Starting phenix.real_space_refine (version: 1.21rc1) on Tue Apr 25 17:32:21 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i54_35191/04_2023/8i54_35191.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i54_35191/04_2023/8i54_35191.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i54_35191/04_2023/8i54_35191.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i54_35191/04_2023/8i54_35191.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i54_35191/04_2023/8i54_35191.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8i54_35191/04_2023/8i54_35191.pdb" } resolution = 3.95 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= 0.001 sd= 0.013 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1091 atoms to isotropic. 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 65 5.49 5 S 25 5.16 5 C 6474 2.51 5 N 1794 2.21 5 O 2203 1.98 5 H 9100 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 4": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 19661 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 18269 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1113, 18269 Classifications: {'peptide': 1113} Link IDs: {'PTRANS': 23, 'TRANS': 1089} Chain breaks: 4 Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 4 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 33, 690 Classifications: {'RNA': 33} Modifications used: {'5*END': 1, 'rna2p_pur': 5, 'rna2p_pyr': 4, 'rna3p_pur': 9, 'rna3p_pyr': 15} Link IDs: {'rna2p': 9, 'rna3p': 23} Chain: "C" Number of atoms: 520 Number of conformers: 1 Conformer: "" Number of residues, atoms: 25, 520 Classifications: {'DNA': 25} Link IDs: {'rna3p': 24} Chain: "D" Number of atoms: 182 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 182 Classifications: {'DNA': 9} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 8} Time building chain proxies: 10.42, per 1000 atoms: 0.53 Number of scatterers: 19661 At special positions: 0 Unit cell: (103.87, 104.975, 141.44, 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 25 16.00 P 65 15.00 O 2203 8.00 N 1794 7.00 C 6474 6.00 H 9100 1.00 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: 16.38 Conformation dependent library (CDL) restraints added in 1.5 seconds 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2136 Finding SS restraints... Secondary structure from input PDB file: 38 helices and 4 sheets defined 33.4% alpha, 3.6% beta 10 base pairs and 25 stacking pairs defined. Time for finding SS restraints: 7.57 Creating SS restraints... Processing helix chain 'A' and resid 52 through 63 removed outlier: 4.257A pdb=" N LYS A 58 " --> pdb=" O ASP A 54 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N GLN A 59 " --> pdb=" O GLU A 55 " (cutoff:3.500A) Processing helix chain 'A' and resid 72 through 76 removed outlier: 3.735A pdb=" N ALA A 76 " --> pdb=" O LEU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 92 through 98 Processing helix chain 'A' and resid 103 through 109 Processing helix chain 'A' and resid 119 through 124 Processing helix chain 'A' and resid 154 through 158 Processing helix chain 'A' and resid 172 through 188 removed outlier: 3.939A pdb=" N PHE A 179 " --> pdb=" O ILE A 175 " (cutoff:3.500A) Proline residue: A 180 - end of helix Processing helix chain 'A' and resid 194 through 199 removed outlier: 3.644A pdb=" N ALA A 199 " --> pdb=" O ALA A 195 " (cutoff:3.500A) Processing helix chain 'A' and resid 215 through 220 Processing helix chain 'A' and resid 225 through 236 removed outlier: 5.406A pdb=" N GLN A 231 " --> pdb=" O THR A 227 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N VAL A 232 " --> pdb=" O TYR A 228 " (cutoff:3.500A) Processing helix chain 'A' and resid 330 through 335 Processing helix chain 'A' and resid 338 through 345 removed outlier: 3.934A pdb=" N LEU A 343 " --> pdb=" O THR A 339 " (cutoff:3.500A) removed outlier: 3.846A pdb=" N ASN A 345 " --> pdb=" O ASP A 341 " (cutoff:3.500A) Processing helix chain 'A' and resid 387 through 391 Processing helix chain 'A' and resid 431 through 436 removed outlier: 4.307A pdb=" N LYS A 434 " --> pdb=" O LYS A 431 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ILE A 436 " --> pdb=" O VAL A 433 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 450 Processing helix chain 'A' and resid 480 through 488 removed outlier: 3.934A pdb=" N MET A 486 " --> pdb=" O SER A 482 " (cutoff:3.500A) Processing helix chain 'A' and resid 497 through 501 removed outlier: 3.956A pdb=" N LYS A 500 " --> pdb=" O SER A 497 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N VAL A 501 " --> pdb=" O THR A 498 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 497 through 501' Processing helix chain 'A' and resid 518 through 523 removed outlier: 4.032A pdb=" N LEU A 523 " --> pdb=" O GLU A 519 " (cutoff:3.500A) Processing helix chain 'A' and resid 542 through 548 removed outlier: 4.011A pdb=" N PHE A 546 " --> pdb=" O ASN A 543 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N ASN A 548 " --> pdb=" O ALA A 545 " (cutoff:3.500A) Processing helix chain 'A' and resid 568 through 576 Proline residue: A 574 - end of helix Processing helix chain 'A' and resid 579 through 586 Processing helix chain 'A' and resid 589 through 599 Processing helix chain 'A' and resid 608 through 625 Processing helix chain 'A' and resid 644 through 656 Processing helix chain 'A' and resid 665 through 674 removed outlier: 3.774A pdb=" N GLU A 674 " --> pdb=" O ASN A 670 " (cutoff:3.500A) Processing helix chain 'A' and resid 697 through 707 removed outlier: 3.517A pdb=" N LEU A 701 " --> pdb=" O ASN A 697 " (cutoff:3.500A) removed outlier: 3.695A pdb=" N TYR A 702 " --> pdb=" O LEU A 698 " (cutoff:3.500A) removed outlier: 4.073A pdb=" N PHE A 707 " --> pdb=" O PHE A 703 " (cutoff:3.500A) Processing helix chain 'A' and resid 796 through 805 removed outlier: 4.540A pdb=" N SER A 801 " --> pdb=" O ASP A 797 " (cutoff:3.500A) removed outlier: 6.186A pdb=" N ALA A 802 " --> pdb=" O ALA A 798 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N ILE A 805 " --> pdb=" O SER A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 857 through 868 Processing helix chain 'A' and resid 878 through 900 removed outlier: 3.737A pdb=" N ASN A 890 " --> pdb=" O SER A 886 " (cutoff:3.500A) Processing helix chain 'A' and resid 922 through 936 removed outlier: 3.998A pdb=" N LYS A 926 " --> pdb=" O GLN A 922 " (cutoff:3.500A) Processing helix chain 'A' and resid 1005 through 1015 removed outlier: 3.602A pdb=" N GLY A1015 " --> pdb=" O ARG A1011 " (cutoff:3.500A) Processing helix chain 'A' and resid 1033 through 1037 removed outlier: 3.720A pdb=" N SER A1036 " --> pdb=" O ASP A1033 " (cutoff:3.500A) Processing helix chain 'A' and resid 1062 through 1066 removed outlier: 4.367A pdb=" N LYS A1065 " --> pdb=" O ASN A1062 " (cutoff:3.500A) Processing helix chain 'A' and resid 1080 through 1088 removed outlier: 3.854A pdb=" N TYR A1087 " --> pdb=" O LEU A1083 " (cutoff:3.500A) Processing helix chain 'A' and resid 1097 through 1102 Processing helix chain 'A' and resid 1106 through 1121 removed outlier: 3.834A pdb=" N LEU A1121 " --> pdb=" O LEU A1117 " (cutoff:3.500A) Processing helix chain 'A' and resid 1159 through 1182 removed outlier: 3.564A pdb=" N TRP A1174 " --> pdb=" O ARG A1170 " (cutoff:3.500A) removed outlier: 3.666A pdb=" N LYS A1182 " --> pdb=" O GLN A1178 " (cutoff:3.500A) Processing helix chain 'A' and resid 1193 through 1203 Processing sheet with id=AA1, first strand: chain 'A' and resid 14 through 16 Processing sheet with id=AA2, first strand: chain 'A' and resid 19 through 20 removed outlier: 4.247A pdb=" N PHE A 777 " --> pdb=" O LEU A 20 " (cutoff:3.500A) removed outlier: 3.814A pdb=" N LYS A 776 " --> pdb=" O ARG A 728 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N ARG A 728 " --> pdb=" O LYS A 776 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 657 through 662 removed outlier: 3.534A pdb=" N LYS A 560 " --> pdb=" O THR A 662 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N LEU A 526 " --> pdb=" O VAL A 561 " (cutoff:3.500A) removed outlier: 8.583A pdb=" N TYR A 563 " --> pdb=" O GLY A 524 " (cutoff:3.500A) removed outlier: 11.152A pdb=" N GLY A 524 " --> pdb=" O TYR A 563 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N LEU A 527 " --> pdb=" O TYR A 534 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N TYR A 533 " --> pdb=" O ILE A 683 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 824 through 827 removed outlier: 3.561A pdb=" N VAL A 811 " --> pdb=" O ILE A 827 " (cutoff:3.500A) 216 hydrogen bonds defined for protein. 591 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 22 hydrogen bonds 36 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 25 stacking parallelities Total time for adding SS restraints: 7.20 Time building geometry restraints manager: 16.91 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.17: 9093 1.17 - 1.52: 7169 1.52 - 1.87: 3725 1.87 - 2.22: 0 2.22 - 2.57: 1 Bond restraints: 19988 Sorted by residual: bond pdb=" C SER A 289 " pdb=" N TYR A 319 " ideal model delta sigma weight residual 1.332 2.566 -1.233 1.40e-02 5.10e+03 7.76e+03 bond pdb=" ND2 ASN A 29 " pdb="HD21 ASN A 29 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" ND2 ASN A 512 " pdb="HD22 ASN A 512 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.55e+01 bond pdb=" ND2 ASN A 512 " pdb="HD21 ASN A 512 " ideal model delta sigma weight residual 0.860 0.979 -0.119 2.00e-02 2.50e+03 3.52e+01 bond pdb=" ND2 ASN A 29 " pdb="HD22 ASN A 29 " ideal model delta sigma weight residual 0.860 0.973 -0.113 2.00e-02 2.50e+03 3.19e+01 ... (remaining 19983 not shown) Histogram of bond angle deviations from ideal: 72.23 - 84.65: 4 84.65 - 97.08: 1 97.08 - 109.50: 13474 109.50 - 121.92: 18669 121.92 - 134.34: 3542 Bond angle restraints: 35690 Sorted by residual: angle pdb=" O SER A 289 " pdb=" C SER A 289 " pdb=" N TYR A 319 " ideal model delta sigma weight residual 122.59 87.05 35.54 1.33e+00 5.65e-01 7.14e+02 angle pdb=" CA SER A 289 " pdb=" C SER A 289 " pdb=" N TYR A 319 " ideal model delta sigma weight residual 116.84 79.31 37.53 1.71e+00 3.42e-01 4.82e+02 angle pdb=" C MET A 258 " pdb=" CA MET A 258 " pdb=" HA MET A 258 " ideal model delta sigma weight residual 110.00 72.23 37.77 3.00e+00 1.11e-01 1.58e+02 angle pdb=" N MET A 258 " pdb=" CA MET A 258 " pdb=" HA MET A 258 " ideal model delta sigma weight residual 110.00 74.22 35.78 3.00e+00 1.11e-01 1.42e+02 angle pdb=" CB MET A 258 " pdb=" CA MET A 258 " pdb=" HA MET A 258 " ideal model delta sigma weight residual 109.00 81.82 27.18 3.00e+00 1.11e-01 8.21e+01 ... (remaining 35685 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.16: 7872 34.16 - 68.32: 281 68.32 - 102.48: 21 102.48 - 136.64: 3 136.64 - 170.80: 5 Dihedral angle restraints: 8182 sinusoidal: 4263 harmonic: 3919 Sorted by residual: dihedral pdb=" O4' C B 2 " pdb=" C1' C B 2 " pdb=" N1 C B 2 " pdb=" C2 C B 2 " ideal model delta sinusoidal sigma weight residual 200.00 40.94 159.06 1 1.50e+01 4.44e-03 8.25e+01 dihedral pdb=" O4' U B -17 " pdb=" C1' U B -17 " pdb=" N1 U B -17 " pdb=" C2 U B -17 " ideal model delta sinusoidal sigma weight residual 232.00 71.34 160.66 1 1.70e+01 3.46e-03 6.46e+01 dihedral pdb=" CA ASP A 323 " pdb=" C ASP A 323 " pdb=" N LEU A 324 " pdb=" CA LEU A 324 " ideal model delta harmonic sigma weight residual -180.00 -150.92 -29.08 0 5.00e+00 4.00e-02 3.38e+01 ... (remaining 8179 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.089: 1572 0.089 - 0.179: 78 0.179 - 0.268: 3 0.268 - 0.358: 2 0.358 - 0.447: 1 Chirality restraints: 1656 Sorted by residual: chirality pdb=" CA MET A 258 " pdb=" N MET A 258 " pdb=" C MET A 258 " pdb=" CB MET A 258 " both_signs ideal model delta sigma weight residual False 2.51 2.06 0.45 2.00e-01 2.50e+01 4.99e+00 chirality pdb=" CA ASN A 29 " pdb=" N ASN A 29 " pdb=" C ASN A 29 " pdb=" CB ASN A 29 " both_signs ideal model delta sigma weight residual False 2.51 2.22 0.29 2.00e-01 2.50e+01 2.12e+00 chirality pdb=" CA LEU A 510 " pdb=" N LEU A 510 " pdb=" C LEU A 510 " pdb=" CB LEU A 510 " both_signs ideal model delta sigma weight residual False 2.51 2.24 0.27 2.00e-01 2.50e+01 1.86e+00 ... (remaining 1653 not shown) Planarity restraints: 2775 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 29 " -0.310 2.00e-02 2.50e+03 4.04e-01 2.45e+03 pdb=" CG ASN A 29 " 0.008 2.00e-02 2.50e+03 pdb=" OD1 ASN A 29 " 0.303 2.00e-02 2.50e+03 pdb=" ND2 ASN A 29 " -0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 29 " 0.631 2.00e-02 2.50e+03 pdb="HD22 ASN A 29 " -0.626 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASN A 512 " -0.245 2.00e-02 2.50e+03 2.51e-01 9.44e+02 pdb=" CG ASN A 512 " 0.023 2.00e-02 2.50e+03 pdb=" OD1 ASN A 512 " 0.229 2.00e-02 2.50e+03 pdb=" ND2 ASN A 512 " 0.004 2.00e-02 2.50e+03 pdb="HD21 ASN A 512 " 0.358 2.00e-02 2.50e+03 pdb="HD22 ASN A 512 " -0.369 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER A 289 " -0.190 2.00e-02 2.50e+03 2.73e-01 7.47e+02 pdb=" C SER A 289 " 0.442 2.00e-02 2.50e+03 pdb=" O SER A 289 " -0.259 2.00e-02 2.50e+03 pdb=" N TYR A 319 " 0.008 2.00e-02 2.50e+03 ... (remaining 2772 not shown) Histogram of nonbonded interaction distances: 1.68 - 2.27: 2766 2.27 - 2.85: 42416 2.85 - 3.43: 47792 3.43 - 4.02: 63235 4.02 - 4.60: 95215 Nonbonded interactions: 251424 Sorted by model distance: nonbonded pdb=" H PHE A 968 " pdb=" OP1 DG C -4 " model vdw 1.684 1.850 nonbonded pdb=" H MET A 258 " pdb=" HA MET A 258 " model vdw 1.706 1.816 nonbonded pdb=" O PHE A1013 " pdb=" H PHE A1016 " model vdw 1.723 1.850 nonbonded pdb=" O ASP A 121 " pdb=" H LEU A 125 " model vdw 1.725 1.850 nonbonded pdb=" OE1 GLU A 627 " pdb=" H GLU A 627 " model vdw 1.729 1.850 ... (remaining 251419 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.130 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.280 Extract box with map and model: 5.200 Check model and map are aligned: 0.310 Set scattering table: 0.190 Process input model: 69.710 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.050 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:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 79.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7024 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 : 0.013 1.233 10888 Z= 1.082 Angle : 1.027 37.532 14957 Z= 0.608 Chirality : 0.046 0.447 1656 Planarity : 0.009 0.273 1691 Dihedral : 17.997 170.798 4300 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.36 % Allowed : 12.81 % Favored : 86.83 % Rotamer Outliers : 0.98 % 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: -3.16 (0.24), residues: 1101 helix: -1.22 (0.27), residues: 345 sheet: -3.34 (0.49), residues: 79 loop : -2.54 (0.23), residues: 677 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2202 Ramachandran restraints generated. 1101 Oldfield, 0 Emsley, 1101 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 85 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 75 time to evaluate : 1.595 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 85 average time/residue: 0.5122 time to fit residues: 61.3565 Evaluate side-chains 68 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 63 time to evaluate : 1.720 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 5 average time/residue: 0.3259 time to fit residues: 4.6800 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.8980 chunk 87 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 30 optimal weight: 8.9990 chunk 59 optimal weight: 3.9990 chunk 46 optimal weight: 5.9990 chunk 90 optimal weight: 3.9990 chunk 35 optimal weight: 9.9990 chunk 55 optimal weight: 0.9990 chunk 67 optimal weight: 10.0000 chunk 105 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 286 ASN ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 820 ASN ** A 836 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7150 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.072 10888 Z= 0.249 Angle : 0.632 10.933 14957 Z= 0.356 Chirality : 0.041 0.460 1656 Planarity : 0.004 0.042 1691 Dihedral : 20.092 175.505 1943 Min Nonbonded Distance : 1.907 Molprobity Statistics. All-atom Clashscore : 22.31 Ramachandran Plot: Outliers : 0.36 % Allowed : 13.24 % Favored : 86.40 % Rotamer Outliers : 1.08 % 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: -3.03 (0.24), residues: 1103 helix: -0.82 (0.28), residues: 349 sheet: -3.47 (0.47), residues: 90 loop : -2.58 (0.23), residues: 664 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 74 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 63 time to evaluate : 1.724 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 68 average time/residue: 0.5472 time to fit residues: 52.1936 Evaluate side-chains 69 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 1.603 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 3 residues processed: 10 average time/residue: 0.3341 time to fit residues: 7.3294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 9.9990 chunk 87 optimal weight: 4.9990 chunk 71 optimal weight: 6.9990 chunk 29 optimal weight: 10.0000 chunk 105 optimal weight: 5.9990 chunk 114 optimal weight: 9.9990 chunk 93 optimal weight: 5.9990 chunk 104 optimal weight: 0.6980 chunk 35 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 GLN A 45 ASN ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 917 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1053 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7286 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 10888 Z= 0.325 Angle : 0.705 10.990 14957 Z= 0.397 Chirality : 0.042 0.466 1656 Planarity : 0.004 0.040 1691 Dihedral : 20.545 170.012 1943 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 31.57 Ramachandran Plot: Outliers : 0.27 % Allowed : 16.59 % Favored : 83.14 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.23), residues: 1103 helix: -1.45 (0.26), residues: 352 sheet: -3.73 (0.48), residues: 90 loop : -2.89 (0.22), residues: 661 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 70 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 63 time to evaluate : 1.661 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 68 average time/residue: 0.5911 time to fit residues: 55.7285 Evaluate side-chains 62 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 1.722 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.3753 time to fit residues: 4.3952 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 chunk 50 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 112 optimal weight: 8.9990 chunk 55 optimal weight: 4.9990 chunk 100 optimal weight: 3.9990 chunk 30 optimal weight: 10.0000 overall best weight: 3.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 582 ASN ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 748 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.2839 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.049 10888 Z= 0.266 Angle : 0.640 10.923 14957 Z= 0.361 Chirality : 0.041 0.455 1656 Planarity : 0.004 0.035 1691 Dihedral : 20.362 179.424 1943 Min Nonbonded Distance : 1.844 Molprobity Statistics. All-atom Clashscore : 30.45 Ramachandran Plot: Outliers : 0.27 % Allowed : 16.86 % Favored : 82.86 % Rotamer Outliers : 1.28 % 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: -3.60 (0.24), residues: 1103 helix: -1.41 (0.27), residues: 350 sheet: -3.62 (0.50), residues: 90 loop : -2.90 (0.23), residues: 663 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 77 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 1.751 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 10 residues processed: 71 average time/residue: 0.5873 time to fit residues: 58.5060 Evaluate side-chains 68 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 58 time to evaluate : 1.689 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 2 residues processed: 10 average time/residue: 0.2926 time to fit residues: 7.0863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 0.9990 chunk 63 optimal weight: 0.7980 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 3.9990 chunk 46 optimal weight: 7.9990 chunk 95 optimal weight: 1.9990 chunk 77 optimal weight: 10.0000 chunk 0 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 100 optimal weight: 1.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 887 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7195 moved from start: 0.2801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10888 Z= 0.173 Angle : 0.566 10.239 14957 Z= 0.315 Chirality : 0.038 0.442 1656 Planarity : 0.003 0.035 1691 Dihedral : 20.079 176.388 1943 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 23.19 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.23 % Favored : 85.58 % Rotamer Outliers : 0.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.24), residues: 1103 helix: -1.07 (0.28), residues: 350 sheet: -3.46 (0.50), residues: 90 loop : -2.74 (0.23), residues: 663 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 65 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 62 time to evaluate : 1.744 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 65 average time/residue: 0.6010 time to fit residues: 53.5812 Evaluate side-chains 61 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.694 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 2 residues processed: 3 average time/residue: 0.4506 time to fit residues: 4.0433 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 9.9990 chunk 100 optimal weight: 5.9990 chunk 22 optimal weight: 9.9990 chunk 65 optimal weight: 3.9990 chunk 27 optimal weight: 20.0000 chunk 112 optimal weight: 10.0000 chunk 93 optimal weight: 8.9990 chunk 51 optimal weight: 0.2980 chunk 9 optimal weight: 0.7980 chunk 58 optimal weight: 0.1980 chunk 108 optimal weight: 3.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7227 moved from start: 0.3051 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 10888 Z= 0.202 Angle : 0.570 10.320 14957 Z= 0.321 Chirality : 0.039 0.444 1656 Planarity : 0.003 0.035 1691 Dihedral : 20.092 169.643 1943 Min Nonbonded Distance : 1.898 Molprobity Statistics. All-atom Clashscore : 25.54 Ramachandran Plot: Outliers : 0.18 % Allowed : 16.23 % Favored : 83.59 % Rotamer Outliers : 0.98 % 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: -3.28 (0.24), residues: 1103 helix: -1.00 (0.28), residues: 339 sheet: -3.52 (0.49), residues: 90 loop : -2.75 (0.23), residues: 674 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 59 time to evaluate : 1.858 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 9 residues processed: 64 average time/residue: 0.5595 time to fit residues: 50.1019 Evaluate side-chains 67 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 58 time to evaluate : 1.471 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2995 time to fit residues: 6.2105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 3.9990 chunk 94 optimal weight: 0.8980 chunk 62 optimal weight: 4.9990 chunk 111 optimal weight: 10.0000 chunk 69 optimal weight: 0.9980 chunk 68 optimal weight: 0.7980 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 3.9990 chunk 66 optimal weight: 0.7980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7143 moved from start: 0.3038 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 10888 Z= 0.146 Angle : 0.529 10.446 14957 Z= 0.294 Chirality : 0.038 0.447 1656 Planarity : 0.003 0.035 1691 Dihedral : 19.882 164.305 1943 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 21.42 Ramachandran Plot: Outliers : 0.18 % Allowed : 13.15 % Favored : 86.67 % Rotamer Outliers : 0.20 % 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: -3.00 (0.25), residues: 1103 helix: -0.77 (0.28), residues: 345 sheet: -3.24 (0.51), residues: 90 loop : -2.61 (0.23), residues: 668 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 64 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 62 time to evaluate : 1.795 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 64 average time/residue: 0.6318 time to fit residues: 55.4192 Evaluate side-chains 61 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.773 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4772 time to fit residues: 3.3129 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 10.0000 chunk 21 optimal weight: 0.0040 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 2.9990 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 3.9990 chunk 101 optimal weight: 4.9990 chunk 107 optimal weight: 5.9990 chunk 97 optimal weight: 0.7980 chunk 104 optimal weight: 2.9990 overall best weight: 1.9598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7215 moved from start: 0.3259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10888 Z= 0.199 Angle : 0.557 9.780 14957 Z= 0.314 Chirality : 0.038 0.451 1656 Planarity : 0.004 0.069 1691 Dihedral : 19.966 169.027 1943 Min Nonbonded Distance : 1.901 Molprobity Statistics. All-atom Clashscore : 25.34 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.78 % Favored : 84.04 % Rotamer Outliers : 0.88 % 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: -3.11 (0.25), residues: 1103 helix: -0.85 (0.28), residues: 345 sheet: -3.34 (0.50), residues: 90 loop : -2.68 (0.23), residues: 668 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 69 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 60 time to evaluate : 1.791 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 9 residues processed: 63 average time/residue: 0.5898 time to fit residues: 52.2077 Evaluate side-chains 66 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 1.653 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 2 residues processed: 9 average time/residue: 0.2973 time to fit residues: 6.4488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 chunk 45 optimal weight: 4.9990 chunk 81 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 0.8980 chunk 98 optimal weight: 4.9990 chunk 103 optimal weight: 8.9990 chunk 68 optimal weight: 1.9990 chunk 110 optimal weight: 3.9990 chunk 67 optimal weight: 9.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7244 moved from start: 0.3501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 10888 Z= 0.212 Angle : 0.573 10.454 14957 Z= 0.322 Chirality : 0.039 0.465 1656 Planarity : 0.003 0.050 1691 Dihedral : 20.114 176.226 1943 Min Nonbonded Distance : 1.883 Molprobity Statistics. All-atom Clashscore : 27.70 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.96 % Favored : 83.86 % Rotamer Outliers : 0.20 % 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: -3.22 (0.25), residues: 1103 helix: -1.02 (0.28), residues: 348 sheet: -3.35 (0.50), residues: 90 loop : -2.71 (0.23), residues: 665 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 61 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 1.673 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 61 average time/residue: 0.5738 time to fit residues: 48.7946 Evaluate side-chains 60 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 58 time to evaluate : 1.596 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 2 average time/residue: 0.4846 time to fit residues: 3.3931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 115 optimal weight: 10.0000 chunk 106 optimal weight: 0.0670 chunk 92 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 71 optimal weight: 5.9990 chunk 56 optimal weight: 4.9990 chunk 73 optimal weight: 0.0980 chunk 98 optimal weight: 0.9990 chunk 28 optimal weight: 20.0000 overall best weight: 1.8324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.3583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.044 10888 Z= 0.185 Angle : 0.557 9.963 14957 Z= 0.311 Chirality : 0.038 0.463 1656 Planarity : 0.003 0.052 1691 Dihedral : 20.059 174.841 1943 Min Nonbonded Distance : 1.912 Molprobity Statistics. All-atom Clashscore : 25.69 Ramachandran Plot: Outliers : 0.18 % Allowed : 15.50 % Favored : 84.32 % Rotamer Outliers : 0.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.19 (0.25), residues: 1103 helix: -0.99 (0.28), residues: 347 sheet: -3.38 (0.50), residues: 90 loop : -2.69 (0.24), residues: 666 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2206 Ramachandran restraints generated. 1103 Oldfield, 0 Emsley, 1103 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue THR 96 is missing expected H atoms. Skipping. Residue SER 624 is missing expected H atoms. Skipping. Evaluate side-chains 63 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 1.680 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 4 residues processed: 61 average time/residue: 0.5889 time to fit residues: 50.2193 Evaluate side-chains 61 residues out of total 1022 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 57 time to evaluate : 1.616 Switching outliers to nearest non-outliers revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 4 average time/residue: 0.3878 time to fit residues: 4.3545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.9990 chunk 13 optimal weight: 9.9990 chunk 25 optimal weight: 0.9980 chunk 92 optimal weight: 3.9990 chunk 38 optimal weight: 7.9990 chunk 94 optimal weight: 5.9990 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 6.9990 chunk 66 optimal weight: 0.5980 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 222 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 336 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 685 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4245 r_free = 0.4245 target = 0.083769 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3885 r_free = 0.3885 target = 0.069392 restraints weight = 198574.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.3945 r_free = 0.3945 target = 0.071918 restraints weight = 101238.202| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.3983 r_free = 0.3983 target = 0.073484 restraints weight = 63499.741| |-----------------------------------------------------------------------------| r_work (final): 0.3935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7282 moved from start: 0.3707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 10888 Z= 0.183 Angle : 0.552 10.071 14957 Z= 0.308 Chirality : 0.038 0.469 1656 Planarity : 0.003 0.048 1691 Dihedral : 20.042 175.218 1943 Min Nonbonded Distance : 1.913 Molprobity Statistics. All-atom Clashscore : 26.57 Ramachandran Plot: Outliers : 0.18 % Allowed : 14.69 % Favored : 85.13 % Rotamer Outliers : 0.59 % 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: -3.14 (0.25), residues: 1103 helix: -1.01 (0.28), residues: 354 sheet: -3.30 (0.51), residues: 90 loop : -2.64 (0.24), residues: 659 =============================================================================== Job complete usr+sys time: 3426.75 seconds wall clock time: 62 minutes 21.41 seconds (3741.41 seconds total)