Starting phenix.real_space_refine on Mon Mar 11 05:27:29 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/03_2024/8efe_28081_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/03_2024/8efe_28081.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/03_2024/8efe_28081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/03_2024/8efe_28081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/03_2024/8efe_28081_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/03_2024/8efe_28081_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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: 6 Type Number sf(0) Gaussians P 2 5.49 5 Mg 1 5.21 5 S 40 5.16 5 C 4534 2.51 5 N 1215 2.21 5 O 1343 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 230": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A PHE 465": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 588": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 123": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7135 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 740, 5967 Classifications: {'peptide': 740} Link IDs: {'PTRANS': 28, 'TRANS': 711} Chain breaks: 3 Chain: "B" Number of atoms: 1140 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1140 Classifications: {'peptide': 146} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 142} Chain: "A" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' MG': 1, 'ADP': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.56, per 1000 atoms: 0.64 Number of scatterers: 7135 At special positions: 0 Unit cell: (139.062, 88.396, 104.566, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) S 40 16.00 P 2 15.00 Mg 1 11.99 O 1343 8.00 N 1215 7.00 C 4534 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: 3.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1658 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 42 helices and 7 sheets defined 49.8% alpha, 9.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.69 Creating SS restraints... Processing helix chain 'A' and resid 10 through 16 Proline residue: A 14 - end of helix Processing helix chain 'A' and resid 20 through 27 Processing helix chain 'A' and resid 73 through 75 No H-bonds generated for 'chain 'A' and resid 73 through 75' Processing helix chain 'A' and resid 82 through 84 No H-bonds generated for 'chain 'A' and resid 82 through 84' Processing helix chain 'A' and resid 98 through 110 removed outlier: 3.940A pdb=" N LEU A 102 " --> pdb=" O GLU A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 132 through 134 No H-bonds generated for 'chain 'A' and resid 132 through 134' Processing helix chain 'A' and resid 136 through 142 Processing helix chain 'A' and resid 154 through 168 Processing helix chain 'A' and resid 184 through 196 Processing helix chain 'A' and resid 217 through 231 Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 270 through 274 Processing helix chain 'A' and resid 284 through 290 Processing helix chain 'A' and resid 295 through 300 Processing helix chain 'A' and resid 307 through 309 No H-bonds generated for 'chain 'A' and resid 307 through 309' Processing helix chain 'A' and resid 311 through 314 No H-bonds generated for 'chain 'A' and resid 311 through 314' Processing helix chain 'A' and resid 326 through 337 Processing helix chain 'A' and resid 343 through 361 removed outlier: 4.259A pdb=" N GLY A 360 " --> pdb=" O ILE A 356 " (cutoff:3.500A) removed outlier: 5.271A pdb=" N ASN A 361 " --> pdb=" O MET A 357 " (cutoff:3.500A) Processing helix chain 'A' and resid 380 through 388 Processing helix chain 'A' and resid 392 through 400 Processing helix chain 'A' and resid 417 through 447 Processing helix chain 'A' and resid 473 through 504 Processing helix chain 'A' and resid 518 through 525 Processing helix chain 'A' and resid 530 through 539 removed outlier: 3.568A pdb=" N MET A 539 " --> pdb=" O GLU A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 545 through 556 Processing helix chain 'A' and resid 593 through 597 Processing helix chain 'A' and resid 604 through 611 Processing helix chain 'A' and resid 615 through 619 Processing helix chain 'A' and resid 647 through 664 removed outlier: 4.087A pdb=" N SER A 664 " --> pdb=" O THR A 660 " (cutoff:3.500A) Processing helix chain 'A' and resid 686 through 696 Processing helix chain 'A' and resid 698 through 707 Processing helix chain 'A' and resid 715 through 724 removed outlier: 3.916A pdb=" N ARG A 723 " --> pdb=" O ARG A 719 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 724 " --> pdb=" O GLN A 720 " (cutoff:3.500A) Processing helix chain 'A' and resid 740 through 749 Processing helix chain 'A' and resid 767 through 795 Processing helix chain 'B' and resid 44 through 56 Processing helix chain 'B' and resid 69 through 75 Processing helix chain 'B' and resid 82 through 88 Processing helix chain 'B' and resid 94 through 97 No H-bonds generated for 'chain 'B' and resid 94 through 97' Processing helix chain 'B' and resid 104 through 116 Proline residue: B 109 - end of helix removed outlier: 3.785A pdb=" N ASN B 116 " --> pdb=" O GLN B 112 " (cutoff:3.500A) Processing helix chain 'B' and resid 123 through 131 Processing helix chain 'B' and resid 143 through 152 Processing helix chain 'B' and resid 159 through 166 Processing helix chain 'B' and resid 178 through 187 Processing sheet with id= A, first strand: chain 'A' and resid 36 through 39 removed outlier: 7.388A pdb=" N THR A 60 " --> pdb=" O VAL A 52 " (cutoff:3.500A) removed outlier: 5.986A pdb=" N ARG A 54 " --> pdb=" O LYS A 58 " (cutoff:3.500A) removed outlier: 7.810A pdb=" N LYS A 58 " --> pdb=" O ARG A 54 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 115 through 118 removed outlier: 3.831A pdb=" N SER A 118 " --> pdb=" O PHE A 121 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N PHE A 121 " --> pdb=" O SER A 118 " (cutoff:3.500A) removed outlier: 7.773A pdb=" N PHE A 669 " --> pdb=" O CYS A 122 " (cutoff:3.500A) removed outlier: 8.538A pdb=" N THR A 124 " --> pdb=" O PHE A 669 " (cutoff:3.500A) removed outlier: 6.285A pdb=" N ARG A 671 " --> pdb=" O THR A 124 " (cutoff:3.500A) removed outlier: 7.733A pdb=" N ASN A 126 " --> pdb=" O ARG A 671 " (cutoff:3.500A) removed outlier: 7.755A pdb=" N ILE A 673 " --> pdb=" O ASN A 126 " (cutoff:3.500A) removed outlier: 8.079A pdb=" N VAL A 670 " --> pdb=" O SER A 173 " (cutoff:3.500A) removed outlier: 6.577A pdb=" N LEU A 175 " --> pdb=" O VAL A 670 " (cutoff:3.500A) removed outlier: 7.862A pdb=" N CYS A 672 " --> pdb=" O LEU A 175 " (cutoff:3.500A) removed outlier: 6.748A pdb=" N THR A 177 " --> pdb=" O CYS A 672 " (cutoff:3.500A) removed outlier: 9.068A pdb=" N ILE A 674 " --> pdb=" O THR A 177 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N GLY A 178 " --> pdb=" O ILE A 462 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 403 through 406 Processing sheet with id= D, first strand: chain 'A' and resid 577 through 580 removed outlier: 4.031A pdb=" N PHE A 577 " --> pdb=" O TYR A 588 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 711 through 714 removed outlier: 3.721A pdb=" N ASN A 711 " --> pdb=" O PHE A 765 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'B' and resid 63 through 65 Processing sheet with id= G, first strand: chain 'B' and resid 140 through 142 306 hydrogen bonds defined for protein. 897 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: 2.22 Time building geometry restraints manager: 3.25 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2328 1.34 - 1.46: 947 1.46 - 1.57: 3926 1.57 - 1.69: 3 1.69 - 1.81: 70 Bond restraints: 7274 Sorted by residual: bond pdb=" C LYS A 365 " pdb=" O LYS A 365 " ideal model delta sigma weight residual 1.235 1.217 0.018 1.26e-02 6.30e+03 2.01e+00 bond pdb=" CA LYS A 365 " pdb=" C LYS A 365 " ideal model delta sigma weight residual 1.523 1.506 0.017 1.34e-02 5.57e+03 1.69e+00 bond pdb=" CA GLN A 372 " pdb=" C GLN A 372 " ideal model delta sigma weight residual 1.525 1.509 0.016 1.28e-02 6.10e+03 1.47e+00 bond pdb=" C4 ADP A2002 " pdb=" C5 ADP A2002 " ideal model delta sigma weight residual 1.490 1.467 0.023 2.00e-02 2.50e+03 1.32e+00 bond pdb=" CA LYS A 367 " pdb=" C LYS A 367 " ideal model delta sigma weight residual 1.523 1.508 0.015 1.28e-02 6.10e+03 1.30e+00 ... (remaining 7269 not shown) Histogram of bond angle deviations from ideal: 99.05 - 106.51: 180 106.51 - 113.97: 4062 113.97 - 121.42: 3899 121.42 - 128.88: 1624 128.88 - 136.33: 34 Bond angle restraints: 9799 Sorted by residual: angle pdb=" CA PRO A 375 " pdb=" C PRO A 375 " pdb=" O PRO A 375 " ideal model delta sigma weight residual 122.12 118.67 3.45 1.24e+00 6.50e-01 7.75e+00 angle pdb=" CA PRO A 375 " pdb=" C PRO A 375 " pdb=" N ASP A 376 " ideal model delta sigma weight residual 114.65 117.92 -3.27 1.27e+00 6.20e-01 6.61e+00 angle pdb=" O MET A 362 " pdb=" C MET A 362 " pdb=" N LYS A 363 " ideal model delta sigma weight residual 122.96 120.28 2.68 1.13e+00 7.83e-01 5.63e+00 angle pdb=" CB MET A 546 " pdb=" CG MET A 546 " pdb=" SD MET A 546 " ideal model delta sigma weight residual 112.70 119.40 -6.70 3.00e+00 1.11e-01 4.98e+00 angle pdb=" CA MET A 362 " pdb=" C MET A 362 " pdb=" N LYS A 363 " ideal model delta sigma weight residual 115.49 118.16 -2.67 1.24e+00 6.50e-01 4.65e+00 ... (remaining 9794 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 3917 17.28 - 34.56: 390 34.56 - 51.84: 81 51.84 - 69.13: 17 69.13 - 86.41: 6 Dihedral angle restraints: 4411 sinusoidal: 1840 harmonic: 2571 Sorted by residual: dihedral pdb=" CB GLU A 269 " pdb=" CG GLU A 269 " pdb=" CD GLU A 269 " pdb=" OE1 GLU A 269 " ideal model delta sinusoidal sigma weight residual 0.00 -86.41 86.41 1 3.00e+01 1.11e-03 1.00e+01 dihedral pdb=" CG ARG B 74 " pdb=" CD ARG B 74 " pdb=" NE ARG B 74 " pdb=" CZ ARG B 74 " ideal model delta sinusoidal sigma weight residual 90.00 132.97 -42.97 2 1.50e+01 4.44e-03 9.91e+00 dihedral pdb=" CB GLU A 280 " pdb=" CG GLU A 280 " pdb=" CD GLU A 280 " pdb=" OE1 GLU A 280 " ideal model delta sinusoidal sigma weight residual 0.00 -85.37 85.37 1 3.00e+01 1.11e-03 9.81e+00 ... (remaining 4408 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 705 0.027 - 0.054: 230 0.054 - 0.081: 68 0.081 - 0.108: 42 0.108 - 0.135: 19 Chirality restraints: 1064 Sorted by residual: chirality pdb=" CA ILE A 174 " pdb=" N ILE A 174 " pdb=" C ILE A 174 " pdb=" CB ILE A 174 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 467 " pdb=" N ILE A 467 " pdb=" C ILE A 467 " pdb=" CB ILE A 467 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.52e-01 chirality pdb=" CA ILE A 751 " pdb=" N ILE A 751 " pdb=" C ILE A 751 " pdb=" CB ILE A 751 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.09e-01 ... (remaining 1061 not shown) Planarity restraints: 1270 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP A 112 " 0.011 2.00e-02 2.50e+03 8.27e-03 1.71e+00 pdb=" CG TRP A 112 " -0.021 2.00e-02 2.50e+03 pdb=" CD1 TRP A 112 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TRP A 112 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP A 112 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP A 112 " -0.003 2.00e-02 2.50e+03 pdb=" CE3 TRP A 112 " -0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP A 112 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP A 112 " 0.003 2.00e-02 2.50e+03 pdb=" CH2 TRP A 112 " 0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 46 " -0.009 2.00e-02 2.50e+03 8.37e-03 1.22e+00 pdb=" CG PHE A 46 " 0.019 2.00e-02 2.50e+03 pdb=" CD1 PHE A 46 " -0.005 2.00e-02 2.50e+03 pdb=" CD2 PHE A 46 " -0.001 2.00e-02 2.50e+03 pdb=" CE1 PHE A 46 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 46 " -0.004 2.00e-02 2.50e+03 pdb=" CZ PHE A 46 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 135 " 0.018 5.00e-02 4.00e+02 2.75e-02 1.21e+00 pdb=" N PRO A 136 " -0.048 5.00e-02 4.00e+02 pdb=" CA PRO A 136 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 136 " 0.015 5.00e-02 4.00e+02 ... (remaining 1267 not shown) Histogram of nonbonded interaction distances: 1.95 - 2.54: 66 2.54 - 3.13: 5918 3.13 - 3.72: 11676 3.72 - 4.31: 15114 4.31 - 4.90: 25071 Nonbonded interactions: 57845 Sorted by model distance: nonbonded pdb=" OG SER A 19 " pdb=" OE1 GLU A 22 " model vdw 1.948 2.440 nonbonded pdb=" O LYS A 189 " pdb=" NE2 GLN A 193 " model vdw 2.054 2.520 nonbonded pdb="MG MG A2001 " pdb=" O3B ADP A2002 " model vdw 2.072 2.170 nonbonded pdb=" OH TYR A 162 " pdb=" O GLY A 256 " model vdw 2.151 2.440 nonbonded pdb=" OG1 THR A 185 " pdb="MG MG A2001 " model vdw 2.234 2.170 ... (remaining 57840 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: 5.990 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: 17.130 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 23.810 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.990 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 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 : 0.002 0.039 7274 Z= 0.155 Angle : 0.515 6.695 9799 Z= 0.278 Chirality : 0.036 0.135 1064 Planarity : 0.003 0.028 1270 Dihedral : 14.481 86.407 2753 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 8.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 0.52 % Allowed : 0.13 % Favored : 99.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.15 (0.30), residues: 876 helix: 2.21 (0.25), residues: 462 sheet: -1.11 (0.63), residues: 75 loop : -0.84 (0.32), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 112 HIS 0.002 0.000 HIS A 153 PHE 0.019 0.001 PHE A 46 TYR 0.013 0.001 TYR A 194 ARG 0.002 0.000 ARG A 272 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 59 time to evaluate : 0.903 Fit side-chains revert: symmetry clash REVERT: A 362 MET cc_start: 0.8874 (mpp) cc_final: 0.8606 (mpp) REVERT: A 465 PHE cc_start: 0.7935 (t80) cc_final: 0.7718 (t80) outliers start: 4 outliers final: 1 residues processed: 62 average time/residue: 0.2156 time to fit residues: 18.0118 Evaluate side-chains 50 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 44 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 68 optimal weight: 6.9990 chunk 26 optimal weight: 2.9990 chunk 41 optimal weight: 0.9990 chunk 51 optimal weight: 0.7980 chunk 79 optimal weight: 6.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 372 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 91 ASN B 184 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 7274 Z= 0.241 Angle : 0.541 5.783 9799 Z= 0.274 Chirality : 0.040 0.151 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.560 45.183 966 Min Nonbonded Distance : 1.864 Molprobity Statistics. All-atom Clashscore : 9.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 0.78 % Allowed : 6.37 % Favored : 92.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.02 (0.29), residues: 876 helix: 2.06 (0.25), residues: 462 sheet: -0.74 (0.67), residues: 71 loop : -0.96 (0.32), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 130 HIS 0.018 0.002 HIS B 148 PHE 0.012 0.001 PHE A 359 TYR 0.016 0.002 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 0.782 Fit side-chains revert: symmetry clash REVERT: A 659 MET cc_start: 0.8838 (mmm) cc_final: 0.8634 (mmm) REVERT: A 776 MET cc_start: 0.9712 (ttm) cc_final: 0.9511 (ptm) outliers start: 6 outliers final: 2 residues processed: 59 average time/residue: 0.1778 time to fit residues: 14.8965 Evaluate side-chains 51 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 672 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 54 optimal weight: 0.4980 chunk 22 optimal weight: 0.1980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 79 optimal weight: 3.9990 chunk 27 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 193 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 372 GLN A 479 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8364 moved from start: 0.1360 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7274 Z= 0.210 Angle : 0.511 5.728 9799 Z= 0.260 Chirality : 0.039 0.143 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.647 49.211 966 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer: Outliers : 0.91 % Allowed : 9.23 % Favored : 89.86 % 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: 0.91 (0.29), residues: 876 helix: 1.97 (0.25), residues: 464 sheet: -0.84 (0.69), residues: 68 loop : -1.01 (0.31), residues: 344 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 130 HIS 0.005 0.001 HIS B 148 PHE 0.009 0.001 PHE A 46 TYR 0.011 0.001 TYR B 178 ARG 0.004 0.000 ARG A 369 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 53 time to evaluate : 0.826 Fit side-chains revert: symmetry clash REVERT: A 659 MET cc_start: 0.8867 (mmm) cc_final: 0.8542 (mmm) outliers start: 7 outliers final: 6 residues processed: 58 average time/residue: 0.1789 time to fit residues: 14.9102 Evaluate side-chains 55 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 49 time to evaluate : 0.828 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 5.9990 chunk 60 optimal weight: 0.9980 chunk 41 optimal weight: 0.9980 chunk 8 optimal weight: 0.0020 chunk 38 optimal weight: 0.9980 chunk 53 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 85 optimal weight: 0.9990 chunk 76 optimal weight: 0.7980 chunk 22 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 overall best weight: 0.6988 ------------------------------------------------------------------------------- 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: 0.8373 moved from start: 0.1641 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 7274 Z= 0.209 Angle : 0.515 5.742 9799 Z= 0.262 Chirality : 0.039 0.144 1064 Planarity : 0.003 0.031 1270 Dihedral : 4.693 50.942 966 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 10.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer: Outliers : 1.95 % Allowed : 10.92 % Favored : 87.13 % 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: 0.84 (0.29), residues: 876 helix: 1.94 (0.25), residues: 463 sheet: -0.85 (0.70), residues: 68 loop : -1.09 (0.31), residues: 345 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 508 HIS 0.007 0.001 HIS B 148 PHE 0.011 0.001 PHE A 46 TYR 0.011 0.001 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 49 time to evaluate : 0.897 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 195 PHE cc_start: 0.8912 (OUTLIER) cc_final: 0.8337 (m-80) REVERT: A 659 MET cc_start: 0.8868 (mmm) cc_final: 0.8571 (mmm) outliers start: 15 outliers final: 9 residues processed: 61 average time/residue: 0.1835 time to fit residues: 15.9913 Evaluate side-chains 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 49 time to evaluate : 0.865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 0.3980 chunk 63 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 72 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 0 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 76 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 28 optimal weight: 2.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 668 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7274 Z= 0.216 Angle : 0.517 5.725 9799 Z= 0.262 Chirality : 0.039 0.144 1064 Planarity : 0.003 0.031 1270 Dihedral : 4.770 52.615 966 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 1.69 % Allowed : 12.87 % Favored : 85.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.84 (0.29), residues: 876 helix: 1.94 (0.25), residues: 464 sheet: -0.95 (0.69), residues: 70 loop : -1.07 (0.31), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 508 HIS 0.005 0.001 HIS B 148 PHE 0.012 0.001 PHE A 46 TYR 0.012 0.001 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 48 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 195 PHE cc_start: 0.8971 (OUTLIER) cc_final: 0.8391 (m-80) REVERT: A 659 MET cc_start: 0.8906 (mmm) cc_final: 0.8553 (mmm) REVERT: A 713 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8750 (mp) outliers start: 13 outliers final: 11 residues processed: 59 average time/residue: 0.1870 time to fit residues: 16.1643 Evaluate side-chains 60 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 195 PHE Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain A residue 713 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 10.0000 chunk 16 optimal weight: 0.9990 chunk 49 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 85 optimal weight: 4.9990 chunk 70 optimal weight: 0.0170 chunk 39 optimal weight: 0.9980 chunk 7 optimal weight: 0.0870 chunk 28 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 172 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8372 moved from start: 0.2018 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 7274 Z= 0.165 Angle : 0.512 12.766 9799 Z= 0.253 Chirality : 0.039 0.138 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.667 51.614 966 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 11.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.08 % Allowed : 13.91 % Favored : 84.01 % 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: 0.82 (0.29), residues: 876 helix: 1.86 (0.25), residues: 469 sheet: -0.88 (0.70), residues: 70 loop : -1.05 (0.31), residues: 337 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 112 HIS 0.003 0.001 HIS B 148 PHE 0.012 0.001 PHE A 46 TYR 0.012 0.001 TYR B 178 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 48 time to evaluate : 0.856 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 546 MET cc_start: 0.7994 (mmm) cc_final: 0.7786 (mmm) REVERT: A 659 MET cc_start: 0.8912 (mmm) cc_final: 0.8491 (mmm) outliers start: 16 outliers final: 14 residues processed: 62 average time/residue: 0.1806 time to fit residues: 16.2138 Evaluate side-chains 62 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 48 time to evaluate : 0.847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 1.9990 chunk 48 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 84 optimal weight: 0.9990 chunk 53 optimal weight: 0.2980 chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 33 optimal weight: 0.8980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2187 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 7274 Z= 0.194 Angle : 0.526 11.750 9799 Z= 0.262 Chirality : 0.039 0.142 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.691 50.814 966 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 11.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.08 % Allowed : 14.82 % Favored : 83.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.81 (0.29), residues: 876 helix: 1.87 (0.25), residues: 468 sheet: -0.96 (0.69), residues: 70 loop : -1.04 (0.31), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP A 130 HIS 0.003 0.001 HIS A 153 PHE 0.012 0.001 PHE A 46 TYR 0.012 0.001 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.873 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 659 MET cc_start: 0.8942 (mmm) cc_final: 0.8623 (mmm) outliers start: 16 outliers final: 14 residues processed: 60 average time/residue: 0.2020 time to fit residues: 17.2103 Evaluate side-chains 60 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 46 time to evaluate : 0.836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 457 ILE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 53 optimal weight: 1.9990 chunk 57 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 7 optimal weight: 0.7980 chunk 66 optimal weight: 0.5980 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 3.9990 chunk 74 optimal weight: 0.2980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 361 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.2307 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7274 Z= 0.190 Angle : 0.535 11.886 9799 Z= 0.264 Chirality : 0.039 0.141 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.680 50.157 966 Min Nonbonded Distance : 1.915 Molprobity Statistics. All-atom Clashscore : 12.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.34 % Favored : 95.66 % Rotamer: Outliers : 2.08 % Allowed : 15.08 % Favored : 82.83 % 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: 0.78 (0.29), residues: 876 helix: 1.84 (0.25), residues: 468 sheet: -1.02 (0.69), residues: 70 loop : -1.05 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 508 HIS 0.003 0.001 HIS A 153 PHE 0.013 0.001 PHE A 46 TYR 0.012 0.001 TYR B 178 ARG 0.004 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 46 time to evaluate : 0.688 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7005 (mmp) cc_final: 0.6732 (mmp) REVERT: A 659 MET cc_start: 0.8947 (mmm) cc_final: 0.8493 (mmm) outliers start: 16 outliers final: 14 residues processed: 60 average time/residue: 0.1683 time to fit residues: 14.5436 Evaluate side-chains 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 45 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 7.9990 chunk 81 optimal weight: 4.9990 chunk 47 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 71 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 51 optimal weight: 0.5980 chunk 83 optimal weight: 0.0040 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 711 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8389 moved from start: 0.2440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7274 Z= 0.202 Angle : 0.547 11.936 9799 Z= 0.268 Chirality : 0.039 0.140 1064 Planarity : 0.003 0.029 1270 Dihedral : 4.657 49.002 966 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 2.08 % Allowed : 15.73 % Favored : 82.18 % 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 (0.30), residues: 876 helix: 1.81 (0.25), residues: 469 sheet: -1.38 (0.64), residues: 80 loop : -1.02 (0.32), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 508 HIS 0.003 0.001 HIS A 153 PHE 0.013 0.001 PHE A 46 TYR 0.012 0.001 TYR B 178 ARG 0.003 0.000 ARG A 169 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 45 time to evaluate : 0.804 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.7002 (mmp) cc_final: 0.6743 (mmp) REVERT: A 659 MET cc_start: 0.8957 (mmm) cc_final: 0.8494 (mmm) outliers start: 16 outliers final: 15 residues processed: 59 average time/residue: 0.1748 time to fit residues: 14.9675 Evaluate side-chains 60 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 45 time to evaluate : 0.882 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 184 LYS Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 510 PHE Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 648 SER Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.6980 chunk 39 optimal weight: 0.1980 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 69 optimal weight: 0.6980 chunk 7 optimal weight: 0.0770 chunk 53 optimal weight: 1.9990 chunk 42 optimal weight: 0.0980 chunk 55 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 overall best weight: 0.3538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 222 GLN A 486 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 moved from start: 0.2439 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7274 Z= 0.148 Angle : 0.527 12.437 9799 Z= 0.256 Chirality : 0.039 0.138 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.480 44.850 966 Min Nonbonded Distance : 1.972 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer: Outliers : 1.69 % Allowed : 15.73 % Favored : 82.57 % 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: 0.81 (0.29), residues: 876 helix: 1.87 (0.26), residues: 457 sheet: -0.92 (0.70), residues: 70 loop : -0.96 (0.31), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 508 HIS 0.003 0.001 HIS A 153 PHE 0.011 0.001 PHE A 764 TYR 0.012 0.001 TYR B 178 ARG 0.002 0.000 ARG A 169 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1752 Ramachandran restraints generated. 876 Oldfield, 0 Emsley, 876 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 49 time to evaluate : 0.878 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 113 MET cc_start: 0.6979 (mmp) cc_final: 0.6725 (mmp) REVERT: A 659 MET cc_start: 0.8938 (mmm) cc_final: 0.8457 (mmm) outliers start: 13 outliers final: 12 residues processed: 60 average time/residue: 0.1668 time to fit residues: 15.1208 Evaluate side-chains 57 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 45 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 THR Chi-restraints excluded: chain A residue 97 HIS Chi-restraints excluded: chain A residue 105 LEU Chi-restraints excluded: chain A residue 125 VAL Chi-restraints excluded: chain A residue 185 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 359 PHE Chi-restraints excluded: chain A residue 378 THR Chi-restraints excluded: chain A residue 515 MET Chi-restraints excluded: chain A residue 672 CYS Chi-restraints excluded: chain A residue 673 ILE Chi-restraints excluded: chain B residue 184 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 19 optimal weight: 0.9990 chunk 69 optimal weight: 4.9990 chunk 29 optimal weight: 0.5980 chunk 71 optimal weight: 0.9990 chunk 8 optimal weight: 0.6980 chunk 12 optimal weight: 0.0770 chunk 61 optimal weight: 1.9990 chunk 3 optimal weight: 0.0470 overall best weight: 0.4838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 486 GLN B 98 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3671 r_free = 0.3671 target = 0.057996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3127 r_free = 0.3127 target = 0.039098 restraints weight = 49734.662| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.040189 restraints weight = 25358.640| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 57)----------------| | r_work = 0.3191 r_free = 0.3191 target = 0.040892 restraints weight = 16463.409| |-----------------------------------------------------------------------------| r_work (final): 0.3142 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8457 moved from start: 0.2528 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7274 Z= 0.169 Angle : 0.539 12.380 9799 Z= 0.260 Chirality : 0.039 0.138 1064 Planarity : 0.003 0.032 1270 Dihedral : 4.415 39.621 966 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 11.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer: Outliers : 2.21 % Allowed : 15.34 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.29), residues: 876 helix: 1.81 (0.25), residues: 463 sheet: -0.90 (0.71), residues: 70 loop : -1.01 (0.31), residues: 343 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 508 HIS 0.003 0.001 HIS A 153 PHE 0.027 0.001 PHE A 46 TYR 0.012 0.001 TYR B 178 ARG 0.003 0.000 ARG A 169 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1740.97 seconds wall clock time: 32 minutes 31.56 seconds (1951.56 seconds total)