Starting phenix.real_space_refine (version: 1.21rc1) on Thu Apr 20 14:19:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln9_0928/04_2023/6ln9_0928_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln9_0928/04_2023/6ln9_0928.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln9_0928/04_2023/6ln9_0928.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln9_0928/04_2023/6ln9_0928.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln9_0928/04_2023/6ln9_0928_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6ln9_0928/04_2023/6ln9_0928_updated.pdb" } resolution = 3.4 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= 0.007 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: 7 Type Number sf(0) Gaussians Mg 1 5.21 5 S 54 5.16 5 Be 1 3.05 5 C 4860 2.51 5 N 1273 2.21 5 O 1420 1.98 5 F 3 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A GLU 55": "OE1" <-> "OE2" Residue "A GLU 58": "OE1" <-> "OE2" Residue "A GLU 121": "OE1" <-> "OE2" Residue "A GLU 123": "OE1" <-> "OE2" Residue "A GLU 238": "OE1" <-> "OE2" Residue "A ARG 290": "NH1" <-> "NH2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 435": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 466": "OE1" <-> "OE2" Residue "A ARG 467": "NH1" <-> "NH2" Residue "A ARG 489": "NH1" <-> "NH2" Residue "A GLU 578": "OE1" <-> "OE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A GLU 659": "OE1" <-> "OE2" Residue "A GLU 784": "OE1" <-> "OE2" Residue "A GLU 883": "OE1" <-> "OE2" Residue "A GLU 950": "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: 7612 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7612 Number of conformers: 1 Conformer: "" Number of residues, atoms: 989, 7612 Unusual residues: {' MG': 1, 'BEF': 1} Classifications: {'peptide': 987, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 46, 'TRANS': 940, None: 2} Not linked: pdbres="SER A1031 " pdbres="BEF A2001 " Not linked: pdbres="BEF A2001 " pdbres=" MG A2002 " Chain breaks: 6 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 14 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" BE BEF A2001 " occ=0.00 ... (2 atoms not shown) pdb=" F3 BEF A2001 " occ=0.00 Time building chain proxies: 4.55, per 1000 atoms: 0.60 Number of scatterers: 7612 At special positions: 0 Unit cell: (87.15, 95.865, 144.42, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 54 16.00 Mg 1 11.99 F 3 9.00 O 1420 8.00 N 1273 7.00 C 4860 6.00 Be 1 4.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.03 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: 3.22 Conformation dependent library (CDL) restraints added in 1.2 seconds 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1852 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 34 helices and 5 sheets defined 44.0% alpha, 9.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.22 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 Processing helix chain 'A' and resid 26 through 35 Processing helix chain 'A' and resid 49 through 56 removed outlier: 5.057A pdb=" N VAL A 53 " --> pdb=" O LEU A 50 " (cutoff:3.500A) Processing helix chain 'A' and resid 61 through 75 Processing helix chain 'A' and resid 90 through 115 removed outlier: 4.435A pdb=" N ILE A 94 " --> pdb=" O GLU A 90 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N LEU A 95 " --> pdb=" O PRO A 91 " (cutoff:3.500A) removed outlier: 4.044A pdb=" N ALA A 102 " --> pdb=" O LEU A 98 " (cutoff:3.500A) removed outlier: 3.743A pdb=" N VAL A 104 " --> pdb=" O ALA A 100 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N GLY A 105 " --> pdb=" O ASN A 101 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N GLU A 113 " --> pdb=" O GLU A 109 " (cutoff:3.500A) Processing helix chain 'A' and resid 117 through 119 No H-bonds generated for 'chain 'A' and resid 117 through 119' Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 248 through 276 Processing helix chain 'A' and resid 292 through 305 Processing helix chain 'A' and resid 309 through 329 removed outlier: 4.466A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N LYS A 328 " --> pdb=" O ARG A 324 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N LYS A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 408 through 418 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 470 through 475 Processing helix chain 'A' and resid 538 through 551 Processing helix chain 'A' and resid 581 through 585 removed outlier: 3.634A pdb=" N LYS A 585 " --> pdb=" O ASN A 582 " (cutoff:3.500A) Processing helix chain 'A' and resid 607 through 615 removed outlier: 3.995A pdb=" N LYS A 611 " --> pdb=" O ALA A 607 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 662 through 671 Processing helix chain 'A' and resid 680 through 692 Processing helix chain 'A' and resid 707 through 710 No H-bonds generated for 'chain 'A' and resid 707 through 710' Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 740 through 779 removed outlier: 3.521A pdb=" N ARG A 761 " --> pdb=" O LYS A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 788 through 808 removed outlier: 4.290A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix removed outlier: 3.947A pdb=" N PHE A 808 " --> pdb=" O THR A 804 " (cutoff:3.500A) Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.559A pdb=" N PHE A 834 " --> pdb=" O GLY A 830 " (cutoff:3.500A) removed outlier: 3.632A pdb=" N GLY A 840 " --> pdb=" O TYR A 836 " (cutoff:3.500A) Processing helix chain 'A' and resid 889 through 891 No H-bonds generated for 'chain 'A' and resid 889 through 891' Processing helix chain 'A' and resid 893 through 913 Processing helix chain 'A' and resid 921 through 923 No H-bonds generated for 'chain 'A' and resid 921 through 923' Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 948 removed outlier: 3.639A pdb=" N LEU A 947 " --> pdb=" O HIS A 943 " (cutoff:3.500A) Processing helix chain 'A' and resid 952 through 954 No H-bonds generated for 'chain 'A' and resid 952 through 954' Processing helix chain 'A' and resid 963 through 989 Proline residue: A 975 - end of helix removed outlier: 3.959A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1015 through 1027 removed outlier: 4.276A pdb=" N MET A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) Proline residue: A1024 - end of helix Processing sheet with id= A, first strand: chain 'A' and resid 138 through 141 removed outlier: 4.492A pdb=" N LYS A 128 " --> pdb=" O GLU A 152 " (cutoff:3.500A) removed outlier: 4.213A pdb=" N ILE A 150 " --> pdb=" O TYR A 130 " (cutoff:3.500A) removed outlier: 5.805A pdb=" N VAL A 222 " --> pdb=" O LEU A 165 " (cutoff:3.500A) removed outlier: 5.229A pdb=" N LEU A 165 " --> pdb=" O VAL A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 331 through 333 Processing sheet with id= C, first strand: chain 'A' and resid 394 through 396 removed outlier: 3.669A pdb=" N GLU A 394 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N CYS A 364 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 7.199A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 4.838A pdb=" N MET A 366 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N CYS A 595 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 5.647A pdb=" N ILE A 368 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 9.234A pdb=" N VAL A 593 " --> pdb=" O ILE A 368 " (cutoff:3.500A) removed outlier: 7.042A pdb=" N LEU A 563 " --> pdb=" O VAL A 593 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N CYS A 595 " --> pdb=" O LEU A 561 " (cutoff:3.500A) removed outlier: 6.340A pdb=" N LEU A 561 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLY A 597 " --> pdb=" O ARG A 559 " (cutoff:3.500A) removed outlier: 5.938A pdb=" N ARG A 559 " --> pdb=" O GLY A 597 " (cutoff:3.500A) removed outlier: 4.180A pdb=" N MET A 511 " --> pdb=" O HIS A 566 " (cutoff:3.500A) removed outlier: 6.384A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.428A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 424 through 428 removed outlier: 3.562A pdb=" N ASN A 428 " --> pdb=" O VAL A 433 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N VAL A 433 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 532 through 535 removed outlier: 6.187A pdb=" N LEU A 590 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 5.180A pdb=" N ILE A 527 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 5.969A pdb=" N PHE A 592 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.633A pdb=" N VAL A 529 " --> pdb=" O PHE A 592 " (cutoff:3.500A) 329 hydrogen bonds defined for protein. 957 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.40 Time building geometry restraints manager: 3.47 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2477 1.34 - 1.46: 1256 1.46 - 1.58: 3933 1.58 - 1.69: 0 1.69 - 1.81: 83 Bond restraints: 7749 Sorted by residual: bond pdb=" BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 1.476 1.561 -0.085 2.00e-02 2.50e+03 1.82e+01 bond pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 1.476 1.545 -0.069 2.00e-02 2.50e+03 1.19e+01 bond pdb=" BE BEF A2001 " pdb=" F1 BEF A2001 " ideal model delta sigma weight residual 1.476 1.533 -0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" N ASP A 878 " pdb=" CA ASP A 878 " ideal model delta sigma weight residual 1.458 1.487 -0.029 1.90e-02 2.77e+03 2.39e+00 bond pdb=" N GLY A 46 " pdb=" CA GLY A 46 " ideal model delta sigma weight residual 1.443 1.451 -0.008 8.60e-03 1.35e+04 8.98e-01 ... (remaining 7744 not shown) Histogram of bond angle deviations from ideal: 100.10 - 106.88: 242 106.88 - 113.66: 4420 113.66 - 120.44: 2942 120.44 - 127.22: 2829 127.22 - 133.99: 81 Bond angle restraints: 10514 Sorted by residual: angle pdb=" F2 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 119.96 106.99 12.97 3.00e+00 1.11e-01 1.87e+01 angle pdb=" F1 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F3 BEF A2001 " ideal model delta sigma weight residual 120.12 109.44 10.68 3.00e+00 1.11e-01 1.27e+01 angle pdb=" F1 BEF A2001 " pdb=" BE BEF A2001 " pdb=" F2 BEF A2001 " ideal model delta sigma weight residual 119.91 111.90 8.01 3.00e+00 1.11e-01 7.12e+00 angle pdb=" CA LYS A 400 " pdb=" CB LYS A 400 " pdb=" CG LYS A 400 " ideal model delta sigma weight residual 114.10 118.74 -4.64 2.00e+00 2.50e-01 5.38e+00 angle pdb=" N THR A 798 " pdb=" CA THR A 798 " pdb=" C THR A 798 " ideal model delta sigma weight residual 113.01 110.32 2.69 1.20e+00 6.94e-01 5.01e+00 ... (remaining 10509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.94: 4351 17.94 - 35.87: 298 35.87 - 53.81: 43 53.81 - 71.74: 5 71.74 - 89.68: 4 Dihedral angle restraints: 4701 sinusoidal: 1850 harmonic: 2851 Sorted by residual: dihedral pdb=" CB CYS A 875 " pdb=" SG CYS A 875 " pdb=" SG CYS A 887 " pdb=" CB CYS A 887 " ideal model delta sinusoidal sigma weight residual -86.00 -53.11 -32.89 1 1.00e+01 1.00e-02 1.54e+01 dihedral pdb=" CA LYS A 397 " pdb=" C LYS A 397 " pdb=" N ASP A 398 " pdb=" CA ASP A 398 " ideal model delta harmonic sigma weight residual 180.00 163.05 16.95 0 5.00e+00 4.00e-02 1.15e+01 dihedral pdb=" CB GLU A 950 " pdb=" CG GLU A 950 " pdb=" CD GLU A 950 " pdb=" OE1 GLU A 950 " ideal model delta sinusoidal sigma weight residual 0.00 -89.68 89.68 1 3.00e+01 1.11e-03 1.06e+01 ... (remaining 4698 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 901 0.039 - 0.078: 250 0.078 - 0.116: 81 0.116 - 0.155: 8 0.155 - 0.194: 2 Chirality restraints: 1242 Sorted by residual: chirality pdb=" CA ASP A 878 " pdb=" N ASP A 878 " pdb=" C ASP A 878 " pdb=" CB ASP A 878 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.40e-01 chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.05e-01 chirality pdb=" CB ILE A 715 " pdb=" CA ILE A 715 " pdb=" CG1 ILE A 715 " pdb=" CG2 ILE A 715 " both_signs ideal model delta sigma weight residual False 2.64 2.49 0.15 2.00e-01 2.50e+01 5.82e-01 ... (remaining 1239 not shown) Planarity restraints: 1335 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.011 2.00e-02 2.50e+03 2.25e-02 5.06e+00 pdb=" C LEU A 796 " -0.039 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.015 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 759 " -0.012 2.00e-02 2.50e+03 1.11e-02 2.15e+00 pdb=" CG PHE A 759 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 PHE A 759 " -0.007 2.00e-02 2.50e+03 pdb=" CD2 PHE A 759 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 759 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 PHE A 759 " -0.003 2.00e-02 2.50e+03 pdb=" CZ PHE A 759 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 974 " -0.024 5.00e-02 4.00e+02 3.62e-02 2.10e+00 pdb=" N PRO A 975 " 0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 975 " -0.018 5.00e-02 4.00e+02 pdb=" CD PRO A 975 " -0.020 5.00e-02 4.00e+02 ... (remaining 1332 not shown) Histogram of nonbonded interaction distances: 2.08 - 2.64: 87 2.64 - 3.21: 7202 3.21 - 3.77: 11863 3.77 - 4.34: 15661 4.34 - 4.90: 25997 Nonbonded interactions: 60810 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.075 2.170 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.092 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.097 2.170 nonbonded pdb=" OD2 ASP A 351 " pdb=" F2 BEF A2001 " model vdw 2.128 2.390 nonbonded pdb=" OG SER A 916 " pdb=" O GLN A 919 " model vdw 2.195 2.440 ... (remaining 60805 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.220 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 1.730 Check model and map are aligned: 0.120 Set scattering table: 0.080 Process input model: 24.170 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 29.200 ------------------------------------------------------------------------------- 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 : 0.003 0.085 7749 Z= 0.176 Angle : 0.544 12.974 10514 Z= 0.293 Chirality : 0.040 0.194 1242 Planarity : 0.004 0.036 1335 Dihedral : 12.315 89.677 2846 Min Nonbonded Distance : 2.075 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.11 % Favored : 95.89 % 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: -3.36 (0.23), residues: 973 helix: -1.54 (0.20), residues: 452 sheet: -3.05 (0.37), residues: 109 loop : -2.68 (0.27), residues: 412 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.995 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.2282 time to fit residues: 44.2506 Evaluate side-chains 101 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 101 time to evaluate : 0.849 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3255 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.8980 chunk 74 optimal weight: 3.9990 chunk 41 optimal weight: 0.0980 chunk 25 optimal weight: 0.7980 chunk 50 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 76 optimal weight: 3.9990 chunk 29 optimal weight: 0.3980 chunk 46 optimal weight: 9.9990 chunk 57 optimal weight: 2.9990 chunk 88 optimal weight: 0.5980 overall best weight: 0.5580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 244 GLN A 259 GLN A 396 HIS A 421 ASN ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 913 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7060 moved from start: 0.1192 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.028 7749 Z= 0.160 Angle : 0.533 6.924 10514 Z= 0.265 Chirality : 0.041 0.156 1242 Planarity : 0.004 0.034 1335 Dihedral : 3.628 18.930 1040 Min Nonbonded Distance : 2.038 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 1.31 % 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: -1.94 (0.26), residues: 973 helix: -0.12 (0.24), residues: 452 sheet: -2.56 (0.40), residues: 109 loop : -2.23 (0.29), residues: 412 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 113 time to evaluate : 0.929 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 119 average time/residue: 0.1953 time to fit residues: 32.3201 Evaluate side-chains 104 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 98 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0715 time to fit residues: 2.0927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 49 optimal weight: 10.0000 chunk 27 optimal weight: 0.0870 chunk 74 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 24 optimal weight: 2.9990 chunk 89 optimal weight: 0.4980 chunk 96 optimal weight: 2.9990 chunk 79 optimal weight: 2.9990 chunk 88 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 71 optimal weight: 0.6980 overall best weight: 0.6358 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 5 HIS ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7066 moved from start: 0.1513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 7749 Z= 0.160 Angle : 0.531 7.173 10514 Z= 0.262 Chirality : 0.041 0.162 1242 Planarity : 0.004 0.032 1335 Dihedral : 3.711 17.244 1040 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer Outliers : 0.84 % 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: -1.36 (0.26), residues: 973 helix: 0.35 (0.24), residues: 455 sheet: -2.10 (0.42), residues: 114 loop : -1.98 (0.29), residues: 404 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 107 time to evaluate : 0.910 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 4 residues processed: 111 average time/residue: 0.2088 time to fit residues: 31.7520 Evaluate side-chains 104 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 100 time to evaluate : 0.919 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0753 time to fit residues: 1.9574 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 88 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 46 optimal weight: 5.9990 chunk 9 optimal weight: 0.9990 chunk 42 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 89 optimal weight: 4.9990 chunk 94 optimal weight: 3.9990 chunk 84 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 469 ASN ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7129 moved from start: 0.1886 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 7749 Z= 0.210 Angle : 0.556 8.520 10514 Z= 0.276 Chirality : 0.042 0.169 1242 Planarity : 0.004 0.034 1335 Dihedral : 3.897 16.959 1040 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.93 % Favored : 95.07 % Rotamer Outliers : 1.91 % 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: -1.17 (0.26), residues: 973 helix: 0.49 (0.24), residues: 448 sheet: -1.96 (0.43), residues: 114 loop : -1.81 (0.30), residues: 411 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 118 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 102 time to evaluate : 0.846 Fit side-chains revert: symmetry clash outliers start: 16 outliers final: 10 residues processed: 111 average time/residue: 0.1674 time to fit residues: 26.7609 Evaluate side-chains 103 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 93 time to evaluate : 0.852 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0695 time to fit residues: 2.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 53 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 70 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 80 optimal weight: 0.9980 chunk 65 optimal weight: 4.9990 chunk 0 optimal weight: 9.9990 chunk 48 optimal weight: 6.9990 chunk 85 optimal weight: 0.9990 chunk 23 optimal weight: 3.9990 chunk 31 optimal weight: 0.4980 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 989 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7156 moved from start: 0.2069 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.036 7749 Z= 0.231 Angle : 0.564 7.176 10514 Z= 0.281 Chirality : 0.043 0.222 1242 Planarity : 0.004 0.034 1335 Dihedral : 3.977 16.900 1040 Min Nonbonded Distance : 1.941 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.14 % Favored : 94.86 % Rotamer Outliers : 1.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.02 (0.26), residues: 973 helix: 0.61 (0.24), residues: 445 sheet: -1.92 (0.43), residues: 111 loop : -1.72 (0.30), residues: 417 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 95 time to evaluate : 0.844 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 107 average time/residue: 0.1742 time to fit residues: 26.7285 Evaluate side-chains 96 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.842 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0716 time to fit residues: 2.2443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 85 optimal weight: 5.9990 chunk 18 optimal weight: 0.0980 chunk 55 optimal weight: 20.0000 chunk 23 optimal weight: 1.9990 chunk 94 optimal weight: 0.7980 chunk 78 optimal weight: 0.9990 chunk 43 optimal weight: 0.9980 chunk 7 optimal weight: 0.0000 chunk 31 optimal weight: 3.9990 chunk 49 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 overall best weight: 0.5184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7090 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 7749 Z= 0.155 Angle : 0.520 8.448 10514 Z= 0.256 Chirality : 0.041 0.160 1242 Planarity : 0.004 0.033 1335 Dihedral : 3.829 16.554 1040 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 1.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.68 (0.27), residues: 973 helix: 0.91 (0.25), residues: 444 sheet: -1.53 (0.48), residues: 106 loop : -1.65 (0.30), residues: 423 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 101 time to evaluate : 0.941 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 105 average time/residue: 0.1899 time to fit residues: 28.0772 Evaluate side-chains 99 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 94 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0767 time to fit residues: 2.0438 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 10 optimal weight: 0.0770 chunk 54 optimal weight: 5.9990 chunk 69 optimal weight: 1.9990 chunk 53 optimal weight: 6.9990 chunk 79 optimal weight: 0.0670 chunk 52 optimal weight: 9.9990 chunk 94 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 57 optimal weight: 0.6980 chunk 43 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 overall best weight: 0.5276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7077 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 7749 Z= 0.155 Angle : 0.527 7.531 10514 Z= 0.259 Chirality : 0.041 0.161 1242 Planarity : 0.004 0.032 1335 Dihedral : 3.760 16.785 1040 Min Nonbonded Distance : 1.987 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.01 % Favored : 95.99 % Rotamer Outliers : 0.95 % 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: -0.52 (0.27), residues: 973 helix: 1.01 (0.25), residues: 445 sheet: -1.34 (0.48), residues: 111 loop : -1.56 (0.30), residues: 417 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 98 time to evaluate : 0.911 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 102 average time/residue: 0.2030 time to fit residues: 29.7822 Evaluate side-chains 99 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 95 time to evaluate : 0.928 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0696 time to fit residues: 1.7488 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 37 optimal weight: 5.9990 chunk 56 optimal weight: 0.6980 chunk 28 optimal weight: 0.9990 chunk 18 optimal weight: 4.9990 chunk 60 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 46 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 74 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 90 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7113 moved from start: 0.2337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7749 Z= 0.192 Angle : 0.545 8.441 10514 Z= 0.269 Chirality : 0.042 0.166 1242 Planarity : 0.004 0.032 1335 Dihedral : 3.901 19.827 1040 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 1.31 % 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: -0.50 (0.27), residues: 973 helix: 1.04 (0.25), residues: 443 sheet: -1.33 (0.47), residues: 114 loop : -1.55 (0.30), residues: 416 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 93 time to evaluate : 0.901 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 6 residues processed: 100 average time/residue: 0.1694 time to fit residues: 25.0501 Evaluate side-chains 99 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 93 time to evaluate : 0.922 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0781 time to fit residues: 2.1575 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 3.9990 chunk 88 optimal weight: 0.9980 chunk 90 optimal weight: 4.9990 chunk 52 optimal weight: 5.9990 chunk 38 optimal weight: 0.0980 chunk 69 optimal weight: 2.9990 chunk 27 optimal weight: 0.8980 chunk 79 optimal weight: 0.5980 chunk 83 optimal weight: 0.7980 chunk 87 optimal weight: 0.9990 chunk 57 optimal weight: 0.7980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7081 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.041 7749 Z= 0.164 Angle : 0.535 8.189 10514 Z= 0.263 Chirality : 0.041 0.161 1242 Planarity : 0.004 0.032 1335 Dihedral : 3.777 16.261 1040 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 0.36 % 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: -0.35 (0.27), residues: 973 helix: 1.12 (0.25), residues: 441 sheet: -1.18 (0.49), residues: 109 loop : -1.42 (0.30), residues: 423 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 97 time to evaluate : 0.930 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 100 average time/residue: 0.1611 time to fit residues: 24.1202 Evaluate side-chains 95 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.945 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2525 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 93 optimal weight: 2.9990 chunk 56 optimal weight: 6.9990 chunk 44 optimal weight: 3.9990 chunk 64 optimal weight: 0.3980 chunk 97 optimal weight: 0.8980 chunk 89 optimal weight: 4.9990 chunk 77 optimal weight: 0.5980 chunk 8 optimal weight: 6.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 421 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 767 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7128 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 7749 Z= 0.213 Angle : 0.576 8.755 10514 Z= 0.282 Chirality : 0.043 0.182 1242 Planarity : 0.004 0.032 1335 Dihedral : 3.880 15.785 1040 Min Nonbonded Distance : 1.952 Molprobity Statistics. All-atom Clashscore : 9.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.24 % 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: -0.33 (0.27), residues: 973 helix: 1.14 (0.25), residues: 437 sheet: -1.29 (0.48), residues: 106 loop : -1.37 (0.30), residues: 430 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1946 Ramachandran restraints generated. 973 Oldfield, 0 Emsley, 973 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 94 time to evaluate : 0.928 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 95 average time/residue: 0.1661 time to fit residues: 23.3506 Evaluate side-chains 94 residues out of total 844 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 93 time to evaluate : 0.927 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0737 time to fit residues: 1.4510 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 98 random chunks: chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 21 optimal weight: 0.6980 chunk 77 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 79 optimal weight: 0.0870 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 0.8980 chunk 68 optimal weight: 0.4980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 206 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 795 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 = 0.4252 r_free = 0.4252 target = 0.205595 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3836 r_free = 0.3836 target = 0.161994 restraints weight = 7925.184| |-----------------------------------------------------------------------------| r_work (start): 0.3814 rms_B_bonded: 1.90 r_work: 0.3683 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.3531 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.3531 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7271 moved from start: 0.2519 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.039 7749 Z= 0.162 Angle : 0.553 9.135 10514 Z= 0.268 Chirality : 0.041 0.162 1242 Planarity : 0.004 0.033 1335 Dihedral : 3.776 15.704 1040 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 10.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer Outliers : 0.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.24 (0.27), residues: 973 helix: 1.21 (0.25), residues: 440 sheet: -1.21 (0.48), residues: 106 loop : -1.33 (0.30), residues: 427 =============================================================================== Job complete usr+sys time: 1731.02 seconds wall clock time: 32 minutes 7.17 seconds (1927.17 seconds total)