 LEU C 212 " both_signs ideal model delta sigma weight residual False -2.59 -2.44 -0.15 2.00e-01 2.50e+01 5.47e-01 ... (remaining 780 not shown) Planarity restraints: 940 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS C 172 " 0.084 5.00e-02 4.00e+02 1.24e-01 2.47e+01 pdb=" N PRO C 173 " -0.215 5.00e-02 4.00e+02 pdb=" CA PRO C 173 " 0.066 5.00e-02 4.00e+02 pdb=" CD PRO C 173 " 0.065 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA GLY A 107 " -0.011 2.00e-02 2.50e+03 2.27e-02 5.15e+00 pdb=" C GLY A 107 " 0.039 2.00e-02 2.50e+03 pdb=" O GLY A 107 " -0.015 2.00e-02 2.50e+03 pdb=" N PHE A 108 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP A 24 " -0.017 2.00e-02 2.50e+03 1.31e-02 4.31e+00 pdb=" CG TRP A 24 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TRP A 24 " -0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP A 24 " 0.002 2.00e-02 2.50e+03 pdb=" NE1 TRP A 24 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP A 24 " 0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP A 24 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 24 " 0.003 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 24 " -0.002 2.00e-02 2.50e+03 pdb=" CH2 TRP A 24 " -0.009 2.00e-02 2.50e+03 ... (remaining 937 not shown) Histogram of nonbonded interaction distances: 2.10 - 2.66: 107 2.66 - 3.22: 5036 3.22 - 3.78: 8356 3.78 - 4.34: 11320 4.34 - 4.90: 18569 Nonbonded interactions: 43388 Sorted by model distance: nonbonded pdb=" OG1 THR C 227 " pdb=" OD1 ASN C 274 " model vdw 2.097 3.040 nonbonded pdb=" NE2 GLN A 76 " pdb=" OD1 ASN A 122 " model vdw 2.157 3.120 nonbonded pdb=" OD1 ASP A 379 " pdb=" N PHE A 380 " model vdw 2.180 3.120 nonbonded pdb=" O GLU A 275 " pdb=" OG SER A 293 " model vdw 2.189 3.040 nonbonded pdb=" OH TYR A 284 " pdb=" O PRO A 327 " model vdw 2.190 3.040 ... (remaining 43383 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: 0.880 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.350 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.030 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:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.490 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7767 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 5317 Z= 0.318 Angle : 0.795 12.018 7222 Z= 0.432 Chirality : 0.048 0.167 783 Planarity : 0.006 0.124 940 Dihedral : 13.608 80.437 1951 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 17.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.13 % Favored : 92.87 % Rotamer: Outliers : 0.00 % Allowed : 0.18 % Favored : 99.82 % 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: -1.31 (0.32), residues: 645 helix: 0.41 (0.49), residues: 121 sheet: -1.10 (0.34), residues: 193 loop : -1.14 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.003 TRP A 24 HIS 0.005 0.001 HIS A 64 PHE 0.010 0.001 PHE A 243 TYR 0.021 0.002 TYR A 409 ARG 0.011 0.001 ARG A 172 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.602 Fit side-chains REVERT: C 109 LEU cc_start: 0.9293 (tp) cc_final: 0.9038 (tp) REVERT: C 111 ASN cc_start: 0.8693 (m-40) cc_final: 0.8381 (m-40) REVERT: C 183 GLU cc_start: 0.8659 (tt0) cc_final: 0.8353 (tt0) REVERT: C 252 TYR cc_start: 0.8183 (m-80) cc_final: 0.7965 (m-80) REVERT: A 33 ASP cc_start: 0.7141 (m-30) cc_final: 0.6819 (m-30) REVERT: A 40 LEU cc_start: 0.9024 (mt) cc_final: 0.8779 (mt) REVERT: A 72 THR cc_start: 0.8702 (m) cc_final: 0.8492 (m) REVERT: A 79 LEU cc_start: 0.8577 (tp) cc_final: 0.8311 (tp) REVERT: A 102 LYS cc_start: 0.7214 (mttt) cc_final: 0.6846 (mttt) REVERT: A 282 ASN cc_start: 0.8648 (t0) cc_final: 0.7842 (t0) REVERT: A 319 GLU cc_start: 0.7109 (tt0) cc_final: 0.6851 (mt-10) REVERT: A 395 GLU cc_start: 0.7747 (mm-30) cc_final: 0.7381 (mm-30) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1995 time to fit residues: 35.1828 Evaluate side-chains 118 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.622 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 54 optimal weight: 0.9980 chunk 48 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 19 optimal weight: 0.9990 chunk 30 optimal weight: 0.6980 chunk 37 optimal weight: 0.4980 chunk 58 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 311 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7743 moved from start: 0.1539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5317 Z= 0.230 Angle : 0.702 10.137 7222 Z= 0.355 Chirality : 0.048 0.163 783 Planarity : 0.005 0.080 940 Dihedral : 5.544 23.213 695 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 13.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer: Outliers : 2.28 % Allowed : 9.49 % Favored : 88.22 % 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: -1.18 (0.32), residues: 645 helix: 1.07 (0.48), residues: 116 sheet: -1.39 (0.36), residues: 185 loop : -1.02 (0.33), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP C 121 HIS 0.006 0.001 HIS A 316 PHE 0.015 0.001 PHE C 256 TYR 0.017 0.002 TYR C 124 ARG 0.005 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 122 time to evaluate : 0.606 Fit side-chains REVERT: C 109 LEU cc_start: 0.9311 (tp) cc_final: 0.9030 (tp) REVERT: C 111 ASN cc_start: 0.8723 (m-40) cc_final: 0.8377 (m-40) REVERT: C 163 TRP cc_start: 0.7736 (m100) cc_final: 0.7337 (m100) REVERT: C 183 GLU cc_start: 0.8726 (tt0) cc_final: 0.8470 (tt0) REVERT: C 192 ARG cc_start: 0.8291 (mtp-110) cc_final: 0.7479 (mtp85) REVERT: A 24 TRP cc_start: 0.9059 (t60) cc_final: 0.8833 (t60) REVERT: A 33 ASP cc_start: 0.7285 (m-30) cc_final: 0.6873 (m-30) REVERT: A 79 LEU cc_start: 0.8547 (tp) cc_final: 0.8234 (tp) REVERT: A 101 GLU cc_start: 0.7927 (OUTLIER) cc_final: 0.7528 (pp20) REVERT: A 102 LYS cc_start: 0.7322 (mttt) cc_final: 0.6766 (mttt) REVERT: A 282 ASN cc_start: 0.8630 (t0) cc_final: 0.7850 (t0) REVERT: A 311 HIS cc_start: 0.7842 (t70) cc_final: 0.7434 (t-90) REVERT: A 319 GLU cc_start: 0.7435 (tt0) cc_final: 0.7027 (tt0) REVERT: A 395 GLU cc_start: 0.7707 (mm-30) cc_final: 0.7498 (mm-30) outliers start: 13 outliers final: 7 residues processed: 126 average time/residue: 0.1524 time to fit residues: 25.6744 Evaluate side-chains 118 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.620 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 101 GLU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 32 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 48 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 58 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 57 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 chunk 46 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 103 GLN B 125 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7726 moved from start: 0.2016 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5317 Z= 0.203 Angle : 0.664 10.507 7222 Z= 0.333 Chirality : 0.047 0.162 783 Planarity : 0.004 0.066 940 Dihedral : 5.227 25.450 695 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 12.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.28 % Allowed : 13.36 % Favored : 84.36 % 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: -1.02 (0.32), residues: 645 helix: 1.13 (0.48), residues: 122 sheet: -1.22 (0.36), residues: 184 loop : -0.98 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP B 122 HIS 0.005 0.001 HIS A 316 PHE 0.014 0.001 PHE C 256 TYR 0.015 0.002 TYR A 409 ARG 0.004 0.001 ARG A 341 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 136 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 123 time to evaluate : 0.631 Fit side-chains revert: symmetry clash REVERT: C 109 LEU cc_start: 0.9295 (tp) cc_final: 0.8995 (tp) REVERT: C 111 ASN cc_start: 0.8698 (m-40) cc_final: 0.8335 (m-40) REVERT: C 125 GLU cc_start: 0.8534 (tp30) cc_final: 0.8149 (tp30) REVERT: C 163 TRP cc_start: 0.7728 (m100) cc_final: 0.7137 (m100) REVERT: C 188 LEU cc_start: 0.9032 (tt) cc_final: 0.8737 (tp) REVERT: C 194 LYS cc_start: 0.8805 (tttt) cc_final: 0.8590 (tttt) REVERT: A 24 TRP cc_start: 0.8993 (t60) cc_final: 0.8698 (t60) REVERT: A 33 ASP cc_start: 0.7354 (m-30) cc_final: 0.6887 (m-30) REVERT: A 79 LEU cc_start: 0.8593 (tp) cc_final: 0.8332 (tp) REVERT: A 282 ASN cc_start: 0.8582 (t0) cc_final: 0.7806 (t0) REVERT: A 311 HIS cc_start: 0.7747 (t70) cc_final: 0.7372 (t-90) REVERT: A 319 GLU cc_start: 0.7376 (tt0) cc_final: 0.7165 (tt0) REVERT: A 321 PHE cc_start: 0.8670 (m-80) cc_final: 0.8321 (m-80) REVERT: A 395 GLU cc_start: 0.7687 (mm-30) cc_final: 0.7430 (mm-30) outliers start: 13 outliers final: 8 residues processed: 130 average time/residue: 0.1697 time to fit residues: 28.4771 Evaluate side-chains 118 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 110 time to evaluate : 0.639 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 57 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 6 optimal weight: 0.0060 chunk 27 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 overall best weight: 0.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5317 Z= 0.226 Angle : 0.700 14.487 7222 Z= 0.340 Chirality : 0.047 0.188 783 Planarity : 0.004 0.058 940 Dihedral : 5.162 26.052 695 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 11.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.98 % Favored : 93.02 % Rotamer: Outliers : 2.99 % Allowed : 14.41 % Favored : 82.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.33), residues: 645 helix: 1.33 (0.48), residues: 122 sheet: -0.83 (0.35), residues: 192 loop : -0.97 (0.34), residues: 331 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP B 122 HIS 0.003 0.001 HIS A 226 PHE 0.014 0.001 PHE C 256 TYR 0.017 0.002 TYR A 409 ARG 0.006 0.000 ARG C 185 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 135 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 118 time to evaluate : 0.607 Fit side-chains REVERT: C 109 LEU cc_start: 0.9292 (tp) cc_final: 0.9004 (tp) REVERT: C 111 ASN cc_start: 0.8711 (m-40) cc_final: 0.8356 (m-40) REVERT: C 127 PHE cc_start: 0.8368 (t80) cc_final: 0.8165 (t80) REVERT: C 163 TRP cc_start: 0.7864 (m100) cc_final: 0.7380 (m100) REVERT: C 252 TYR cc_start: 0.8287 (m-80) cc_final: 0.8050 (m-80) REVERT: A 24 TRP cc_start: 0.8995 (t60) cc_final: 0.8668 (t60) REVERT: A 33 ASP cc_start: 0.7382 (m-30) cc_final: 0.6957 (m-30) REVERT: A 79 LEU cc_start: 0.8628 (tp) cc_final: 0.8393 (tp) REVERT: A 282 ASN cc_start: 0.8665 (t0) cc_final: 0.7854 (t0) REVERT: A 395 GLU cc_start: 0.7670 (mm-30) cc_final: 0.7374 (mm-30) outliers start: 17 outliers final: 12 residues processed: 128 average time/residue: 0.1714 time to fit residues: 28.3976 Evaluate side-chains 123 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 111 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 275 GLU Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 35 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 46 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7819 moved from start: 0.2251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 5317 Z= 0.435 Angle : 0.772 14.365 7222 Z= 0.386 Chirality : 0.051 0.197 783 Planarity : 0.005 0.060 940 Dihedral : 5.686 27.343 695 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 14.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.22 % Favored : 91.78 % Rotamer: Outliers : 3.16 % Allowed : 16.34 % Favored : 80.49 % 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: -1.15 (0.32), residues: 645 helix: 1.16 (0.48), residues: 116 sheet: -1.23 (0.36), residues: 179 loop : -1.14 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP B 122 HIS 0.005 0.001 HIS A 373 PHE 0.024 0.002 PHE C 256 TYR 0.024 0.002 TYR A 98 ARG 0.004 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 120 time to evaluate : 0.619 Fit side-chains REVERT: C 111 ASN cc_start: 0.8823 (m-40) cc_final: 0.8513 (m-40) REVERT: C 115 LEU cc_start: 0.8961 (mm) cc_final: 0.8609 (mt) REVERT: C 163 TRP cc_start: 0.8110 (m100) cc_final: 0.7742 (m100) REVERT: A 33 ASP cc_start: 0.7507 (m-30) cc_final: 0.7174 (m-30) REVERT: A 79 LEU cc_start: 0.8714 (tp) cc_final: 0.8451 (tp) REVERT: A 282 ASN cc_start: 0.8908 (t0) cc_final: 0.8027 (t0) REVERT: A 316 HIS cc_start: 0.8127 (OUTLIER) cc_final: 0.7887 (m-70) REVERT: A 395 GLU cc_start: 0.7798 (mm-30) cc_final: 0.7440 (mm-30) outliers start: 18 outliers final: 12 residues processed: 130 average time/residue: 0.1640 time to fit residues: 27.8429 Evaluate side-chains 119 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.688 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 183 GLU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain A residue 28 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 84 VAL Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 36 optimal weight: 0.4980 chunk 15 optimal weight: 4.9990 chunk 61 optimal weight: 0.1980 chunk 51 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 chunk 5 optimal weight: 0.6980 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 0.0570 chunk 6 optimal weight: 0.9980 chunk 35 optimal weight: 0.5980 overall best weight: 0.4098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 277 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7721 moved from start: 0.2590 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 5317 Z= 0.190 Angle : 0.720 13.637 7222 Z= 0.346 Chirality : 0.047 0.158 783 Planarity : 0.004 0.051 940 Dihedral : 5.223 27.934 695 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 12.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.89 % Favored : 94.11 % Rotamer: Outliers : 2.11 % Allowed : 18.45 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.32), residues: 645 helix: 1.03 (0.48), residues: 122 sheet: -0.84 (0.35), residues: 195 loop : -1.00 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP B 122 HIS 0.002 0.001 HIS A 373 PHE 0.023 0.001 PHE C 256 TYR 0.021 0.002 TYR C 124 ARG 0.009 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 127 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 115 time to evaluate : 0.623 Fit side-chains revert: symmetry clash REVERT: C 111 ASN cc_start: 0.8767 (m-40) cc_final: 0.8405 (m-40) REVERT: C 163 TRP cc_start: 0.8106 (m100) cc_final: 0.7626 (m100) REVERT: C 196 ARG cc_start: 0.7197 (ptp-170) cc_final: 0.6978 (ptp-110) REVERT: C 238 PHE cc_start: 0.8191 (m-80) cc_final: 0.7899 (m-80) REVERT: C 268 ASP cc_start: 0.8575 (p0) cc_final: 0.8365 (p0) REVERT: A 33 ASP cc_start: 0.7410 (m-30) cc_final: 0.6975 (m-30) REVERT: A 79 LEU cc_start: 0.8674 (tp) cc_final: 0.8459 (tp) REVERT: A 277 ASN cc_start: 0.8208 (m-40) cc_final: 0.7986 (m110) REVERT: A 282 ASN cc_start: 0.8631 (t0) cc_final: 0.7879 (t0) REVERT: A 316 HIS cc_start: 0.8084 (OUTLIER) cc_final: 0.7659 (m-70) REVERT: A 321 PHE cc_start: 0.8650 (m-80) cc_final: 0.8250 (m-80) REVERT: A 395 GLU cc_start: 0.7659 (mm-30) cc_final: 0.7308 (mm-30) REVERT: A 399 MET cc_start: 0.7721 (tmm) cc_final: 0.7441 (tmm) outliers start: 12 outliers final: 9 residues processed: 122 average time/residue: 0.1596 time to fit residues: 25.8276 Evaluate side-chains 119 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 109 time to evaluate : 0.666 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 45 optimal weight: 5.9990 chunk 35 optimal weight: 0.1980 chunk 52 optimal weight: 1.9990 chunk 34 optimal weight: 0.0010 chunk 61 optimal weight: 2.9990 chunk 38 optimal weight: 5.9990 chunk 37 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 36 optimal weight: 0.8980 chunk 18 optimal weight: 0.6980 overall best weight: 0.5186 ------------------------------------------------------------------------------- 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: 0.7723 moved from start: 0.2728 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5317 Z= 0.199 Angle : 0.686 13.174 7222 Z= 0.333 Chirality : 0.047 0.149 783 Planarity : 0.004 0.049 940 Dihedral : 5.075 27.814 695 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 11.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.51 % Favored : 93.49 % Rotamer: Outliers : 2.46 % Allowed : 18.45 % Favored : 79.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.32), residues: 645 helix: 1.15 (0.48), residues: 122 sheet: -0.86 (0.35), residues: 193 loop : -0.99 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.002 TRP B 122 HIS 0.003 0.001 HIS A 373 PHE 0.024 0.001 PHE C 256 TYR 0.020 0.002 TYR C 124 ARG 0.006 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 115 time to evaluate : 0.679 Fit side-chains revert: symmetry clash REVERT: C 111 ASN cc_start: 0.8727 (m-40) cc_final: 0.8357 (m-40) REVERT: C 163 TRP cc_start: 0.8037 (m100) cc_final: 0.7621 (m100) REVERT: A 33 ASP cc_start: 0.7400 (m-30) cc_final: 0.7020 (m-30) REVERT: A 282 ASN cc_start: 0.8609 (t0) cc_final: 0.7869 (t0) REVERT: A 321 PHE cc_start: 0.8537 (m-80) cc_final: 0.8102 (m-80) REVERT: A 395 GLU cc_start: 0.7679 (mm-30) cc_final: 0.7321 (mm-30) outliers start: 14 outliers final: 12 residues processed: 122 average time/residue: 0.1666 time to fit residues: 26.8442 Evaluate side-chains 121 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 109 time to evaluate : 0.634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 12 optimal weight: 3.9990 chunk 11 optimal weight: 0.0010 chunk 39 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 53 optimal weight: 0.0470 chunk 57 optimal weight: 0.5980 overall best weight: 0.5086 ------------------------------------------------------------------------------- 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: 0.7712 moved from start: 0.2842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5317 Z= 0.201 Angle : 0.719 14.288 7222 Z= 0.343 Chirality : 0.047 0.155 783 Planarity : 0.004 0.047 940 Dihedral : 5.020 27.281 695 Min Nonbonded Distance : 2.473 Molprobity Statistics. All-atom Clashscore : 11.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.99 % Allowed : 19.51 % Favored : 77.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.86 (0.32), residues: 645 helix: 1.10 (0.48), residues: 122 sheet: -0.80 (0.35), residues: 193 loop : -1.02 (0.33), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 122 HIS 0.003 0.001 HIS A 226 PHE 0.022 0.001 PHE C 256 TYR 0.019 0.002 TYR C 124 ARG 0.006 0.001 ARG C 192 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 114 time to evaluate : 0.512 Fit side-chains revert: symmetry clash REVERT: C 111 ASN cc_start: 0.8726 (m-40) cc_final: 0.8354 (m-40) REVERT: C 163 TRP cc_start: 0.8050 (m100) cc_final: 0.7682 (m100) REVERT: A 33 ASP cc_start: 0.7419 (m-30) cc_final: 0.6999 (m-30) REVERT: A 282 ASN cc_start: 0.8510 (t0) cc_final: 0.7784 (t0) REVERT: A 316 HIS cc_start: 0.8152 (OUTLIER) cc_final: 0.7779 (m-70) REVERT: A 321 PHE cc_start: 0.8535 (m-80) cc_final: 0.8107 (m-80) REVERT: A 395 GLU cc_start: 0.7684 (mm-30) cc_final: 0.7326 (mm-30) outliers start: 17 outliers final: 13 residues processed: 124 average time/residue: 0.1694 time to fit residues: 27.5613 Evaluate side-chains 122 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 108 time to evaluate : 0.717 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 2.9990 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 5.9990 chunk 17 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 54 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 37 optimal weight: 0.5980 chunk 60 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.004 0.064 5317 Z= 0.269 Angle : 0.750 14.314 7222 Z= 0.367 Chirality : 0.049 0.193 783 Planarity : 0.004 0.051 940 Dihedral : 5.188 26.404 695 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 12.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.82 % Favored : 93.18 % Rotamer: Outliers : 3.34 % Allowed : 19.86 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.32), residues: 645 helix: 0.95 (0.49), residues: 122 sheet: -0.89 (0.37), residues: 178 loop : -1.06 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 122 HIS 0.003 0.001 HIS A 226 PHE 0.013 0.001 PHE A 243 TYR 0.017 0.002 TYR C 124 ARG 0.013 0.001 ARG C 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: C 111 ASN cc_start: 0.8722 (m-40) cc_final: 0.8364 (m-40) REVERT: C 163 TRP cc_start: 0.8088 (m100) cc_final: 0.7740 (m100) REVERT: C 196 ARG cc_start: 0.7065 (mtt90) cc_final: 0.6818 (ptp-170) REVERT: A 33 ASP cc_start: 0.7367 (m-30) cc_final: 0.7017 (m-30) REVERT: A 108 PHE cc_start: 0.7792 (OUTLIER) cc_final: 0.7381 (m-80) REVERT: A 282 ASN cc_start: 0.8660 (t0) cc_final: 0.7816 (t0) REVERT: A 316 HIS cc_start: 0.8073 (OUTLIER) cc_final: 0.7609 (m-70) REVERT: A 321 PHE cc_start: 0.8594 (m-80) cc_final: 0.8136 (m-80) REVERT: A 395 GLU cc_start: 0.7751 (mm-30) cc_final: 0.7407 (mm-30) outliers start: 19 outliers final: 15 residues processed: 121 average time/residue: 0.1630 time to fit residues: 26.0931 Evaluate side-chains 123 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.635 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 42 optimal weight: 0.9990 chunk 63 optimal weight: 0.0370 chunk 58 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 39 optimal weight: 0.2980 chunk 31 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 1.9990 chunk 15 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7715 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.063 5317 Z= 0.226 Angle : 0.747 14.188 7222 Z= 0.364 Chirality : 0.048 0.179 783 Planarity : 0.004 0.048 940 Dihedral : 5.079 27.253 695 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 3.16 % Allowed : 20.56 % Favored : 76.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.32), residues: 645 helix: 0.92 (0.49), residues: 122 sheet: -0.85 (0.37), residues: 178 loop : -1.03 (0.32), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP B 122 HIS 0.003 0.001 HIS A 226 PHE 0.014 0.001 PHE A 243 TYR 0.019 0.002 TYR C 124 ARG 0.013 0.001 ARG C 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1290 Ramachandran restraints generated. 645 Oldfield, 0 Emsley, 645 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 110 time to evaluate : 0.728 Fit side-chains revert: symmetry clash REVERT: C 111 ASN cc_start: 0.8693 (m-40) cc_final: 0.8319 (m-40) REVERT: C 163 TRP cc_start: 0.8012 (m100) cc_final: 0.7704 (m100) REVERT: A 33 ASP cc_start: 0.7361 (m-30) cc_final: 0.6982 (m-30) REVERT: A 108 PHE cc_start: 0.7672 (OUTLIER) cc_final: 0.7224 (m-80) REVERT: A 282 ASN cc_start: 0.8507 (t0) cc_final: 0.7699 (t0) REVERT: A 316 HIS cc_start: 0.8158 (OUTLIER) cc_final: 0.7765 (m-70) REVERT: A 321 PHE cc_start: 0.8559 (m-80) cc_final: 0.8114 (m-80) REVERT: A 395 GLU cc_start: 0.7723 (mm-30) cc_final: 0.7380 (mm-30) outliers start: 18 outliers final: 15 residues processed: 121 average time/residue: 0.1691 time to fit residues: 27.6373 Evaluate side-chains 123 residues out of total 584 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 109 LEU Chi-restraints excluded: chain C residue 188 LEU Chi-restraints excluded: chain C residue 254 VAL Chi-restraints excluded: chain C residue 255 THR Chi-restraints excluded: chain C residue 266 ILE Chi-restraints excluded: chain A residue 37 THR Chi-restraints excluded: chain A residue 72 THR Chi-restraints excluded: chain A residue 102 LYS Chi-restraints excluded: chain A residue 108 PHE Chi-restraints excluded: chain A residue 114 LYS Chi-restraints excluded: chain A residue 193 LEU Chi-restraints excluded: chain A residue 227 THR Chi-restraints excluded: chain A residue 293 SER Chi-restraints excluded: chain A residue 316 HIS Chi-restraints excluded: chain A residue 333 LEU Chi-restraints excluded: chain A residue 338 THR Chi-restraints excluded: chain A residue 391 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 64 random chunks: chunk 7 optimal weight: 0.0670 chunk 14 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 21 optimal weight: 0.3980 chunk 52 optimal weight: 0.9990 chunk 6 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 44 optimal weight: 0.0670 chunk 2 optimal weight: 0.0980 chunk 36 optimal weight: 0.9990 chunk 58 optimal weight: 0.9990 overall best weight: 0.3056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 199 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 = 0.3861 r_free = 0.3861 target = 0.142661 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3457 r_free = 0.3457 target = 0.111495 restraints weight = 9100.986| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.115271 restraints weight = 4683.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 31)----------------| | r_work = 0.3543 r_free = 0.3543 target = 0.117757 restraints weight = 3154.024| |-----------------------------------------------------------------------------| r_work (final): 0.3537 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7662 moved from start: 0.3279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 5317 Z= 0.193 Angle : 0.742 14.706 7222 Z= 0.357 Chirality : 0.048 0.188 783 Planarity : 0.004 0.046 940 Dihedral : 4.979 28.874 695 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 12.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 2.64 % Allowed : 20.56 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.95 (0.32), residues: 645 helix: 0.86 (0.48), residues: 123 sheet: -0.78 (0.37), residues: 179 loop : -1.07 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP B 122 HIS 0.002 0.001 HIS A 316 PHE 0.013 0.001 PHE A 243 TYR 0.020 0.002 TYR C 124 ARG 0.005 0.001 ARG C 192 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1579.25 seconds wall clock time: 29 minutes 1.02 seconds (1741.02 seconds total)