Starting phenix.real_space_refine (version: dev) on Sat Feb 18 04:04:18 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/02_2023/8efe_28081_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/02_2023/8efe_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_28081/02_2023/8efe_28081.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/02_2023/8efe_28081.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/02_2023/8efe_28081_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8efe_28081/02_2023/8efe_28081_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 4.64, per 1000 atoms: 0.65 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: 3.10 Conformation dependent library (CDL) restraints added in 1.0 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: 1.34 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: 2.44 Time building geometry restraints manager: 3.32 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 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. 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: 4.490 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: 16.980 Check model and map are aligned: 0.110 Process input model: 23.420 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.090 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.140 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 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 % 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 *********************** 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 : 0.840 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 62 average time/residue: 0.2257 time to fit residues: 18.9825 Evaluate side-chains 50 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 49 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0685 time to fit residues: 1.4284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 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: 0.8380 ------------------------------------------------------------------------------- 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** A 479 ASN B 91 ASN B 184 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8312 moved from start: 0.1149 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.025 7274 Z= 0.246 Angle : 0.552 5.831 9799 Z= 0.280 Chirality : 0.040 0.154 1064 Planarity : 0.003 0.033 1270 Dihedral : 4.394 32.063 965 Min Nonbonded Distance : 1.874 Molprobity Statistics. All-atom Clashscore : 9.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.99 (0.29), residues: 876 helix: 2.04 (0.25), residues: 462 sheet: -0.72 (0.68), residues: 71 loop : -0.99 (0.32), residues: 343 *********************** 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 60 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 55 time to evaluate : 0.807 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 1 residues processed: 60 average time/residue: 0.1886 time to fit residues: 15.9938 Evaluate side-chains 51 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 50 time to evaluate : 0.858 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0616 time to fit residues: 1.2444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 66 optimal weight: 3.9990 chunk 54 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 80 optimal weight: 3.9990 chunk 86 optimal weight: 0.6980 chunk 71 optimal weight: 2.9990 chunk 79 optimal weight: 6.9990 chunk 27 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8321 moved from start: 0.1471 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= 0.220 Angle : 0.519 5.725 9799 Z= 0.264 Chirality : 0.040 0.146 1064 Planarity : 0.003 0.033 1270 Dihedral : 4.429 31.495 965 Min Nonbonded Distance : 1.909 Molprobity Statistics. All-atom Clashscore : 10.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.78 % 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 (0.29), residues: 876 helix: 1.96 (0.25), residues: 464 sheet: -0.85 (0.69), residues: 68 loop : -1.05 (0.31), residues: 344 *********************** 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 59 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 53 time to evaluate : 1.204 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 6 residues processed: 57 average time/residue: 0.2300 time to fit residues: 19.0322 Evaluate side-chains 54 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.965 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1321 time to fit residues: 2.4397 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 7.9990 chunk 60 optimal weight: 0.8980 chunk 41 optimal weight: 0.9990 chunk 8 optimal weight: 0.0870 chunk 38 optimal weight: 0.6980 chunk 53 optimal weight: 0.5980 chunk 80 optimal weight: 0.9990 chunk 85 optimal weight: 0.8980 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 70 optimal weight: 5.9990 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.1680 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 7274 Z= 0.192 Angle : 0.504 5.795 9799 Z= 0.256 Chirality : 0.039 0.141 1064 Planarity : 0.003 0.028 1270 Dihedral : 4.401 30.813 965 Min Nonbonded Distance : 1.930 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 1.04 % 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: 1.93 (0.25), residues: 463 sheet: -0.95 (0.69), residues: 70 loop : -1.06 (0.31), residues: 343 *********************** 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 57 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 49 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 56 average time/residue: 0.1794 time to fit residues: 14.7795 Evaluate side-chains 51 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 48 time to evaluate : 0.930 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0693 time to fit residues: 1.6360 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 63 optimal weight: 3.9990 chunk 35 optimal weight: 0.7980 chunk 72 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 0.4980 chunk 76 optimal weight: 4.9990 chunk 21 optimal weight: 0.9990 chunk 28 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 172 GLN A 668 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8343 moved from start: 0.1977 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= 0.229 Angle : 0.531 6.138 9799 Z= 0.270 Chirality : 0.039 0.146 1064 Planarity : 0.003 0.031 1270 Dihedral : 4.505 32.164 965 Min Nonbonded Distance : 1.948 Molprobity Statistics. All-atom Clashscore : 12.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.78 % 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: 0.72 (0.29), residues: 876 helix: 1.84 (0.25), residues: 469 sheet: -0.96 (0.69), residues: 70 loop : -1.18 (0.31), residues: 337 *********************** 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 54 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.940 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 4 residues processed: 53 average time/residue: 0.1938 time to fit residues: 14.9427 Evaluate side-chains 51 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 47 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0856 time to fit residues: 1.8611 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.5980 chunk 49 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 chunk 70 optimal weight: 0.0570 chunk 39 optimal weight: 0.6980 chunk 7 optimal weight: 0.0020 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 82 optimal weight: 4.9990 overall best weight: 0.3706 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8311 moved from start: 0.2003 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= 0.147 Angle : 0.497 7.268 9799 Z= 0.249 Chirality : 0.038 0.138 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.309 29.606 965 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.22 % Favored : 95.78 % Rotamer Outliers : 0.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.86 (0.29), residues: 876 helix: 1.93 (0.25), residues: 463 sheet: -0.88 (0.70), residues: 70 loop : -1.04 (0.31), residues: 343 *********************** 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 51 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 49 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 0.1894 time to fit residues: 14.2289 Evaluate side-chains 49 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.929 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0628 time to fit residues: 1.4114 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 3.9990 chunk 62 optimal weight: 0.9980 chunk 71 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 84 optimal weight: 2.9990 chunk 53 optimal weight: 0.0050 chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 0.2980 chunk 52 optimal weight: 0.0070 chunk 33 optimal weight: 0.9980 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 361 ASN A 486 GLN A 726 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8301 moved from start: 0.2075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7274 Z= 0.141 Angle : 0.497 7.880 9799 Z= 0.247 Chirality : 0.038 0.137 1064 Planarity : 0.003 0.031 1270 Dihedral : 4.175 29.704 965 Min Nonbonded Distance : 1.943 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.00 % Favored : 96.00 % Rotamer Outliers : 0.78 % 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 (0.29), residues: 876 helix: 1.90 (0.25), residues: 468 sheet: -0.91 (0.69), residues: 70 loop : -1.01 (0.31), residues: 338 *********************** 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 54 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 48 time to evaluate : 0.928 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 53 average time/residue: 0.1866 time to fit residues: 14.4722 Evaluate side-chains 48 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 45 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0715 time to fit residues: 1.6849 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.7980 chunk 25 optimal weight: 0.0870 chunk 16 optimal weight: 0.8980 chunk 53 optimal weight: 2.9990 chunk 57 optimal weight: 0.0770 chunk 41 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 66 optimal weight: 0.9990 chunk 77 optimal weight: 7.9990 chunk 81 optimal weight: 0.0270 chunk 74 optimal weight: 0.7980 overall best weight: 0.2574 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 482 ASN A 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.2185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 7274 Z= 0.134 Angle : 0.511 8.043 9799 Z= 0.253 Chirality : 0.039 0.137 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.106 29.898 965 Min Nonbonded Distance : 1.949 Molprobity Statistics. All-atom Clashscore : 10.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.88 % Favored : 96.12 % Rotamer Outliers : 0.39 % 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 (0.29), residues: 876 helix: 1.88 (0.25), residues: 459 sheet: -0.86 (0.69), residues: 70 loop : -0.88 (0.31), residues: 347 *********************** 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 54 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 51 time to evaluate : 1.100 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 53 average time/residue: 0.1962 time to fit residues: 15.2345 Evaluate side-chains 49 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 47 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0755 time to fit residues: 1.4920 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.5980 chunk 81 optimal weight: 0.0970 chunk 47 optimal weight: 0.6980 chunk 34 optimal weight: 0.0020 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 chunk 71 optimal weight: 2.9990 chunk 74 optimal weight: 0.6980 chunk 78 optimal weight: 0.8980 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 0.7980 overall best weight: 0.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 726 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2275 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 7274 Z= 0.156 Angle : 0.534 9.019 9799 Z= 0.264 Chirality : 0.039 0.194 1064 Planarity : 0.003 0.031 1270 Dihedral : 4.104 29.046 965 Min Nonbonded Distance : 1.939 Molprobity Statistics. All-atom Clashscore : 11.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % Rotamer Outliers : 0.26 % 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 (0.29), residues: 876 helix: 1.87 (0.25), residues: 458 sheet: -0.81 (0.70), residues: 70 loop : -0.86 (0.31), residues: 348 *********************** 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 50 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 0.2065 time to fit residues: 14.7208 Evaluate side-chains 48 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 46 time to evaluate : 0.909 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0762 time to fit residues: 1.5346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.5980 chunk 39 optimal weight: 0.9990 chunk 58 optimal weight: 0.9980 chunk 87 optimal weight: 5.9990 chunk 80 optimal weight: 0.7980 chunk 69 optimal weight: 0.9980 chunk 7 optimal weight: 0.0070 chunk 53 optimal weight: 2.9990 chunk 42 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 chunk 74 optimal weight: 0.9980 overall best weight: 0.5798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 711 ASN A 726 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8322 moved from start: 0.2380 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= 0.184 Angle : 0.543 8.555 9799 Z= 0.268 Chirality : 0.039 0.163 1064 Planarity : 0.003 0.031 1270 Dihedral : 4.162 28.352 965 Min Nonbonded Distance : 1.920 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.00 % 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 (0.29), residues: 876 helix: 1.88 (0.26), residues: 458 sheet: -0.80 (0.71), residues: 70 loop : -0.90 (0.31), residues: 348 ********************** 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 47 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.875 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 47 average time/residue: 0.1965 time to fit residues: 13.3410 Evaluate side-chains 46 residues out of total 769 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.875 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 chunk 29 optimal weight: 0.9990 chunk 71 optimal weight: 0.8980 chunk 8 optimal weight: 0.0000 chunk 12 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 3 optimal weight: 0.3980 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 97 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 222 GLN A 492 HIS A 726 ASN B 98 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3670 r_free = 0.3670 target = 0.057642 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3110 r_free = 0.3110 target = 0.038112 restraints weight = 48074.832| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.039277 restraints weight = 24438.485| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.039998 restraints weight = 15805.988| |-----------------------------------------------------------------------------| r_work (final): 0.3140 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8397 moved from start: 0.2491 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= 0.183 Angle : 0.544 8.567 9799 Z= 0.268 Chirality : 0.039 0.154 1064 Planarity : 0.003 0.030 1270 Dihedral : 4.220 29.049 965 Min Nonbonded Distance : 1.911 Molprobity Statistics. All-atom Clashscore : 12.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.45 % Favored : 95.55 % Rotamer Outliers : 0.52 % 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 (0.29), residues: 876 helix: 1.92 (0.26), residues: 452 sheet: -0.88 (0.71), residues: 70 loop : -0.89 (0.31), residues: 354 =============================================================================== Job complete usr+sys time: 1706.52 seconds wall clock time: 32 minutes 18.17 seconds (1938.17 seconds total)