Starting phenix.real_space_refine on Fri Jul 19 01:16:35 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/07_2024/8i6j_35199.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/07_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_35199/07_2024/8i6j_35199.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/07_2024/8i6j_35199.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/07_2024/8i6j_35199.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i6j_35199/07_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 Residue "Q GLU 66": "OE1" <-> "OE2" Residue "Q GLU 105": "OE1" <-> "OE2" Residue "C GLU 89": "OE1" <-> "OE2" Residue "C GLU 187": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/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: 3.93, per 1000 atoms: 0.74 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 - 3.50 Amino acid : False - 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: 1.89 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.57 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: 1.32 Time building geometry restraints manager: 2.06 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: 98.84 - 106.28: 136 106.28 - 113.72: 3101 113.72 - 121.15: 2596 121.15 - 128.59: 1373 128.59 - 136.03: 31 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 2.440 nonbonded pdb=" O VAL Q 183 " pdb=" NZ LYS Q 197 " model vdw 2.292 2.520 nonbonded pdb=" OE1 GLU C 497 " pdb=" NZ LYS C 502 " model vdw 2.341 2.520 nonbonded pdb=" O ASN Q 157 " pdb=" ND2 ASN Q 157 " model vdw 2.344 2.520 nonbonded pdb=" O SER C 158 " pdb=" OG1 THR C 161 " model vdw 2.348 2.440 ... (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 ========== 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: 1.810 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: 0.030 Set scattering table: 0.050 Process input model: 18.870 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:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.610 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.634 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: 0.2000 time to fit residues: 21.3036 Evaluate side-chains 75 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.608 ------------------------------------------------------------------------------- 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: 8.9990 chunk 50 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 34 optimal weight: 0.0770 chunk 27 optimal weight: 0.9980 chunk 52 optimal weight: 0.5980 chunk 20 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 39 optimal weight: 2.9990 chunk 60 optimal weight: 9.9990 overall best weight: 0.6740 ------------------------------------------------------------------------------- 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: 0.6942 moved from start: 0.1088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5360 Z= 0.190 Angle : 0.637 6.746 7237 Z= 0.316 Chirality : 0.044 0.133 846 Planarity : 0.003 0.038 921 Dihedral : 7.104 135.094 736 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.71 % Favored : 91.29 % Rotamer: Outliers : 0.86 % Allowed : 11.34 % 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: -0.87 (0.33), residues: 666 helix: 1.66 (0.31), residues: 310 sheet: -0.67 (0.62), residues: 77 loop : -3.38 (0.30), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 435 HIS 0.003 0.001 HIS C 74 PHE 0.012 0.002 PHE C 362 TYR 0.015 0.002 TYR C 247 ARG 0.004 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 85 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 80 time to evaluate : 0.638 Fit side-chains revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7757 (mmt) cc_final: 0.7330 (mmm) REVERT: C 190 ARG cc_start: 0.7359 (mmp80) cc_final: 0.7139 (mmp80) REVERT: C 275 ILE cc_start: 0.9005 (mm) cc_final: 0.8753 (mm) outliers start: 5 outliers final: 5 residues processed: 83 average time/residue: 0.2017 time to fit residues: 21.5086 Evaluate side-chains 75 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.594 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 188 ASN Chi-restraints excluded: chain C residue 364 THR 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: 0.5980 chunk 18 optimal weight: 2.9990 chunk 50 optimal weight: 2.9990 chunk 41 optimal weight: 0.9980 chunk 16 optimal weight: 4.9990 chunk 60 optimal weight: 0.9990 chunk 65 optimal weight: 0.8980 chunk 54 optimal weight: 0.5980 chunk 20 optimal weight: 0.3980 chunk 48 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- 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: 0.6954 moved from start: 0.1341 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5360 Z= 0.185 Angle : 0.625 6.668 7237 Z= 0.313 Chirality : 0.044 0.143 846 Planarity : 0.003 0.038 921 Dihedral : 7.073 135.535 736 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.16 % Favored : 90.84 % Rotamer: Outliers : 1.72 % Allowed : 15.46 % Favored : 82.82 % 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: -0.76 (0.33), residues: 666 helix: 1.78 (0.30), residues: 309 sheet: -0.53 (0.63), residues: 77 loop : -3.36 (0.30), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 435 HIS 0.002 0.001 HIS C 74 PHE 0.009 0.001 PHE Q 167 TYR 0.011 0.001 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 89 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.716 Fit side-chains revert: symmetry clash REVERT: Q 187 MET cc_start: 0.7690 (mmt) cc_final: 0.7271 (mmm) REVERT: C 128 LYS cc_start: 0.8111 (pptt) cc_final: 0.7773 (pptt) REVERT: C 275 ILE cc_start: 0.8871 (mm) cc_final: 0.8508 (mm) outliers start: 10 outliers final: 7 residues processed: 84 average time/residue: 0.1812 time to fit residues: 19.9785 Evaluate side-chains 80 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 73 time to evaluate : 0.618 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 166 ILE Chi-restraints excluded: chain Q residue 168 VAL Chi-restraints excluded: chain C residue 100 ILE Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 364 THR 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: 4.9990 chunk 6 optimal weight: 0.0370 chunk 29 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 61 optimal weight: 1.9990 chunk 64 optimal weight: 2.9990 chunk 57 optimal weight: 7.9990 chunk 17 optimal weight: 0.9980 chunk 53 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.4064 ------------------------------------------------------------------------------- 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: 0.7062 moved from start: 0.1682 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 5360 Z= 0.298 Angle : 0.692 8.507 7237 Z= 0.349 Chirality : 0.046 0.203 846 Planarity : 0.004 0.041 921 Dihedral : 7.265 135.571 736 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 10.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 3.78 % Allowed : 16.15 % Favored : 80.07 % 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: -0.93 (0.33), residues: 666 helix: 1.56 (0.30), residues: 317 sheet: -0.89 (0.62), residues: 78 loop : -3.40 (0.31), residues: 271 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 435 HIS 0.004 0.001 HIS C 74 PHE 0.022 0.002 PHE Q 167 TYR 0.012 0.001 TYR C 198 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 102 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 80 time to evaluate : 0.648 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 112 PHE cc_start: 0.7118 (OUTLIER) cc_final: 0.6897 (m-10) REVERT: C 376 LEU cc_start: 0.8474 (OUTLIER) cc_final: 0.8206 (pt) outliers start: 22 outliers final: 16 residues processed: 91 average time/residue: 0.1707 time to fit residues: 20.2813 Evaluate side-chains 93 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 75 time to evaluate : 0.614 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET 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 364 THR 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.6980 chunk 26 optimal weight: 8.9990 chunk 55 optimal weight: 0.8980 chunk 44 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 0.9990 chunk 58 optimal weight: 10.0000 chunk 16 optimal weight: 10.0000 chunk 21 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 442 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7012 moved from start: 0.1809 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= 0.205 Angle : 0.649 8.425 7237 Z= 0.324 Chirality : 0.044 0.150 846 Planarity : 0.003 0.038 921 Dihedral : 7.145 136.273 736 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 10.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.31 % Favored : 90.69 % Rotamer: Outliers : 3.61 % Allowed : 17.70 % Favored : 78.69 % 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 (0.33), residues: 666 helix: 1.72 (0.30), residues: 311 sheet: -0.66 (0.63), residues: 77 loop : -3.35 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 435 HIS 0.003 0.001 HIS C 74 PHE 0.014 0.002 PHE Q 167 TYR 0.012 0.001 TYR C 247 ARG 0.005 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 98 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 77 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: Q 101 ASP cc_start: 0.7350 (OUTLIER) cc_final: 0.7058 (m-30) REVERT: Q 187 MET cc_start: 0.7715 (mmt) cc_final: 0.7421 (mmm) REVERT: C 128 LYS cc_start: 0.7912 (pptt) cc_final: 0.7556 (pptt) REVERT: C 190 ARG cc_start: 0.7348 (mmp80) cc_final: 0.7088 (mmp80) REVERT: C 376 LEU cc_start: 0.8385 (OUTLIER) cc_final: 0.8121 (pt) outliers start: 21 outliers final: 17 residues processed: 87 average time/residue: 0.1760 time to fit residues: 19.8969 Evaluate side-chains 94 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 75 time to evaluate : 0.604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain Q residue 67 ASP Chi-restraints excluded: chain Q residue 101 ASP 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 205 MET Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 211 ASN 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 364 THR 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 1.9990 chunk 64 optimal weight: 0.0870 chunk 53 optimal weight: 0.5980 chunk 30 optimal weight: 0.0270 chunk 5 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 34 optimal weight: 0.8980 chunk 62 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 chunk 36 optimal weight: 0.3980 chunk 47 optimal weight: 0.0670 overall best weight: 0.1332 ------------------------------------------------------------------------------- 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: 0.6879 moved from start: 0.2012 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 5360 Z= 0.144 Angle : 0.606 8.199 7237 Z= 0.299 Chirality : 0.042 0.132 846 Planarity : 0.003 0.035 921 Dihedral : 6.878 135.632 736 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 8.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.26 % Favored : 91.74 % Rotamer: Outliers : 2.58 % Allowed : 19.42 % 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: -0.59 (0.34), residues: 666 helix: 1.92 (0.30), residues: 309 sheet: -0.77 (0.67), residues: 62 loop : -3.06 (0.31), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.002 0.001 HIS C 470 PHE 0.010 0.001 PHE C 264 TYR 0.024 0.001 TYR C 247 ARG 0.004 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 94 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 79 time to evaluate : 0.622 Fit side-chains revert: symmetry clash REVERT: C 376 LEU cc_start: 0.8331 (OUTLIER) cc_final: 0.8048 (pt) REVERT: C 402 LEU cc_start: 0.6639 (OUTLIER) cc_final: 0.5925 (tt) outliers start: 15 outliers final: 10 residues processed: 87 average time/residue: 0.1827 time to fit residues: 20.7404 Evaluate side-chains 88 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 76 time to evaluate : 0.629 ------------------------------------------------------------------------------- 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 168 VAL Chi-restraints excluded: chain Q residue 195 GLU Chi-restraints excluded: chain Q residue 205 MET Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain C residue 47 MET Chi-restraints excluded: chain C residue 98 VAL Chi-restraints excluded: chain C residue 111 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 376 LEU Chi-restraints excluded: chain C residue 402 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 0.7980 chunk 54 optimal weight: 0.5980 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 39 optimal weight: 0.5980 chunk 29 optimal weight: 5.9990 chunk 25 optimal weight: 7.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 12 optimal weight: 3.9990 chunk 41 optimal weight: 2.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- 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: 0.7093 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.042 5360 Z= 0.358 Angle : 0.738 8.148 7237 Z= 0.374 Chirality : 0.048 0.229 846 Planarity : 0.004 0.037 921 Dihedral : 7.221 135.125 736 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 3.44 % Allowed : 20.96 % Favored : 75.60 % 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: -0.88 (0.34), residues: 666 helix: 1.65 (0.31), residues: 312 sheet: -0.72 (0.63), residues: 78 loop : -3.40 (0.31), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 435 HIS 0.005 0.002 HIS C 74 PHE 0.026 0.003 PHE Q 167 TYR 0.014 0.002 TYR C 198 ARG 0.006 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 100 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 80 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 18 residues processed: 90 average time/residue: 0.1773 time to fit residues: 20.9566 Evaluate side-chains 95 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.622 ------------------------------------------------------------------------------- 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 205 MET Chi-restraints excluded: chain Q residue 208 LEU Chi-restraints excluded: chain Q residue 211 ASN 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 182 MET Chi-restraints excluded: chain C residue 364 THR 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: 0.0670 chunk 31 optimal weight: 6.9990 chunk 6 optimal weight: 0.0470 chunk 50 optimal weight: 2.9990 chunk 58 optimal weight: 8.9990 chunk 61 optimal weight: 5.9990 chunk 56 optimal weight: 1.9990 chunk 60 optimal weight: 9.9990 chunk 36 optimal weight: 0.7980 chunk 26 optimal weight: 1.9990 chunk 47 optimal weight: 0.0170 overall best weight: 0.5856 ------------------------------------------------------------------------------- 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: 0.6986 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5360 Z= 0.179 Angle : 0.646 7.463 7237 Z= 0.323 Chirality : 0.044 0.146 846 Planarity : 0.003 0.035 921 Dihedral : 7.021 135.418 736 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.56 % Favored : 91.44 % Rotamer: Outliers : 1.89 % Allowed : 22.34 % Favored : 75.77 % 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: -0.74 (0.34), residues: 666 helix: 1.76 (0.31), residues: 310 sheet: -0.39 (0.63), residues: 77 loop : -3.37 (0.31), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.002 0.001 HIS C 226 PHE 0.012 0.001 PHE Q 167 TYR 0.010 0.001 TYR C 274 ARG 0.007 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 90 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 79 time to evaluate : 0.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 152 MET cc_start: 0.6462 (mtt) cc_final: 0.6223 (mtt) REVERT: C 190 ARG cc_start: 0.7331 (mmp80) cc_final: 0.7060 (mmp80) outliers start: 11 outliers final: 11 residues processed: 84 average time/residue: 0.1668 time to fit residues: 18.4730 Evaluate side-chains 86 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.538 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 MET 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 111 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 402 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 3.9990 chunk 54 optimal weight: 0.5980 chunk 56 optimal weight: 7.9990 chunk 59 optimal weight: 4.9990 chunk 39 optimal weight: 0.0030 chunk 63 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 overall best weight: 1.2794 ------------------------------------------------------------------------------- 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: 0.7068 moved from start: 0.2297 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 5360 Z= 0.279 Angle : 0.708 7.926 7237 Z= 0.356 Chirality : 0.046 0.166 846 Planarity : 0.004 0.038 921 Dihedral : 7.183 135.626 736 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 10.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.41 % Allowed : 21.48 % Favored : 76.12 % 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 (0.33), residues: 666 helix: 1.54 (0.30), residues: 311 sheet: -0.72 (0.63), residues: 78 loop : -3.39 (0.31), residues: 277 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 0.020 0.002 PHE Q 167 TYR 0.014 0.002 TYR C 274 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 90 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 76 time to evaluate : 0.631 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 11 residues processed: 84 average time/residue: 0.1627 time to fit residues: 18.2018 Evaluate side-chains 85 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 74 time to evaluate : 0.572 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 MET 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 111 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 402 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 41 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 7 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- 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: 0.7008 moved from start: 0.2308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 5360 Z= 0.203 Angle : 0.668 9.021 7237 Z= 0.334 Chirality : 0.044 0.151 846 Planarity : 0.004 0.035 921 Dihedral : 7.033 135.384 736 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 2.58 % Allowed : 20.62 % 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: -0.83 (0.34), residues: 666 helix: 1.63 (0.30), residues: 311 sheet: -0.44 (0.64), residues: 77 loop : -3.35 (0.31), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.003 0.001 HIS C 226 PHE 0.013 0.002 PHE Q 167 TYR 0.010 0.002 TYR Q 74 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 88 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 73 time to evaluate : 0.604 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 11 residues processed: 82 average time/residue: 0.1505 time to fit residues: 16.6542 Evaluate side-chains 83 residues out of total 583 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 72 time to evaluate : 0.595 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 205 MET 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 111 HIS Chi-restraints excluded: chain C residue 364 THR Chi-restraints excluded: chain C residue 459 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 0.9990 chunk 6 optimal weight: 0.0020 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 3 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 60 optimal weight: 6.9990 chunk 35 optimal weight: 0.1980 chunk 45 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4469 r_free = 0.4469 target = 0.211004 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.4106 r_free = 0.4106 target = 0.173118 restraints weight = 8217.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.4068 r_free = 0.4068 target = 0.171553 restraints weight = 13843.655| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.4076 r_free = 0.4076 target = 0.172736 restraints weight = 13067.994| |-----------------------------------------------------------------------------| r_work (final): 0.4113 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7058 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5360 Z= 0.184 Angle : 0.668 9.531 7237 Z= 0.331 Chirality : 0.044 0.148 846 Planarity : 0.004 0.039 921 Dihedral : 6.914 134.446 736 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.91 % Favored : 90.09 % Rotamer: Outliers : 2.23 % Allowed : 21.65 % Favored : 76.12 % 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: -0.74 (0.34), residues: 666 helix: 1.73 (0.31), residues: 311 sheet: -0.35 (0.65), residues: 77 loop : -3.37 (0.32), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 435 HIS 0.003 0.001 HIS C 226 PHE 0.013 0.001 PHE C 264 TYR 0.011 0.001 TYR Q 74 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: 1342.00 seconds wall clock time: 24 minutes 56.05 seconds (1496.05 seconds total)