Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 05:12:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/04_2023/7to1_26026_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/04_2023/7to1_26026.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.66 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/04_2023/7to1_26026.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/04_2023/7to1_26026.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/04_2023/7to1_26026_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7to1_26026/04_2023/7to1_26026_updated.pdb" } resolution = 3.66 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= 0.005 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 24 5.49 5 S 31 5.16 5 C 3492 2.51 5 N 947 2.21 5 O 1106 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 279": "OE1" <-> "OE2" Residue "A GLU 315": "OE1" <-> "OE2" Residue "A ARG 316": "NH1" <-> "NH2" Residue "A GLU 335": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A GLU 422": "OE1" <-> "OE2" Residue "A ARG 502": "NH1" <-> "NH2" Residue "A ARG 533": "NH1" <-> "NH2" Residue "A ARG 575": "NH1" <-> "NH2" Residue "A GLU 591": "OE1" <-> "OE2" Residue "A GLU 592": "OE1" <-> "OE2" Residue "A GLU 596": "OE1" <-> "OE2" Residue "A GLU 598": "OE1" <-> "OE2" Residue "A ARG 602": "NH1" <-> "NH2" Residue "A GLU 612": "OE1" <-> "OE2" Residue "A GLU 620": "OE1" <-> "OE2" Residue "A GLU 621": "OE1" <-> "OE2" Residue "A GLU 627": "OE1" <-> "OE2" Residue "A GLU 749": "OE1" <-> "OE2" Residue "A GLU 914": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 5601 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5123 Number of conformers: 1 Conformer: "" Number of residues, atoms: 635, 5123 Classifications: {'peptide': 635} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 27, 'TRANS': 607} Chain breaks: 3 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 18 Unresolved non-hydrogen dihedrals: 14 Planarities with less than four sites: {'ARG:plan': 2} Unresolved non-hydrogen planarities: 10 Chain: "B" Number of atoms: 477 Number of conformers: 1 Conformer: "" Number of residues, atoms: 22, 477 Unusual residues: {'GTP': 1} Classifications: {'RNA': 21, 'undetermined': 1} Modifications used: {'rna3p_pur': 10, 'rna3p_pyr': 11} Link IDs: {'rna3p': 20, None: 1} Not linked: pdbres="GTP B 1 " pdbres=" G B 2 " Chain breaks: 1 Chain: "A" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 4191 SG CYS A 810 43.045 22.013 23.953 1.00 50.21 S ATOM 4630 SG CYS A 864 42.729 20.263 20.098 1.00 64.66 S ATOM 4669 SG CYS A 869 39.685 21.192 21.887 1.00 60.38 S Time building chain proxies: 3.51, per 1000 atoms: 0.63 Number of scatterers: 5601 At special positions: 0 Unit cell: (89.25, 94.5, 66.15, 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) Zn 1 29.99 S 31 16.00 P 24 15.00 O 1106 8.00 N 947 7.00 C 3492 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 2.12 Conformation dependent library (CDL) restraints added in 805.9 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN A1001 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 869 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 864 " pdb="ZN ZN A1001 " - pdb=" SG CYS A 810 " 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1220 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 23 helices and 5 sheets defined 44.4% alpha, 7.4% beta 10 base pairs and 15 stacking pairs defined. Time for finding SS restraints: 1.72 Creating SS restraints... Processing helix chain 'A' and resid 245 through 255 removed outlier: 3.711A pdb=" N LEU A 250 " --> pdb=" O TYR A 246 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N ALA A 251 " --> pdb=" O GLN A 247 " (cutoff:3.500A) Proline residue: A 253 - end of helix Processing helix chain 'A' and resid 267 through 283 Processing helix chain 'A' and resid 300 through 313 Processing helix chain 'A' and resid 334 through 339 Processing helix chain 'A' and resid 348 through 357 Processing helix chain 'A' and resid 374 through 376 No H-bonds generated for 'chain 'A' and resid 374 through 376' Processing helix chain 'A' and resid 382 through 395 Processing helix chain 'A' and resid 420 through 433 Processing helix chain 'A' and resid 449 through 451 No H-bonds generated for 'chain 'A' and resid 449 through 451' Processing helix chain 'A' and resid 470 through 486 Processing helix chain 'A' and resid 493 through 496 No H-bonds generated for 'chain 'A' and resid 493 through 496' Processing helix chain 'A' and resid 507 through 522 removed outlier: 5.010A pdb=" N VAL A 522 " --> pdb=" O LYS A 518 " (cutoff:3.500A) Processing helix chain 'A' and resid 530 through 557 Processing helix chain 'A' and resid 560 through 575 Processing helix chain 'A' and resid 581 through 601 removed outlier: 3.598A pdb=" N GLN A 595 " --> pdb=" O GLU A 591 " (cutoff:3.500A) removed outlier: 4.663A pdb=" N GLU A 596 " --> pdb=" O GLU A 592 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N SER A 599 " --> pdb=" O GLN A 595 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 606 No H-bonds generated for 'chain 'A' and resid 604 through 606' Processing helix chain 'A' and resid 609 through 624 Processing helix chain 'A' and resid 637 through 649 removed outlier: 4.382A pdb=" N ASP A 641 " --> pdb=" O ARG A 637 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N ALA A 642 " --> pdb=" O ALA A 638 " (cutoff:3.500A) removed outlier: 3.550A pdb=" N LYS A 644 " --> pdb=" O VAL A 640 " (cutoff:3.500A) Processing helix chain 'A' and resid 745 through 770 Processing helix chain 'A' and resid 774 through 793 Processing helix chain 'A' and resid 820 through 822 No H-bonds generated for 'chain 'A' and resid 820 through 822' Processing helix chain 'A' and resid 836 through 839 No H-bonds generated for 'chain 'A' and resid 836 through 839' Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing sheet with id= A, first strand: chain 'A' and resid 294 through 296 Processing sheet with id= B, first strand: chain 'A' and resid 694 through 696 removed outlier: 3.586A pdb=" N LEU A 632 " --> pdb=" O LEU A 694 " (cutoff:3.500A) removed outlier: 6.732A pdb=" N LEU A 711 " --> pdb=" O ILE A 631 " (cutoff:3.500A) removed outlier: 7.725A pdb=" N PHE A 633 " --> pdb=" O LEU A 711 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N ILE A 713 " --> pdb=" O PHE A 633 " (cutoff:3.500A) removed outlier: 6.354A pdb=" N LYS A 737 " --> pdb=" O VAL A 712 " (cutoff:3.500A) removed outlier: 7.958A pdb=" N LEU A 714 " --> pdb=" O LYS A 737 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N PHE A 739 " --> pdb=" O LEU A 714 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 893 through 895 removed outlier: 3.857A pdb=" N CYS A 818 " --> pdb=" O LEU A 808 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 823 through 825 Processing sheet with id= E, first strand: chain 'A' and resid 842 through 846 removed outlier: 6.922A pdb=" N HIS A 876 " --> pdb=" O ARG A 859 " (cutoff:3.500A) removed outlier: 5.382A pdb=" N LYS A 861 " --> pdb=" O GLY A 874 " (cutoff:3.500A) removed outlier: 7.134A pdb=" N GLY A 874 " --> pdb=" O LYS A 861 " (cutoff:3.500A) 205 hydrogen bonds defined for protein. 603 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 25 hydrogen bonds 50 hydrogen bond angles 0 basepair planarities 10 basepair parallelities 15 stacking parallelities Total time for adding SS restraints: 1.68 Time building geometry restraints manager: 2.28 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 895 1.32 - 1.44: 1579 1.44 - 1.57: 3195 1.57 - 1.69: 46 1.69 - 1.82: 43 Bond restraints: 5758 Sorted by residual: bond pdb=" C1' GTP B 1 " pdb=" C2' GTP B 1 " ideal model delta sigma weight residual 1.524 1.285 0.239 2.00e-02 2.50e+03 1.43e+02 bond pdb=" C1' GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sigma weight residual 1.410 1.613 -0.203 2.00e-02 2.50e+03 1.03e+02 bond pdb=" C5 GTP B 1 " pdb=" C6 GTP B 1 " ideal model delta sigma weight residual 1.390 1.544 -0.154 2.00e-02 2.50e+03 5.91e+01 bond pdb=" C4 GTP B 1 " pdb=" N3 GTP B 1 " ideal model delta sigma weight residual 1.355 1.490 -0.135 2.00e-02 2.50e+03 4.54e+01 bond pdb=" C2 GTP B 1 " pdb=" N2 GTP B 1 " ideal model delta sigma weight residual 1.330 1.452 -0.122 2.00e-02 2.50e+03 3.73e+01 ... (remaining 5753 not shown) Histogram of bond angle deviations from ideal: 99.72 - 106.64: 260 106.64 - 113.56: 3184 113.56 - 120.47: 2420 120.47 - 127.39: 1935 127.39 - 134.31: 73 Bond angle restraints: 7872 Sorted by residual: angle pdb=" CA GLY A 835 " pdb=" C GLY A 835 " pdb=" O GLY A 835 " ideal model delta sigma weight residual 121.41 118.49 2.92 8.80e-01 1.29e+00 1.10e+01 angle pdb=" C VAL A 453 " pdb=" N TYR A 454 " pdb=" CA TYR A 454 " ideal model delta sigma weight residual 121.54 127.68 -6.14 1.91e+00 2.74e-01 1.03e+01 angle pdb=" CA VAL A 414 " pdb=" C VAL A 414 " pdb=" O VAL A 414 " ideal model delta sigma weight residual 120.34 117.52 2.82 9.10e-01 1.21e+00 9.62e+00 angle pdb=" N ILE A 489 " pdb=" CA ILE A 489 " pdb=" C ILE A 489 " ideal model delta sigma weight residual 113.53 110.85 2.68 9.80e-01 1.04e+00 7.50e+00 angle pdb=" C2' GTP B 1 " pdb=" C3' GTP B 1 " pdb=" C4' GTP B 1 " ideal model delta sigma weight residual 111.00 102.83 8.17 3.00e+00 1.11e-01 7.42e+00 ... (remaining 7867 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 20.24: 3212 20.24 - 40.47: 215 40.47 - 60.70: 22 60.70 - 80.93: 10 80.93 - 101.17: 2 Dihedral angle restraints: 3461 sinusoidal: 1589 harmonic: 1872 Sorted by residual: dihedral pdb=" C8 GTP B 1 " pdb=" C1' GTP B 1 " pdb=" N9 GTP B 1 " pdb=" O4' GTP B 1 " ideal model delta sinusoidal sigma weight residual 104.59 3.43 101.17 1 2.00e+01 2.50e-03 2.86e+01 dihedral pdb=" C4' GTP B 1 " pdb=" C5' GTP B 1 " pdb=" O5' GTP B 1 " pdb=" PA GTP B 1 " ideal model delta sinusoidal sigma weight residual -99.13 -165.63 66.50 1 2.00e+01 2.50e-03 1.44e+01 dihedral pdb=" CA LEU A 449 " pdb=" C LEU A 449 " pdb=" N GLU A 450 " pdb=" CA GLU A 450 " ideal model delta harmonic sigma weight residual -180.00 -161.31 -18.69 0 5.00e+00 4.00e-02 1.40e+01 ... (remaining 3458 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 411 0.041 - 0.081: 265 0.081 - 0.122: 188 0.122 - 0.162: 27 0.162 - 0.203: 2 Chirality restraints: 893 Sorted by residual: chirality pdb=" CA ILE A 360 " pdb=" N ILE A 360 " pdb=" C ILE A 360 " pdb=" CB ILE A 360 " both_signs ideal model delta sigma weight residual False 2.43 2.64 -0.20 2.00e-01 2.50e+01 1.03e+00 chirality pdb=" CA ILE A 261 " pdb=" N ILE A 261 " pdb=" C ILE A 261 " pdb=" CB ILE A 261 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 9.10e-01 chirality pdb=" CA ILE A 386 " pdb=" N ILE A 386 " pdb=" C ILE A 386 " pdb=" CB ILE A 386 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 890 not shown) Planarity restraints: 924 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' U B 62 " 0.028 2.00e-02 2.50e+03 1.31e-02 3.86e+00 pdb=" N1 U B 62 " -0.011 2.00e-02 2.50e+03 pdb=" C2 U B 62 " -0.010 2.00e-02 2.50e+03 pdb=" O2 U B 62 " -0.008 2.00e-02 2.50e+03 pdb=" N3 U B 62 " 0.003 2.00e-02 2.50e+03 pdb=" C4 U B 62 " 0.004 2.00e-02 2.50e+03 pdb=" O4 U B 62 " 0.014 2.00e-02 2.50e+03 pdb=" C5 U B 62 " -0.008 2.00e-02 2.50e+03 pdb=" C6 U B 62 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 697 " -0.006 2.00e-02 2.50e+03 1.20e-02 1.43e+00 pdb=" C THR A 697 " 0.021 2.00e-02 2.50e+03 pdb=" O THR A 697 " -0.008 2.00e-02 2.50e+03 pdb=" N SER A 698 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' G B 60 " 0.017 2.00e-02 2.50e+03 6.79e-03 1.38e+00 pdb=" N9 G B 60 " -0.012 2.00e-02 2.50e+03 pdb=" C8 G B 60 " -0.006 2.00e-02 2.50e+03 pdb=" N7 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" C5 G B 60 " 0.001 2.00e-02 2.50e+03 pdb=" C6 G B 60 " 0.001 2.00e-02 2.50e+03 pdb=" O6 G B 60 " 0.006 2.00e-02 2.50e+03 pdb=" N1 G B 60 " 0.003 2.00e-02 2.50e+03 pdb=" C2 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" N2 G B 60 " -0.003 2.00e-02 2.50e+03 pdb=" N3 G B 60 " -0.001 2.00e-02 2.50e+03 pdb=" C4 G B 60 " -0.004 2.00e-02 2.50e+03 ... (remaining 921 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1638 2.83 - 3.35: 5486 3.35 - 3.87: 9376 3.87 - 4.38: 10293 4.38 - 4.90: 17575 Nonbonded interactions: 44368 Sorted by model distance: nonbonded pdb=" O HIS A 557 " pdb=" OH TYR A 715 " model vdw 2.314 2.440 nonbonded pdb=" OH TYR A 622 " pdb=" OD1 ASN A 692 " model vdw 2.315 2.440 nonbonded pdb=" NH1 ARG A 811 " pdb=" O GLU A 890 " model vdw 2.336 2.520 nonbonded pdb=" O ILE A 337 " pdb=" ND2 ASN A 341 " model vdw 2.339 2.520 nonbonded pdb=" OG SER A 362 " pdb=" OG SER A 364 " model vdw 2.364 2.440 ... (remaining 44363 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: 0.300 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: 0.000 Extract box with map and model: 2.070 Check model and map are aligned: 0.090 Set scattering table: 0.060 Process input model: 19.460 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.010 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: 0.010 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.710 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7863 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 : 0.012 0.239 5758 Z= 0.806 Angle : 1.047 8.173 7872 Z= 0.756 Chirality : 0.063 0.203 893 Planarity : 0.004 0.019 924 Dihedral : 13.191 101.166 2241 Min Nonbonded Distance : 2.314 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.29 % Favored : 91.71 % 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: -2.28 (0.31), residues: 627 helix: 0.24 (0.29), residues: 282 sheet: -3.75 (0.50), residues: 67 loop : -2.85 (0.32), residues: 278 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 132 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 132 average time/residue: 0.2509 time to fit residues: 41.0706 Evaluate side-chains 80 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 80 time to evaluate : 0.700 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 54 optimal weight: 4.9990 chunk 49 optimal weight: 0.8980 chunk 27 optimal weight: 0.0970 chunk 16 optimal weight: 0.5980 chunk 33 optimal weight: 0.9980 chunk 26 optimal weight: 2.9990 chunk 50 optimal weight: 7.9990 chunk 19 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 298 ASN A 380 GLN A 495 ASN A 517 GLN A 595 GLN A 769 GLN A 784 GLN A 876 HIS Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.024 5758 Z= 0.168 Angle : 0.516 8.031 7872 Z= 0.253 Chirality : 0.038 0.232 893 Planarity : 0.003 0.037 924 Dihedral : 6.764 89.246 935 Min Nonbonded Distance : 2.237 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.38 % Favored : 93.62 % Rotamer Outliers : 1.75 % 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: -1.26 (0.34), residues: 627 helix: 1.21 (0.31), residues: 290 sheet: -3.33 (0.52), residues: 75 loop : -2.49 (0.36), residues: 262 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 80 time to evaluate : 0.671 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 86 average time/residue: 0.1854 time to fit residues: 21.2100 Evaluate side-chains 74 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 68 time to evaluate : 0.662 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0625 time to fit residues: 1.5559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 32 optimal weight: 0.2980 chunk 18 optimal weight: 0.9990 chunk 49 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 59 optimal weight: 0.0070 chunk 63 optimal weight: 4.9990 chunk 52 optimal weight: 0.8980 chunk 58 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 47 optimal weight: 2.9990 overall best weight: 0.5198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 381 HIS A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.1746 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.021 5758 Z= 0.143 Angle : 0.498 7.113 7872 Z= 0.244 Chirality : 0.037 0.182 893 Planarity : 0.003 0.044 924 Dihedral : 6.672 89.833 935 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 9.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.81 (0.35), residues: 627 helix: 1.61 (0.32), residues: 290 sheet: -3.03 (0.55), residues: 74 loop : -2.33 (0.36), residues: 263 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 79 time to evaluate : 0.667 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 86 average time/residue: 0.1711 time to fit residues: 19.9677 Evaluate side-chains 75 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.687 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0677 time to fit residues: 1.4286 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 58 optimal weight: 8.9990 chunk 44 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 28 optimal weight: 0.5980 chunk 39 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 62 optimal weight: 0.5980 chunk 31 optimal weight: 0.0020 chunk 56 optimal weight: 1.9990 chunk 16 optimal weight: 2.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- 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: 0.7885 moved from start: 0.1926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 5758 Z= 0.155 Angle : 0.491 7.288 7872 Z= 0.242 Chirality : 0.037 0.149 893 Planarity : 0.003 0.029 924 Dihedral : 6.593 89.507 935 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 8.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 1.93 % 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: -0.53 (0.35), residues: 627 helix: 1.80 (0.31), residues: 291 sheet: -2.61 (0.63), residues: 66 loop : -2.28 (0.35), residues: 270 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.719 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 85 average time/residue: 0.1790 time to fit residues: 20.4494 Evaluate side-chains 77 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 71 time to evaluate : 0.693 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0578 time to fit residues: 1.5718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 52 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 56 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 21 optimal weight: 7.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 619 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7933 moved from start: 0.2086 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 5758 Z= 0.219 Angle : 0.538 7.808 7872 Z= 0.269 Chirality : 0.038 0.157 893 Planarity : 0.003 0.029 924 Dihedral : 6.692 89.552 935 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer Outliers : 1.75 % 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: -0.46 (0.35), residues: 627 helix: 1.94 (0.31), residues: 284 sheet: -2.73 (0.59), residues: 73 loop : -2.15 (0.36), residues: 270 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.677 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 10 outliers final: 5 residues processed: 81 average time/residue: 0.1701 time to fit residues: 18.6589 Evaluate side-chains 75 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 70 time to evaluate : 0.658 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0571 time to fit residues: 1.4161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 56 optimal weight: 0.8980 chunk 12 optimal weight: 0.0670 chunk 36 optimal weight: 0.9990 chunk 15 optimal weight: 0.3980 chunk 62 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 20 optimal weight: 8.9990 chunk 33 optimal weight: 5.9990 chunk 60 optimal weight: 1.9990 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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: 0.7890 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 5758 Z= 0.158 Angle : 0.507 7.337 7872 Z= 0.250 Chirality : 0.037 0.133 893 Planarity : 0.003 0.030 924 Dihedral : 6.547 88.984 935 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 1.23 % 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: -0.30 (0.35), residues: 627 helix: 2.03 (0.31), residues: 285 sheet: -2.43 (0.62), residues: 77 loop : -2.09 (0.36), residues: 265 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 82 time to evaluate : 0.614 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 88 average time/residue: 0.1653 time to fit residues: 19.7239 Evaluate side-chains 77 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 73 time to evaluate : 0.596 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0588 time to fit residues: 1.2932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 7 optimal weight: 6.9990 chunk 35 optimal weight: 0.5980 chunk 45 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 62 optimal weight: 0.1980 chunk 39 optimal weight: 0.7980 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 25 optimal weight: 0.0020 chunk 37 optimal weight: 1.9990 chunk 18 optimal weight: 3.9990 overall best weight: 0.7190 ------------------------------------------------------------------------------- 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: 0.7896 moved from start: 0.2293 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.025 5758 Z= 0.170 Angle : 0.508 7.429 7872 Z= 0.254 Chirality : 0.037 0.138 893 Planarity : 0.004 0.087 924 Dihedral : 6.502 89.134 935 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 9.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 0.70 % 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: -0.20 (0.35), residues: 627 helix: 2.07 (0.31), residues: 285 sheet: -2.33 (0.63), residues: 77 loop : -2.00 (0.37), residues: 265 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 84 time to evaluate : 0.696 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 2 residues processed: 87 average time/residue: 0.1723 time to fit residues: 20.1932 Evaluate side-chains 72 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 70 time to evaluate : 0.671 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0579 time to fit residues: 1.1142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 12 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 5 optimal weight: 0.9980 chunk 49 optimal weight: 0.7980 chunk 56 optimal weight: 0.0270 chunk 60 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 58 optimal weight: 6.9990 chunk 35 optimal weight: 0.7980 overall best weight: 0.7240 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.2347 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5758 Z= 0.171 Angle : 0.522 7.797 7872 Z= 0.259 Chirality : 0.037 0.176 893 Planarity : 0.004 0.076 924 Dihedral : 6.476 88.689 935 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.02 % Favored : 92.98 % Rotamer Outliers : 1.58 % 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: -0.10 (0.35), residues: 627 helix: 2.11 (0.31), residues: 285 sheet: -2.23 (0.65), residues: 71 loop : -1.94 (0.37), residues: 271 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 77 time to evaluate : 0.656 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 85 average time/residue: 0.1674 time to fit residues: 19.4329 Evaluate side-chains 78 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.657 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0600 time to fit residues: 1.5476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 25 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 7.9990 chunk 52 optimal weight: 0.6980 chunk 55 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 38 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 37 optimal weight: 0.9990 chunk 29 optimal weight: 0.8980 chunk 42 optimal weight: 5.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 384 ASN A 876 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5758 Z= 0.192 Angle : 0.539 8.791 7872 Z= 0.266 Chirality : 0.038 0.170 893 Planarity : 0.004 0.069 924 Dihedral : 6.484 88.825 935 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 0.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.35), residues: 627 helix: 2.09 (0.31), residues: 285 sheet: -2.15 (0.70), residues: 63 loop : -1.95 (0.36), residues: 279 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.666 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 75 average time/residue: 0.1736 time to fit residues: 17.6567 Evaluate side-chains 73 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.649 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0580 time to fit residues: 1.1019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 64 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 51 optimal weight: 4.9990 chunk 5 optimal weight: 0.8980 chunk 39 optimal weight: 0.9990 chunk 31 optimal weight: 0.0770 chunk 40 optimal weight: 0.9990 chunk 54 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 47 optimal weight: 0.7980 chunk 7 optimal weight: 5.9990 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7889 moved from start: 0.2454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5758 Z= 0.172 Angle : 0.540 8.675 7872 Z= 0.266 Chirality : 0.038 0.171 893 Planarity : 0.004 0.065 924 Dihedral : 6.445 88.584 935 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.70 % Favored : 93.30 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.09 (0.35), residues: 627 helix: 2.06 (0.31), residues: 285 sheet: -2.10 (0.66), residues: 71 loop : -1.90 (0.37), residues: 271 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1254 Ramachandran restraints generated. 627 Oldfield, 0 Emsley, 627 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.653 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 77 average time/residue: 0.1766 time to fit residues: 18.4062 Evaluate side-chains 70 residues out of total 574 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 69 time to evaluate : 0.652 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0566 time to fit residues: 1.0010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 65 random chunks: chunk 14 optimal weight: 1.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.0170 chunk 53 optimal weight: 0.6980 chunk 6 optimal weight: 0.7980 chunk 9 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 37 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 overall best weight: 0.9020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.138893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3352 r_free = 0.3352 target = 0.113016 restraints weight = 6970.502| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 45)----------------| | r_work = 0.3397 r_free = 0.3397 target = 0.116705 restraints weight = 4298.492| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3426 r_free = 0.3426 target = 0.119271 restraints weight = 3139.785| |-----------------------------------------------------------------------------| r_work (final): 0.3428 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7669 moved from start: 0.2514 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.033 5758 Z= 0.199 Angle : 0.569 8.599 7872 Z= 0.282 Chirality : 0.038 0.167 893 Planarity : 0.003 0.026 924 Dihedral : 6.470 88.592 935 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.34 % Favored : 92.66 % Rotamer Outliers : 0.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.36), residues: 627 helix: 2.08 (0.31), residues: 285 sheet: -1.97 (0.72), residues: 63 loop : -1.93 (0.37), residues: 279 =============================================================================== Job complete usr+sys time: 1371.21 seconds wall clock time: 25 minutes 32.46 seconds (1532.46 seconds total)