Starting phenix.real_space_refine on Thu Nov 14 09:19:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/11_2024/8i6j_35199.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/11_2024/8i6j_35199.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/11_2024/8i6j_35199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/11_2024/8i6j_35199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/11_2024/8i6j_35199.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/11_2024/8i6j_35199.cif" } resolution = 3.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.072 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 36 5.16 5 C 3318 2.51 5 N 925 2.21 5 O 1006 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 4 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 5287 Number of models: 1 Model: "" Number of chains: 3 Chain: "Q" Number of atoms: 1371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 170, 1371 Classifications: {'peptide': 170} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 161} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 3889 Number of conformers: 1 Conformer: "" Number of residues, atoms: 500, 3889 Classifications: {'peptide': 500} Link IDs: {'PTRANS': 16, 'TRANS': 483} Chain: "C" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.19, per 1000 atoms: 0.79 Number of scatterers: 5287 At special positions: 0 Unit cell: (97.18, 74.58, 118.65, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 36 16.00 P 2 15.00 O 1006 8.00 N 925 7.00 C 3318 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: 1.29 Conformation dependent library (CDL) restraints added in 612.8 milliseconds 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1260 Finding SS restraints... Secondary structure from input PDB file: 25 helices and 6 sheets defined 50.7% alpha, 7.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.55 Creating SS restraints... Processing helix chain 'Q' and resid 65 through 81 Processing helix chain 'Q' and resid 82 through 84 No H-bonds generated for 'chain 'Q' and resid 82 through 84' Processing helix chain 'Q' and resid 128 through 141 removed outlier: 4.112A pdb=" N GLN Q 132 " --> pdb=" O ALA Q 128 " (cutoff:3.500A) removed outlier: 3.644A pdb=" N HIS Q 133 " --> pdb=" O LEU Q 129 " (cutoff:3.500A) Processing helix chain 'Q' and resid 180 through 185 removed outlier: 4.529A pdb=" N PHE Q 184 " --> pdb=" O GLY Q 180 " (cutoff:3.500A) Processing helix chain 'Q' and resid 190 through 200 removed outlier: 3.666A pdb=" N LEU Q 194 " --> pdb=" O THR Q 190 " (cutoff:3.500A) Processing helix chain 'Q' and resid 218 through 231 removed outlier: 3.860A pdb=" N LYS Q 231 " --> pdb=" O SER Q 227 " (cutoff:3.500A) Processing helix chain 'C' and resid 21 through 37 removed outlier: 4.281A pdb=" N ASN C 28 " --> pdb=" O SER C 24 " (cutoff:3.500A) removed outlier: 4.174A pdb=" N ALA C 29 " --> pdb=" O GLY C 25 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N ILE C 37 " --> pdb=" O ILE C 33 " (cutoff:3.500A) Processing helix chain 'C' and resid 62 through 70 removed outlier: 3.567A pdb=" N ILE C 66 " --> pdb=" O ASP C 62 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ILE C 70 " --> pdb=" O ILE C 66 " (cutoff:3.500A) Processing helix chain 'C' and resid 74 through 91 removed outlier: 4.008A pdb=" N SER C 84 " --> pdb=" O MET C 80 " (cutoff:3.500A) removed outlier: 3.735A pdb=" N ARG C 85 " --> pdb=" O ILE C 81 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLU C 90 " --> pdb=" O THR C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 95 through 108 removed outlier: 3.985A pdb=" N ILE C 99 " --> pdb=" O THR C 95 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N VAL C 108 " --> pdb=" O GLU C 104 " (cutoff:3.500A) Processing helix chain 'C' and resid 109 through 116 removed outlier: 4.645A pdb=" N LEU C 113 " --> pdb=" O ALA C 109 " (cutoff:3.500A) Processing helix chain 'C' and resid 118 through 140 removed outlier: 3.542A pdb=" N LYS C 128 " --> pdb=" O SER C 124 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE C 140 " --> pdb=" O THR C 136 " (cutoff:3.500A) Processing helix chain 'C' and resid 149 through 160 Processing helix chain 'C' and resid 168 through 184 removed outlier: 3.847A pdb=" N GLN C 184 " --> pdb=" O VAL C 180 " (cutoff:3.500A) Processing helix chain 'C' and resid 208 through 212 removed outlier: 3.731A pdb=" N ASP C 211 " --> pdb=" O ILE C 208 " (cutoff:3.500A) removed outlier: 3.647A pdb=" N SER C 212 " --> pdb=" O ILE C 209 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 208 through 212' Processing helix chain 'C' and resid 249 through 253 removed outlier: 3.549A pdb=" N SER C 252 " --> pdb=" O LYS C 249 " (cutoff:3.500A) Processing helix chain 'C' and resid 260 through 284 removed outlier: 3.932A pdb=" N PHE C 264 " --> pdb=" O ARG C 260 " (cutoff:3.500A) removed outlier: 3.766A pdb=" N GLU C 272 " --> pdb=" O LEU C 268 " (cutoff:3.500A) removed outlier: 3.969A pdb=" N GLU C 273 " --> pdb=" O GLN C 269 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N TYR C 274 " --> pdb=" O MET C 270 " (cutoff:3.500A) Processing helix chain 'C' and resid 297 through 307 removed outlier: 3.745A pdb=" N GLN C 301 " --> pdb=" O SER C 297 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N ALA C 307 " --> pdb=" O TYR C 303 " (cutoff:3.500A) Processing helix chain 'C' and resid 316 through 324 Processing helix chain 'C' and resid 381 through 404 removed outlier: 3.761A pdb=" N LEU C 403 " --> pdb=" O ARG C 399 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP C 404 " --> pdb=" O ASN C 400 " (cutoff:3.500A) Processing helix chain 'C' and resid 412 through 430 Processing helix chain 'C' and resid 433 through 442 removed outlier: 3.931A pdb=" N TYR C 437 " --> pdb=" O GLU C 433 " (cutoff:3.500A) Processing helix chain 'C' and resid 445 through 456 removed outlier: 4.126A pdb=" N ARG C 449 " --> pdb=" O GLU C 445 " (cutoff:3.500A) Processing helix chain 'C' and resid 458 through 473 removed outlier: 3.686A pdb=" N LEU C 462 " --> pdb=" O SER C 458 " (cutoff:3.500A) Processing helix chain 'C' and resid 499 through 519 removed outlier: 3.858A pdb=" N ILE C 519 " --> pdb=" O LEU C 515 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'Q' and resid 145 through 146 removed outlier: 3.735A pdb=" N PHE Q 167 " --> pdb=" O LEU Q 117 " (cutoff:3.500A) removed outlier: 7.555A pdb=" N ILE Q 166 " --> pdb=" O GLN Q 177 " (cutoff:3.500A) removed outlier: 5.627A pdb=" N GLN Q 177 " --> pdb=" O ILE Q 166 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N VAL Q 168 " --> pdb=" O LYS Q 175 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 48 through 51 Processing sheet with id=AA3, first strand: chain 'C' and resid 142 through 143 Processing sheet with id=AA4, first strand: chain 'C' and resid 201 through 205 removed outlier: 3.680A pdb=" N ILE C 204 " --> pdb=" O LEU C 376 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N GLY C 378 " --> pdb=" O ILE C 204 " (cutoff:3.500A) removed outlier: 3.661A pdb=" N THR C 373 " --> pdb=" O LEU C 215 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU C 375 " --> pdb=" O CYS C 213 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 218 through 220 removed outlier: 3.504A pdb=" N ILE C 363 " --> pdb=" O VAL C 218 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N LEU C 350 " --> pdb=" O ILE C 233 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ILE C 233 " --> pdb=" O LEU C 350 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 238 through 240 removed outlier: 3.615A pdb=" N ILE C 291 " --> pdb=" O VAL C 239 " (cutoff:3.500A) removed outlier: 6.526A pdb=" N VAL C 290 " --> pdb=" O ILE C 312 " (cutoff:3.500A) 236 hydrogen bonds defined for protein. 681 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: 1.23 Time building geometry restraints manager: 1.48 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1769 1.34 - 1.46: 950 1.46 - 1.58: 2578 1.58 - 1.70: 3 1.70 - 1.81: 60 Bond restraints: 5360 Sorted by residual: bond pdb=" CG GLU C 511 " pdb=" CD GLU C 511 " ideal model delta sigma weight residual 1.516 1.489 0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CG GLU Q 195 " pdb=" CD GLU Q 195 " ideal model delta sigma weight residual 1.516 1.490 0.026 2.50e-02 1.60e+03 1.08e+00 bond pdb=" C4 ADP C 601 " pdb=" C5 ADP C 601 " ideal model delta sigma weight residual 1.490 1.471 0.019 2.00e-02 2.50e+03 8.77e-01 bond pdb=" CG ARG Q 225 " pdb=" CD ARG Q 225 " ideal model delta sigma weight residual 1.520 1.544 -0.024 3.00e-02 1.11e+03 6.66e-01 bond pdb=" N GLN Q 122 " pdb=" CA GLN Q 122 " ideal model delta sigma weight residual 1.456 1.466 -0.010 1.23e-02 6.61e+03 6.28e-01 ... (remaining 5355 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.62: 6984 1.62 - 3.23: 193 3.23 - 4.85: 42 4.85 - 6.47: 14 6.47 - 8.08: 4 Bond angle restraints: 7237 Sorted by residual: angle pdb=" N ILE C 195 " pdb=" CA ILE C 195 " pdb=" C ILE C 195 " ideal model delta sigma weight residual 113.53 109.98 3.55 9.80e-01 1.04e+00 1.31e+01 angle pdb=" N GLU C 511 " pdb=" CA GLU C 511 " pdb=" CB GLU C 511 " ideal model delta sigma weight residual 110.28 115.50 -5.22 1.55e+00 4.16e-01 1.13e+01 angle pdb=" N MET Q 73 " pdb=" CA MET Q 73 " pdb=" CB MET Q 73 " ideal model delta sigma weight residual 110.28 115.16 -4.88 1.55e+00 4.16e-01 9.91e+00 angle pdb=" N GLU Q 195 " pdb=" CA GLU Q 195 " pdb=" CB GLU Q 195 " ideal model delta sigma weight residual 110.12 114.56 -4.44 1.47e+00 4.63e-01 9.13e+00 angle pdb=" N TYR Q 102 " pdb=" CA TYR Q 102 " pdb=" C TYR Q 102 " ideal model delta sigma weight residual 110.80 116.86 -6.06 2.13e+00 2.20e-01 8.11e+00 ... (remaining 7232 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 27.12: 3189 27.12 - 54.23: 131 54.23 - 81.35: 9 81.35 - 108.46: 5 108.46 - 135.58: 1 Dihedral angle restraints: 3335 sinusoidal: 1393 harmonic: 1942 Sorted by residual: dihedral pdb=" O2A ADP C 601 " pdb=" O3A ADP C 601 " pdb=" PA ADP C 601 " pdb=" PB ADP C 601 " ideal model delta sinusoidal sigma weight residual 300.00 164.42 135.58 1 2.00e+01 2.50e-03 4.11e+01 dihedral pdb=" CA ILE Q 150 " pdb=" C ILE Q 150 " pdb=" N SER Q 151 " pdb=" CA SER Q 151 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 dihedral pdb=" CA TYR Q 169 " pdb=" C TYR Q 169 " pdb=" N LEU Q 170 " pdb=" CA LEU Q 170 " ideal model delta harmonic sigma weight residual 180.00 157.17 22.83 0 5.00e+00 4.00e-02 2.09e+01 ... (remaining 3332 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.032: 514 0.032 - 0.065: 209 0.065 - 0.097: 69 0.097 - 0.129: 47 0.129 - 0.162: 7 Chirality restraints: 846 Sorted by residual: chirality pdb=" CB ILE C 374 " pdb=" CA ILE C 374 " pdb=" CG1 ILE C 374 " pdb=" CG2 ILE C 374 " both_signs ideal model delta sigma weight residual False 2.64 2.48 0.16 2.00e-01 2.50e+01 6.54e-01 chirality pdb=" CA GLU C 511 " pdb=" N GLU C 511 " pdb=" C GLU C 511 " pdb=" CB GLU C 511 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 chirality pdb=" CA TYR Q 102 " pdb=" N TYR Q 102 " pdb=" C TYR Q 102 " pdb=" CB TYR Q 102 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.45e-01 ... (remaining 843 not shown) Planarity restraints: 921 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE C 112 " 0.014 2.00e-02 2.50e+03 1.41e-02 3.47e+00 pdb=" CG PHE C 112 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 PHE C 112 " 0.003 2.00e-02 2.50e+03 pdb=" CD2 PHE C 112 " 0.010 2.00e-02 2.50e+03 pdb=" CE1 PHE C 112 " 0.006 2.00e-02 2.50e+03 pdb=" CE2 PHE C 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ PHE C 112 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE Q 124 " 0.026 5.00e-02 4.00e+02 4.02e-02 2.59e+00 pdb=" N PRO Q 125 " -0.070 5.00e-02 4.00e+02 pdb=" CA PRO Q 125 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO Q 125 " 0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS C 507 " 0.007 2.00e-02 2.50e+03 1.37e-02 1.88e+00 pdb=" C LYS C 507 " -0.024 2.00e-02 2.50e+03 pdb=" O LYS C 507 " 0.009 2.00e-02 2.50e+03 pdb=" N THR C 508 " 0.008 2.00e-02 2.50e+03 ... (remaining 918 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1164 2.79 - 3.32: 5151 3.32 - 3.85: 7858 3.85 - 4.37: 8250 4.37 - 4.90: 14508 Nonbonded interactions: 36931 Sorted by model distance: nonbonded pdb=" OD2 ASP C 132 " pdb=" OH TYR C 437 " model vdw 2.265 3.040 nonbonded pdb=" O VAL Q 183 " pdb=" NZ LYS Q 197 " model vdw 2.292 3.120 nonbonded pdb=" OE1 GLU C 497 " pdb=" NZ LYS C 502 " model vdw 2.341 3.120 nonbonded pdb=" O ASN Q 157 " pdb=" ND2 ASN Q 157 " model vdw 2.344 3.120 nonbonded pdb=" O SER C 158 " pdb=" OG1 THR C 161 " model vdw 2.348 3.040 ... (remaining 36926 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.960 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 16.120 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.340 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6941 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 0.029 5360 Z= 0.196 Angle : 0.697 8.081 7237 Z= 0.359 Chirality : 0.046 0.162 846 Planarity : 0.004 0.040 921 Dihedral : 14.716 135.578 2075 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 7.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 0.17 % Allowed : 0.00 % Favored : 99.83 % 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 (0.33), residues: 666 helix: 1.57 (0.31), residues: 306 sheet: -0.75 (0.66), residues: 70 loop : -3.23 (0.29), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP C 435 HIS 0.004 0.001 HIS C 111 PHE 0.032 0.002 PHE C 112 TYR 0.011 0.002 TYR Q 102 ARG 0.009 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 83 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7745 (mmt) cc_final: 0.7351 (mmm) REVERT: C 190 ARG cc_start: 0.7336 (mmp80) cc_final: 0.7102 (mmp80) outliers start: 1 outliers final: 0 residues processed: 84 average time/residue: 0.2078 time to fit residues: 22.1399 Evaluate side-chains 75 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 75 time to evaluate : 0.637 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 4.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 2.9990 chunk 52 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 0.3980 chunk 39 optimal weight: 3.9990 chunk 60 optimal weight: 9.9990 overall best weight: 1.4184 ------------------------------------------------------------------------------- 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: 0.7044 moved from start: 0.1290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5360 Z= 0.305 Angle : 0.717 9.055 7237 Z= 0.363 Chirality : 0.047 0.155 846 Planarity : 0.004 0.043 921 Dihedral : 7.347 135.221 736 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 1.20 % Allowed : 11.00 % Favored : 87.80 % 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: -0.99 (0.33), residues: 666 helix: 1.48 (0.31), residues: 311 sheet: -0.66 (0.66), residues: 70 loop : -3.31 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 435 HIS 0.006 0.001 HIS C 74 PHE 0.018 0.002 PHE Q 167 TYR 0.015 0.002 TYR C 247 ARG 0.003 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.617 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 69 GLU cc_start: 0.7330 (tp30) cc_final: 0.7100 (tp30) outliers start: 7 outliers final: 7 residues processed: 83 average time/residue: 0.1939 time to fit residues: 20.9119 Evaluate side-chains 82 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 75 time to evaluate : 0.687 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 16 optimal weight: 7.9990 chunk 60 optimal weight: 8.9990 chunk 65 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 0.0030 chunk 48 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 overall best weight: 1.0794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.1572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 5360 Z= 0.243 Angle : 0.668 8.232 7237 Z= 0.336 Chirality : 0.045 0.148 846 Planarity : 0.004 0.044 921 Dihedral : 7.283 136.133 736 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 2.23 % Allowed : 15.64 % Favored : 82.13 % 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: -0.92 (0.33), residues: 666 helix: 1.54 (0.30), residues: 311 sheet: -0.53 (0.67), residues: 70 loop : -3.31 (0.30), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 435 HIS 0.004 0.001 HIS C 74 PHE 0.015 0.002 PHE Q 167 TYR 0.012 0.002 TYR C 247 ARG 0.004 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 82 time to evaluate : 0.620 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 PHE cc_start: 0.7132 (OUTLIER) cc_final: 0.6924 (m-10) REVERT: C 128 LYS cc_start: 0.8100 (pptt) cc_final: 0.7716 (pptt) REVERT: C 376 LEU cc_start: 0.8500 (OUTLIER) cc_final: 0.8251 (pt) outliers start: 13 outliers final: 8 residues processed: 87 average time/residue: 0.1765 time to fit residues: 20.1541 Evaluate side-chains 84 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 74 time to evaluate : 0.623 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 7.9990 chunk 6 optimal weight: 0.9990 chunk 29 optimal weight: 6.9990 chunk 40 optimal weight: 7.9990 chunk 61 optimal weight: 7.9990 chunk 64 optimal weight: 0.5980 chunk 57 optimal weight: 7.9990 chunk 17 optimal weight: 2.9990 chunk 53 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.7092 moved from start: 0.1890 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.036 5360 Z= 0.317 Angle : 0.726 9.035 7237 Z= 0.367 Chirality : 0.047 0.186 846 Planarity : 0.004 0.044 921 Dihedral : 7.415 136.194 736 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Rotamer: Outliers : 3.78 % Allowed : 15.81 % Favored : 80.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.99 (0.33), residues: 666 helix: 1.52 (0.30), residues: 311 sheet: -0.77 (0.67), residues: 71 loop : -3.33 (0.30), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 435 HIS 0.005 0.001 HIS C 74 PHE 0.020 0.002 PHE Q 167 TYR 0.012 0.002 TYR Q 74 ARG 0.005 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 78 time to evaluate : 0.640 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 PHE cc_start: 0.7156 (OUTLIER) cc_final: 0.6927 (m-10) REVERT: C 128 LYS cc_start: 0.8121 (pptt) cc_final: 0.7805 (pptt) REVERT: C 376 LEU cc_start: 0.8503 (OUTLIER) cc_final: 0.8016 (pt) outliers start: 22 outliers final: 17 residues processed: 91 average time/residue: 0.1783 time to fit residues: 21.1519 Evaluate side-chains 95 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 76 time to evaluate : 0.749 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 102 TYR Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 112 PHE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 chunk 44 optimal weight: 0.9980 chunk 0 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 16 optimal weight: 5.9990 chunk 21 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 0.7980 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7040 moved from start: 0.1963 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5360 Z= 0.220 Angle : 0.664 7.681 7237 Z= 0.333 Chirality : 0.045 0.149 846 Planarity : 0.004 0.042 921 Dihedral : 7.303 136.644 736 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.09 % Allowed : 18.90 % Favored : 78.01 % 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: -0.87 (0.33), residues: 666 helix: 1.60 (0.30), residues: 311 sheet: -0.49 (0.67), residues: 70 loop : -3.30 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 435 HIS 0.003 0.001 HIS C 74 PHE 0.023 0.002 PHE C 185 TYR 0.011 0.001 TYR C 247 ARG 0.006 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 74 time to evaluate : 0.625 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8081 (pptt) cc_final: 0.7802 (pptt) REVERT: C 152 MET cc_start: 0.6991 (mtt) cc_final: 0.6306 (mtt) REVERT: C 376 LEU cc_start: 0.8487 (OUTLIER) cc_final: 0.8253 (pt) outliers start: 18 outliers final: 16 residues processed: 86 average time/residue: 0.1839 time to fit residues: 20.6691 Evaluate side-chains 87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 70 time to evaluate : 0.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 391 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.6980 chunk 64 optimal weight: 8.9990 chunk 53 optimal weight: 0.6980 chunk 30 optimal weight: 0.4980 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 47 optimal weight: 0.0370 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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: 0.6973 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5360 Z= 0.164 Angle : 0.642 8.915 7237 Z= 0.317 Chirality : 0.043 0.141 846 Planarity : 0.003 0.041 921 Dihedral : 7.130 136.679 736 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 2.92 % Allowed : 19.24 % Favored : 77.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.71 (0.34), residues: 666 helix: 1.74 (0.30), residues: 311 sheet: -0.45 (0.62), residues: 80 loop : -3.31 (0.32), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 435 HIS 0.002 0.001 HIS C 226 PHE 0.019 0.002 PHE C 185 TYR 0.015 0.001 TYR C 247 ARG 0.006 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 79 time to evaluate : 0.659 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 128 LYS cc_start: 0.8051 (pptt) cc_final: 0.7783 (pptt) REVERT: C 190 ARG cc_start: 0.7250 (mmp80) cc_final: 0.6954 (mmp80) REVERT: C 402 LEU cc_start: 0.6916 (OUTLIER) cc_final: 0.5924 (tt) outliers start: 17 outliers final: 14 residues processed: 91 average time/residue: 0.1813 time to fit residues: 21.6140 Evaluate side-chains 87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 72 time to evaluate : 0.638 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 64 optimal weight: 5.9990 chunk 40 optimal weight: 9.9990 chunk 39 optimal weight: 0.7980 chunk 29 optimal weight: 6.9990 chunk 25 optimal weight: 6.9990 chunk 38 optimal weight: 0.0050 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 overall best weight: 0.6596 ------------------------------------------------------------------------------- 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: 0.6992 moved from start: 0.2082 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 5360 Z= 0.184 Angle : 0.649 9.180 7237 Z= 0.322 Chirality : 0.044 0.145 846 Planarity : 0.003 0.040 921 Dihedral : 7.105 136.011 736 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 3.09 % Allowed : 20.62 % Favored : 76.29 % 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: -0.73 (0.34), residues: 666 helix: 1.69 (0.30), residues: 311 sheet: -0.84 (0.67), residues: 66 loop : -3.05 (0.32), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.002 0.001 HIS C 74 PHE 0.022 0.002 PHE C 185 TYR 0.026 0.002 TYR C 247 ARG 0.007 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 69 time to evaluate : 0.745 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 376 LEU cc_start: 0.8347 (OUTLIER) cc_final: 0.8068 (pt) REVERT: C 402 LEU cc_start: 0.6996 (OUTLIER) cc_final: 0.5843 (mt) outliers start: 18 outliers final: 13 residues processed: 82 average time/residue: 0.1765 time to fit residues: 18.8739 Evaluate side-chains 84 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 69 time to evaluate : 0.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 113 LEU Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 50 optimal weight: 0.8980 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 6.9990 chunk 56 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 36 optimal weight: 0.9990 chunk 26 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 overall best weight: 0.7902 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7013 moved from start: 0.2207 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 5360 Z= 0.201 Angle : 0.667 9.814 7237 Z= 0.332 Chirality : 0.044 0.149 846 Planarity : 0.004 0.040 921 Dihedral : 7.135 134.979 736 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.86 % Favored : 91.14 % Rotamer: Outliers : 2.92 % Allowed : 20.79 % Favored : 76.29 % 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: -0.70 (0.34), residues: 666 helix: 1.71 (0.31), residues: 311 sheet: -0.21 (0.69), residues: 71 loop : -3.25 (0.31), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.003 0.001 HIS C 74 PHE 0.021 0.002 PHE C 185 TYR 0.009 0.001 TYR Q 120 ARG 0.008 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 74 time to evaluate : 0.628 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.6942 (mtt) cc_final: 0.6241 (mtt) REVERT: C 190 ARG cc_start: 0.7251 (mmp80) cc_final: 0.6963 (mmp80) REVERT: C 376 LEU cc_start: 0.8372 (OUTLIER) cc_final: 0.8103 (pt) outliers start: 17 outliers final: 13 residues processed: 87 average time/residue: 0.1710 time to fit residues: 19.6860 Evaluate side-chains 82 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 68 time to evaluate : 0.672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 0.5980 chunk 56 optimal weight: 2.9990 chunk 59 optimal weight: 2.9990 chunk 39 optimal weight: 1.9990 chunk 63 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 30 optimal weight: 0.2980 chunk 44 optimal weight: 0.4980 chunk 66 optimal weight: 9.9990 chunk 61 optimal weight: 7.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7050 moved from start: 0.2291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5360 Z= 0.245 Angle : 0.704 9.407 7237 Z= 0.350 Chirality : 0.045 0.153 846 Planarity : 0.004 0.042 921 Dihedral : 7.212 134.595 736 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 3.44 % Allowed : 20.62 % Favored : 75.95 % 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: -0.80 (0.34), residues: 666 helix: 1.63 (0.31), residues: 311 sheet: -0.24 (0.69), residues: 70 loop : -3.31 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.004 0.001 HIS C 74 PHE 0.022 0.002 PHE C 185 TYR 0.025 0.002 TYR C 247 ARG 0.008 0.000 ARG Q 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 73 time to evaluate : 0.622 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.6888 (mtt) cc_final: 0.6138 (mtt) outliers start: 20 outliers final: 15 residues processed: 88 average time/residue: 0.1809 time to fit residues: 20.8488 Evaluate side-chains 86 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 71 time to evaluate : 0.643 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 91 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 402 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 41 optimal weight: 0.7980 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.8980 chunk 56 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 49 optimal weight: 0.0040 chunk 7 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6998 moved from start: 0.2354 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5360 Z= 0.188 Angle : 0.683 8.653 7237 Z= 0.336 Chirality : 0.044 0.144 846 Planarity : 0.004 0.039 921 Dihedral : 7.100 134.591 736 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 2.58 % Allowed : 21.48 % Favored : 75.95 % 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: -0.75 (0.34), residues: 666 helix: 1.67 (0.31), residues: 311 sheet: -0.08 (0.70), residues: 70 loop : -3.31 (0.31), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.002 0.001 HIS C 470 PHE 0.018 0.002 PHE C 185 TYR 0.015 0.001 TYR C 437 ARG 0.008 0.000 ARG Q 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1332 Ramachandran restraints generated. 666 Oldfield, 0 Emsley, 666 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 75 time to evaluate : 0.619 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: Q 72 GLU cc_start: 0.5335 (OUTLIER) cc_final: 0.4733 (pp20) outliers start: 15 outliers final: 13 residues processed: 87 average time/residue: 0.1417 time to fit residues: 17.0522 Evaluate side-chains 84 residues out of total 583 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 70 time to evaluate : 0.682 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 72 GLU Chi-restraints excluded: chain Q residue 115 VAL Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 72 VAL Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 201 VAL Chi-restraints excluded: chain C residue 375 LEU Chi-restraints excluded: chain C residue 420 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 1.9990 chunk 6 optimal weight: 0.0970 chunk 9 optimal weight: 0.9990 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 0.5980 chunk 60 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 1 optimal weight: 10.0000 chunk 42 optimal weight: 0.6980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 28 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4467 r_free = 0.4467 target = 0.210198 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.4133 r_free = 0.4133 target = 0.175015 restraints weight = 7966.351| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.4138 r_free = 0.4138 target = 0.178417 restraints weight = 14005.004| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4143 r_free = 0.4143 target = 0.178916 restraints weight = 7723.980| |-----------------------------------------------------------------------------| r_work (final): 0.4137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6917 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 5360 Z= 0.183 Angle : 0.681 8.887 7237 Z= 0.335 Chirality : 0.045 0.148 846 Planarity : 0.004 0.037 921 Dihedral : 7.059 133.533 736 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.61 % Favored : 90.39 % Rotamer: Outliers : 2.58 % Allowed : 21.48 % Favored : 75.95 % 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: -0.70 (0.34), residues: 666 helix: 1.71 (0.30), residues: 310 sheet: -0.43 (0.76), residues: 55 loop : -3.02 (0.32), residues: 301 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.002 0.001 HIS C 226 PHE 0.018 0.002 PHE C 185 TYR 0.021 0.002 TYR C 247 ARG 0.009 0.000 ARG Q 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1338.29 seconds wall clock time: 25 minutes 24.38 seconds (1524.38 seconds total)