Starting phenix.real_space_refine (version: dev) on Sat Feb 18 14:09:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz6_15036/02_2023/7zz6_15036_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz6_15036/02_2023/7zz6_15036.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz6_15036/02_2023/7zz6_15036.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz6_15036/02_2023/7zz6_15036.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz6_15036/02_2023/7zz6_15036_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zz6_15036/02_2023/7zz6_15036_updated.pdb" } resolution = 2.15 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.015 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "D GLU 509": "OE1" <-> "OE2" Residue "D GLU 524": "OE1" <-> "OE2" Residue "D ARG 579": "NH1" <-> "NH2" Residue "D ARG 593": "NH1" <-> "NH2" Residue "D PHE 605": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 622": "OE1" <-> "OE2" Residue "D GLU 663": "OE1" <-> "OE2" Residue "D ARG 677": "NH1" <-> "NH2" Residue "D ARG 716": "NH1" <-> "NH2" Residue "D GLU 720": "OE1" <-> "OE2" Residue "D ASP 753": "OD1" <-> "OD2" Residue "D GLU 779": "OE1" <-> "OE2" Residue "D GLU 810": "OE1" <-> "OE2" Residue "D TYR 830": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D ARG 845": "NH1" <-> "NH2" Residue "D GLU 887": "OE1" <-> "OE2" Residue "D GLU 888": "OE1" <-> "OE2" Residue "D GLU 896": "OE1" <-> "OE2" Residue "D GLU 920": "OE1" <-> "OE2" Residue "D GLU 954": "OE1" <-> "OE2" Residue "D GLU 985": "OE1" <-> "OE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A GLU 567": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 593": "NH1" <-> "NH2" Residue "A GLU 622": "OE1" <-> "OE2" Residue "A GLU 663": "OE1" <-> "OE2" Residue "A ARG 677": "NH1" <-> "NH2" Residue "A ARG 716": "NH1" <-> "NH2" Residue "A GLU 720": "OE1" <-> "OE2" Residue "A ASP 753": "OD1" <-> "OD2" Residue "A GLU 779": "OE1" <-> "OE2" Residue "A GLU 810": "OE1" <-> "OE2" Residue "A ARG 845": "NH1" <-> "NH2" Residue "A GLU 848": "OE1" <-> "OE2" Residue "A GLU 888": "OE1" <-> "OE2" Residue "A GLU 920": "OE1" <-> "OE2" Residue "A GLU 954": "OE1" <-> "OE2" Residue "A GLU 965": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 8257 Number of models: 1 Model: "" Number of chains: 6 Chain: "D" Number of atoms: 4047 Number of conformers: 1 Conformer: "" Number of residues, atoms: 509, 4047 Classifications: {'peptide': 509} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 485} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "A" Number of atoms: 4037 Number of conformers: 1 Conformer: "" Number of residues, atoms: 508, 4037 Classifications: {'peptide': 508} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 484} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'KCX:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "D" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 8 Unusual residues: {' MG': 1, ' MN': 1, 'PYR': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "D" Number of atoms: 99 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 99 Classifications: {'water': 99} Link IDs: {None: 98} Chain: "A" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 58, 58 Classifications: {'water': 58} Link IDs: {None: 57} Time building chain proxies: 5.38, per 1000 atoms: 0.65 Number of scatterers: 8257 At special positions: 0 Unit cell: (96.46, 71.02, 110.24, 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) Mn 2 24.99 S 36 16.00 Mg 2 11.99 O 1702 8.00 N 1367 7.00 C 5148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.97 Conformation dependent library (CDL) restraints added in 1.4 seconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1894 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 52 helices and 4 sheets defined 52.9% alpha, 5.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.96 Creating SS restraints... Processing helix chain 'D' and resid 503 through 521 removed outlier: 8.241A pdb=" N ALA D 512 " --> pdb=" O ASP D 508 " (cutoff:3.500A) removed outlier: 9.629A pdb=" N ASP D 513 " --> pdb=" O GLU D 509 " (cutoff:3.500A) removed outlier: 4.341A pdb=" N ALA D 514 " --> pdb=" O GLN D 510 " (cutoff:3.500A) Processing helix chain 'D' and resid 534 through 539 Processing helix chain 'D' and resid 546 through 559 removed outlier: 3.709A pdb=" N GLY D 551 " --> pdb=" O GLN D 547 " (cutoff:3.500A) removed outlier: 4.177A pdb=" N ILE D 552 " --> pdb=" O ASP D 548 " (cutoff:3.500A) removed outlier: 4.689A pdb=" N GLN D 554 " --> pdb=" O LYS D 550 " (cutoff:3.500A) removed outlier: 5.724A pdb=" N ALA D 555 " --> pdb=" O GLY D 551 " (cutoff:3.500A) Processing helix chain 'D' and resid 573 through 581 removed outlier: 3.712A pdb=" N TYR D 578 " --> pdb=" O PHE D 574 " (cutoff:3.500A) Processing helix chain 'D' and resid 585 through 595 Processing helix chain 'D' and resid 618 through 631 Processing helix chain 'D' and resid 645 through 657 removed outlier: 3.802A pdb=" N GLU D 649 " --> pdb=" O PRO D 646 " (cutoff:3.500A) removed outlier: 5.276A pdb=" N LYS D 650 " --> pdb=" O GLN D 647 " (cutoff:3.500A) Processing helix chain 'D' and resid 682 through 694 Processing helix chain 'D' and resid 711 through 724 Processing helix chain 'D' and resid 740 through 750 Processing helix chain 'D' and resid 760 through 762 No H-bonds generated for 'chain 'D' and resid 760 through 762' Processing helix chain 'D' and resid 771 through 777 Processing helix chain 'D' and resid 789 through 809 removed outlier: 3.640A pdb=" N HIS D 797 " --> pdb=" O GLU D 793 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N TYR D 798 " --> pdb=" O GLN D 794 " (cutoff:3.500A) removed outlier: 3.810A pdb=" N LYS D 804 " --> pdb=" O GLU D 800 " (cutoff:3.500A) removed outlier: 4.222A pdb=" N TYR D 805 " --> pdb=" O ASP D 801 " (cutoff:3.500A) removed outlier: 4.110A pdb=" N TYR D 806 " --> pdb=" O VAL D 802 " (cutoff:3.500A) removed outlier: 3.994A pdb=" N ALA D 807 " --> pdb=" O ARG D 803 " (cutoff:3.500A) Proline residue: D 808 - end of helix Processing helix chain 'D' and resid 818 through 821 Processing helix chain 'D' and resid 827 through 840 Processing helix chain 'D' and resid 843 through 860 removed outlier: 3.510A pdb=" N PHE D 846 " --> pdb=" O GLY D 843 " (cutoff:3.500A) removed outlier: 5.055A pdb=" N ASP D 847 " --> pdb=" O HIS D 844 " (cutoff:3.500A) Processing helix chain 'D' and resid 869 through 882 Processing helix chain 'D' and resid 887 through 892 Processing helix chain 'D' and resid 894 through 896 No H-bonds generated for 'chain 'D' and resid 894 through 896' Processing helix chain 'D' and resid 901 through 907 Processing helix chain 'D' and resid 920 through 926 Processing helix chain 'D' and resid 937 through 940 Processing helix chain 'D' and resid 946 through 956 Processing helix chain 'D' and resid 963 through 971 Processing helix chain 'D' and resid 973 through 986 Processing helix chain 'D' and resid 989 through 991 No H-bonds generated for 'chain 'D' and resid 989 through 991' Processing helix chain 'A' and resid 503 through 510 Processing helix chain 'A' and resid 512 through 521 Processing helix chain 'A' and resid 534 through 539 Processing helix chain 'A' and resid 546 through 559 removed outlier: 3.698A pdb=" N GLY A 551 " --> pdb=" O GLN A 547 " (cutoff:3.500A) removed outlier: 4.137A pdb=" N ILE A 552 " --> pdb=" O ASP A 548 " (cutoff:3.500A) removed outlier: 4.749A pdb=" N GLN A 554 " --> pdb=" O LYS A 550 " (cutoff:3.500A) removed outlier: 5.717A pdb=" N ALA A 555 " --> pdb=" O GLY A 551 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 581 removed outlier: 3.889A pdb=" N PHE A 574 " --> pdb=" O GLY A 571 " (cutoff:3.500A) removed outlier: 3.799A pdb=" N ALA A 577 " --> pdb=" O PHE A 574 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N TYR A 578 " --> pdb=" O ASP A 575 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 580 " --> pdb=" O ALA A 577 " (cutoff:3.500A) removed outlier: 4.318A pdb=" N LEU A 581 " --> pdb=" O TYR A 578 " (cutoff:3.500A) Processing helix chain 'A' and resid 585 through 595 Processing helix chain 'A' and resid 618 through 631 Processing helix chain 'A' and resid 645 through 657 removed outlier: 3.754A pdb=" N GLU A 649 " --> pdb=" O PRO A 646 " (cutoff:3.500A) removed outlier: 5.366A pdb=" N LYS A 650 " --> pdb=" O GLN A 647 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 694 Processing helix chain 'A' and resid 711 through 722 Processing helix chain 'A' and resid 740 through 750 Processing helix chain 'A' and resid 760 through 762 No H-bonds generated for 'chain 'A' and resid 760 through 762' Processing helix chain 'A' and resid 771 through 777 Processing helix chain 'A' and resid 789 through 809 removed outlier: 3.626A pdb=" N HIS A 797 " --> pdb=" O GLU A 793 " (cutoff:3.500A) removed outlier: 3.901A pdb=" N TYR A 798 " --> pdb=" O GLN A 794 " (cutoff:3.500A) removed outlier: 3.808A pdb=" N LYS A 804 " --> pdb=" O GLU A 800 " (cutoff:3.500A) removed outlier: 4.285A pdb=" N TYR A 805 " --> pdb=" O ASP A 801 " (cutoff:3.500A) removed outlier: 4.145A pdb=" N TYR A 806 " --> pdb=" O VAL A 802 " (cutoff:3.500A) removed outlier: 3.988A pdb=" N ALA A 807 " --> pdb=" O ARG A 803 " (cutoff:3.500A) Proline residue: A 808 - end of helix Processing helix chain 'A' and resid 818 through 821 Processing helix chain 'A' and resid 827 through 840 Processing helix chain 'A' and resid 843 through 860 removed outlier: 5.395A pdb=" N ASP A 847 " --> pdb=" O HIS A 844 " (cutoff:3.500A) Processing helix chain 'A' and resid 869 through 882 Processing helix chain 'A' and resid 887 through 895 removed outlier: 6.110A pdb=" N ASN A 895 " --> pdb=" O TYR A 891 " (cutoff:3.500A) Processing helix chain 'A' and resid 901 through 907 Processing helix chain 'A' and resid 920 through 927 Processing helix chain 'A' and resid 937 through 940 Processing helix chain 'A' and resid 946 through 956 Processing helix chain 'A' and resid 963 through 971 Processing helix chain 'A' and resid 973 through 986 Processing helix chain 'A' and resid 989 through 991 No H-bonds generated for 'chain 'A' and resid 989 through 991' Processing sheet with id= A, first strand: chain 'D' and resid 526 through 529 Processing sheet with id= B, first strand: chain 'D' and resid 728 through 731 removed outlier: 6.197A pdb=" N ALA D 566 " --> pdb=" O GLN D 602 " (cutoff:3.500A) removed outlier: 7.974A pdb=" N LEU D 604 " --> pdb=" O ALA D 566 " (cutoff:3.500A) removed outlier: 8.769A pdb=" N MET D 568 " --> pdb=" O LEU D 604 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 526 through 529 Processing sheet with id= D, first strand: chain 'A' and resid 728 through 731 removed outlier: 6.184A pdb=" N ALA A 566 " --> pdb=" O GLN A 602 " (cutoff:3.500A) removed outlier: 8.014A pdb=" N LEU A 604 " --> pdb=" O ALA A 566 " (cutoff:3.500A) removed outlier: 8.845A pdb=" N MET A 568 " --> pdb=" O LEU A 604 " (cutoff:3.500A) 337 hydrogen bonds defined for protein. 849 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: 2.34 Time building geometry restraints manager: 4.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2694 1.34 - 1.46: 1840 1.46 - 1.58: 3665 1.58 - 1.70: 0 1.70 - 1.82: 70 Bond restraints: 8269 Sorted by residual: bond pdb=" C1 PYR A1203 " pdb=" C2 PYR A1203 " ideal model delta sigma weight residual 1.558 1.389 0.169 2.00e-02 2.50e+03 7.15e+01 bond pdb=" C1 PYR D1203 " pdb=" C2 PYR D1203 " ideal model delta sigma weight residual 1.558 1.393 0.165 2.00e-02 2.50e+03 6.84e+01 bond pdb=" C2 PYR A1203 " pdb=" O3 PYR A1203 " ideal model delta sigma weight residual 1.210 1.309 -0.099 2.00e-02 2.50e+03 2.47e+01 bond pdb=" C2 PYR D1203 " pdb=" O3 PYR D1203 " ideal model delta sigma weight residual 1.210 1.308 -0.098 2.00e-02 2.50e+03 2.41e+01 bond pdb=" NZ KCX A 703 " pdb=" CX KCX A 703 " ideal model delta sigma weight residual 1.411 1.324 0.087 2.00e-02 2.50e+03 1.91e+01 ... (remaining 8264 not shown) Histogram of bond angle deviations from ideal: 99.64 - 106.53: 226 106.53 - 113.41: 4481 113.41 - 120.30: 3124 120.30 - 127.19: 3275 127.19 - 134.07: 87 Bond angle restraints: 11193 Sorted by residual: angle pdb=" CB MET D 858 " pdb=" CG MET D 858 " pdb=" SD MET D 858 " ideal model delta sigma weight residual 112.70 125.27 -12.57 3.00e+00 1.11e-01 1.75e+01 angle pdb=" CB MET D 982 " pdb=" CG MET D 982 " pdb=" SD MET D 982 " ideal model delta sigma weight residual 112.70 122.56 -9.86 3.00e+00 1.11e-01 1.08e+01 angle pdb=" O1 PYR D1203 " pdb=" C1 PYR D1203 " pdb=" O2 PYR D1203 " ideal model delta sigma weight residual 129.19 119.71 9.48 3.00e+00 1.11e-01 9.98e+00 angle pdb=" O1 PYR A1203 " pdb=" C1 PYR A1203 " pdb=" O2 PYR A1203 " ideal model delta sigma weight residual 129.19 120.00 9.19 3.00e+00 1.11e-01 9.39e+00 angle pdb=" CB MET A 568 " pdb=" CG MET A 568 " pdb=" SD MET A 568 " ideal model delta sigma weight residual 112.70 121.75 -9.05 3.00e+00 1.11e-01 9.11e+00 ... (remaining 11188 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4355 17.86 - 35.72: 443 35.72 - 53.58: 132 53.58 - 71.44: 32 71.44 - 89.30: 21 Dihedral angle restraints: 4983 sinusoidal: 2026 harmonic: 2957 Sorted by residual: dihedral pdb=" CA ASP A 929 " pdb=" C ASP A 929 " pdb=" N LYS A 930 " pdb=" CA LYS A 930 " ideal model delta harmonic sigma weight residual 180.00 -156.71 -23.29 0 5.00e+00 4.00e-02 2.17e+01 dihedral pdb=" CA LEU D 778 " pdb=" C LEU D 778 " pdb=" N GLU D 779 " pdb=" CA GLU D 779 " ideal model delta harmonic sigma weight residual -180.00 -161.43 -18.57 0 5.00e+00 4.00e-02 1.38e+01 dihedral pdb=" CA LEU A 778 " pdb=" C LEU A 778 " pdb=" N GLU A 779 " pdb=" CA GLU A 779 " ideal model delta harmonic sigma weight residual -180.00 -162.03 -17.97 0 5.00e+00 4.00e-02 1.29e+01 ... (remaining 4980 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 596 0.029 - 0.057: 385 0.057 - 0.086: 162 0.086 - 0.114: 66 0.114 - 0.143: 12 Chirality restraints: 1221 Sorted by residual: chirality pdb=" CA VAL A 866 " pdb=" N VAL A 866 " pdb=" C VAL A 866 " pdb=" CB VAL A 866 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA VAL D 866 " pdb=" N VAL D 866 " pdb=" C VAL D 866 " pdb=" CB VAL D 866 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 chirality pdb=" CA ILE D 666 " pdb=" N ILE D 666 " pdb=" C ILE D 666 " pdb=" CB ILE D 666 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.20e-01 ... (remaining 1218 not shown) Planarity restraints: 1466 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ARG D 533 " 0.007 2.00e-02 2.50e+03 1.44e-02 2.09e+00 pdb=" C ARG D 533 " -0.025 2.00e-02 2.50e+03 pdb=" O ARG D 533 " 0.009 2.00e-02 2.50e+03 pdb=" N ASP D 534 " 0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ARG A 533 " -0.007 2.00e-02 2.50e+03 1.42e-02 2.01e+00 pdb=" C ARG A 533 " 0.025 2.00e-02 2.50e+03 pdb=" O ARG A 533 " -0.009 2.00e-02 2.50e+03 pdb=" N ASP A 534 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR D 867 " -0.021 5.00e-02 4.00e+02 3.15e-02 1.59e+00 pdb=" N PRO D 868 " 0.055 5.00e-02 4.00e+02 pdb=" CA PRO D 868 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO D 868 " -0.016 5.00e-02 4.00e+02 ... (remaining 1463 not shown) Histogram of nonbonded interaction distances: 1.38 - 2.09: 3 2.09 - 2.79: 2254 2.79 - 3.49: 12553 3.49 - 4.20: 22783 4.20 - 4.90: 37877 Nonbonded interactions: 75470 Sorted by model distance: nonbonded pdb=" OD1 ASP A 753 " pdb="MG MG A1201 " model vdw 1.385 2.170 nonbonded pdb=" NE2 HIS A 732 " pdb="MN MN A1202 " model vdw 1.835 2.400 nonbonded pdb=" NE2 HIS D 732 " pdb="MN MN D1202 " model vdw 1.838 2.400 nonbonded pdb=" OD1 ASP A 753 " pdb=" O HOH A1301 " model vdw 2.143 2.440 nonbonded pdb="MN MN D1202 " pdb=" O HOH D1335 " model vdw 2.193 2.320 ... (remaining 75465 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'D' and (resid 487 through 994 or resid 1201 through 1203)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Mn 2 7.51 5 Mg 2 5.21 5 S 36 5.16 5 C 5148 2.51 5 N 1367 2.21 5 O 1702 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.480 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: 6.030 Check model and map are aligned: 0.140 Process input model: 26.210 Find NCS groups from input model: 0.500 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.080 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:14.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 48.950 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9010 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 : 0.006 0.169 8269 Z= 0.417 Angle : 0.682 12.566 11193 Z= 0.359 Chirality : 0.045 0.143 1221 Planarity : 0.003 0.032 1466 Dihedral : 17.300 89.298 3089 Min Nonbonded Distance : 1.385 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.64 (0.26), residues: 1007 helix: 1.07 (0.22), residues: 530 sheet: -0.96 (0.47), residues: 86 loop : 0.02 (0.33), residues: 391 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 48 time to evaluate : 1.118 Fit side-chains outliers start: 30 outliers final: 26 residues processed: 75 average time/residue: 1.0325 time to fit residues: 84.3124 Evaluate side-chains 73 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 47 time to evaluate : 0.952 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 25 residues processed: 2 average time/residue: 1.1144 time to fit residues: 3.7382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 84 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 42 optimal weight: 0.7980 chunk 25 optimal weight: 2.9990 chunk 51 optimal weight: 1.9990 chunk 40 optimal weight: 4.9990 chunk 78 optimal weight: 0.9980 chunk 30 optimal weight: 0.8980 chunk 47 optimal weight: 0.5980 chunk 58 optimal weight: 0.6980 chunk 90 optimal weight: 0.8980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 829 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8981 moved from start: 0.0646 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8269 Z= 0.186 Angle : 0.497 6.612 11193 Z= 0.264 Chirality : 0.040 0.147 1221 Planarity : 0.004 0.033 1466 Dihedral : 4.960 39.420 1119 Min Nonbonded Distance : 1.947 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 4.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.76 (0.27), residues: 1007 helix: 1.12 (0.22), residues: 534 sheet: -0.89 (0.50), residues: 86 loop : 0.14 (0.34), residues: 387 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 51 time to evaluate : 1.142 Fit side-chains outliers start: 40 outliers final: 25 residues processed: 86 average time/residue: 1.1482 time to fit residues: 107.1408 Evaluate side-chains 73 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 48 time to evaluate : 1.063 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 1.2219 time to fit residues: 4.0097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 50 optimal weight: 0.2980 chunk 28 optimal weight: 3.9990 chunk 75 optimal weight: 1.9990 chunk 61 optimal weight: 3.9990 chunk 25 optimal weight: 0.6980 chunk 90 optimal weight: 3.9990 chunk 98 optimal weight: 1.9990 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 89 optimal weight: 3.9990 overall best weight: 1.5986 ------------------------------------------------------------------------------- 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: 0.9008 moved from start: 0.0561 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 8269 Z= 0.306 Angle : 0.549 6.735 11193 Z= 0.292 Chirality : 0.043 0.142 1221 Planarity : 0.004 0.032 1466 Dihedral : 5.295 44.803 1119 Min Nonbonded Distance : 1.971 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer Outliers : 4.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.48 (0.26), residues: 1007 helix: 0.87 (0.22), residues: 539 sheet: -0.92 (0.50), residues: 86 loop : 0.02 (0.33), residues: 382 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 46 time to evaluate : 1.048 Fit side-chains outliers start: 41 outliers final: 26 residues processed: 80 average time/residue: 0.9944 time to fit residues: 87.3186 Evaluate side-chains 72 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 46 time to evaluate : 1.062 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 1.3992 time to fit residues: 4.5418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 68 optimal weight: 0.9990 chunk 47 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 43 optimal weight: 2.9990 chunk 61 optimal weight: 0.5980 chunk 91 optimal weight: 5.9990 chunk 96 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 overall best weight: 1.2986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 882 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8998 moved from start: 0.0679 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 8269 Z= 0.259 Angle : 0.522 7.010 11193 Z= 0.277 Chirality : 0.042 0.177 1221 Planarity : 0.004 0.031 1466 Dihedral : 5.165 42.863 1119 Min Nonbonded Distance : 2.009 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 4.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.59 (0.27), residues: 1007 helix: 0.93 (0.22), residues: 534 sheet: -0.89 (0.51), residues: 86 loop : 0.14 (0.33), residues: 387 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 47 time to evaluate : 1.070 Fit side-chains outliers start: 42 outliers final: 27 residues processed: 82 average time/residue: 1.0430 time to fit residues: 93.0954 Evaluate side-chains 73 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 46 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 1.2280 time to fit residues: 5.2323 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 1 optimal weight: 2.9990 chunk 71 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 82 optimal weight: 1.9990 chunk 66 optimal weight: 0.5980 chunk 0 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 32 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 overall best weight: 1.2384 ------------------------------------------------------------------------------- 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: 0.8997 moved from start: 0.0704 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8269 Z= 0.250 Angle : 0.520 7.579 11193 Z= 0.275 Chirality : 0.042 0.143 1221 Planarity : 0.004 0.032 1466 Dihedral : 5.151 43.085 1119 Min Nonbonded Distance : 2.007 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 3.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.61 (0.27), residues: 1007 helix: 0.94 (0.22), residues: 535 sheet: -0.88 (0.51), residues: 86 loop : 0.15 (0.33), residues: 386 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 48 time to evaluate : 1.056 Fit side-chains outliers start: 33 outliers final: 27 residues processed: 76 average time/residue: 0.9641 time to fit residues: 80.2854 Evaluate side-chains 72 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 45 time to evaluate : 1.023 Switching outliers to nearest non-outliers outliers start: 27 outliers final: 24 residues processed: 3 average time/residue: 1.1178 time to fit residues: 4.9528 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 19 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 96 optimal weight: 3.9990 chunk 80 optimal weight: 0.9980 chunk 44 optimal weight: 0.8980 chunk 8 optimal weight: 7.9990 chunk 32 optimal weight: 2.9990 chunk 50 optimal weight: 0.7980 chunk 93 optimal weight: 3.9990 chunk 10 optimal weight: 1.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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: 0.8998 moved from start: 0.0710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.037 8269 Z= 0.267 Angle : 0.535 8.077 11193 Z= 0.281 Chirality : 0.042 0.142 1221 Planarity : 0.004 0.032 1466 Dihedral : 5.188 44.130 1119 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 4.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.59 (0.27), residues: 1007 helix: 0.91 (0.22), residues: 536 sheet: -0.89 (0.51), residues: 86 loop : 0.16 (0.33), residues: 385 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 45 time to evaluate : 1.146 Fit side-chains outliers start: 37 outliers final: 26 residues processed: 77 average time/residue: 1.1549 time to fit residues: 97.5314 Evaluate side-chains 71 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 1.086 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 1.1084 time to fit residues: 3.7798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 55 optimal weight: 5.9990 chunk 70 optimal weight: 0.1980 chunk 54 optimal weight: 5.9990 chunk 81 optimal weight: 0.9990 chunk 96 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 58 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 59 optimal weight: 0.7980 chunk 38 optimal weight: 0.5980 chunk 57 optimal weight: 2.9990 overall best weight: 0.6582 ------------------------------------------------------------------------------- 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: 0.8970 moved from start: 0.0990 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8269 Z= 0.167 Angle : 0.486 8.545 11193 Z= 0.252 Chirality : 0.040 0.144 1221 Planarity : 0.003 0.031 1466 Dihedral : 4.806 39.015 1119 Min Nonbonded Distance : 2.086 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 3.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.76 (0.27), residues: 1007 helix: 1.10 (0.23), residues: 535 sheet: -0.84 (0.52), residues: 86 loop : 0.17 (0.33), residues: 386 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 50 time to evaluate : 1.041 Fit side-chains outliers start: 34 outliers final: 26 residues processed: 77 average time/residue: 0.9815 time to fit residues: 83.3703 Evaluate side-chains 72 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 46 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 1.1959 time to fit residues: 4.1285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 29 optimal weight: 0.5980 chunk 18 optimal weight: 4.9990 chunk 61 optimal weight: 3.9990 chunk 65 optimal weight: 1.9990 chunk 47 optimal weight: 0.8980 chunk 8 optimal weight: 8.9990 chunk 75 optimal weight: 0.8980 chunk 87 optimal weight: 0.7980 chunk 92 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 chunk 89 optimal weight: 0.7980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.8972 moved from start: 0.1004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.026 8269 Z= 0.183 Angle : 0.511 9.530 11193 Z= 0.261 Chirality : 0.040 0.143 1221 Planarity : 0.003 0.031 1466 Dihedral : 4.822 39.872 1119 Min Nonbonded Distance : 2.062 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 3.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.77 (0.27), residues: 1007 helix: 1.10 (0.23), residues: 536 sheet: -0.83 (0.52), residues: 86 loop : 0.17 (0.33), residues: 385 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 46 time to evaluate : 1.075 Fit side-chains outliers start: 30 outliers final: 26 residues processed: 70 average time/residue: 0.9890 time to fit residues: 76.1764 Evaluate side-chains 71 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 45 time to evaluate : 1.065 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 24 residues processed: 2 average time/residue: 1.1761 time to fit residues: 3.9130 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 7.9990 chunk 39 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 27 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 84 optimal weight: 2.9990 chunk 89 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 94 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 683 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9020 moved from start: 0.0740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.049 8269 Z= 0.435 Angle : 0.655 12.075 11193 Z= 0.337 Chirality : 0.047 0.139 1221 Planarity : 0.004 0.039 1466 Dihedral : 5.581 49.663 1119 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer Outliers : 3.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.42 (0.26), residues: 1007 helix: 0.78 (0.22), residues: 542 sheet: -0.90 (0.49), residues: 86 loop : 0.02 (0.33), residues: 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 47 time to evaluate : 1.148 Fit side-chains outliers start: 28 outliers final: 25 residues processed: 73 average time/residue: 0.9374 time to fit residues: 75.6026 Evaluate side-chains 70 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 45 time to evaluate : 1.194 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 23 residues processed: 2 average time/residue: 1.2873 time to fit residues: 4.0867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 45 optimal weight: 0.5980 chunk 66 optimal weight: 0.8980 chunk 99 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 8 optimal weight: 5.9990 chunk 61 optimal weight: 0.8980 chunk 48 optimal weight: 0.6980 chunk 63 optimal weight: 0.4980 chunk 84 optimal weight: 0.5980 chunk 24 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.8971 moved from start: 0.1030 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 8269 Z= 0.176 Angle : 0.537 12.636 11193 Z= 0.269 Chirality : 0.040 0.146 1221 Planarity : 0.004 0.032 1466 Dihedral : 4.852 40.405 1119 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 7.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer Outliers : 2.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.76 (0.27), residues: 1007 helix: 1.07 (0.23), residues: 535 sheet: -0.80 (0.52), residues: 86 loop : 0.20 (0.33), residues: 386 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 48 time to evaluate : 0.953 Fit side-chains outliers start: 24 outliers final: 23 residues processed: 71 average time/residue: 0.9848 time to fit residues: 76.6249 Evaluate side-chains 68 residues out of total 861 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 45 time to evaluate : 1.042 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 23 residues processed: 0 time to fit residues: 1.3842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 100 random chunks: chunk 73 optimal weight: 3.9990 chunk 11 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 chunk 81 optimal weight: 0.7980 chunk 10 optimal weight: 0.7980 chunk 14 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 4 optimal weight: 1.9990 chunk 57 optimal weight: 3.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 882 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.061072 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.051911 restraints weight = 20330.328| |-----------------------------------------------------------------------------| r_work (start): 0.3011 rms_B_bonded: 1.30 r_work: 0.2912 rms_B_bonded: 1.73 restraints_weight: 0.5000 r_work: 0.2813 rms_B_bonded: 2.89 restraints_weight: 0.2500 r_work (final): 0.2813 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9159 moved from start: 0.0856 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 8269 Z= 0.267 Angle : 0.594 12.899 11193 Z= 0.297 Chirality : 0.043 0.159 1221 Planarity : 0.004 0.032 1466 Dihedral : 5.165 44.581 1119 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.98 % Favored : 97.02 % Rotamer Outliers : 3.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.69 (0.27), residues: 1007 helix: 1.01 (0.23), residues: 536 sheet: -0.88 (0.51), residues: 86 loop : 0.20 (0.33), residues: 385 =============================================================================== Job complete usr+sys time: 2499.02 seconds wall clock time: 46 minutes 9.72 seconds (2769.72 seconds total)