Starting phenix.real_space_refine (version: dev) on Fri Feb 17 18:44:22 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/02_2023/7n00_24095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/02_2023/7n00_24095.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/02_2023/7n00_24095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/02_2023/7n00_24095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/02_2023/7n00_24095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/02_2023/7n00_24095.pdb" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A PHE 677": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 769": "OD1" <-> "OD2" Residue "A ASP 781": "OD1" <-> "OD2" Residue "A GLU 803": "OE1" <-> "OE2" Residue "A ASP 854": "OD1" <-> "OD2" Residue "A GLU 862": "OE1" <-> "OE2" Residue "A ASP 947": "OD1" <-> "OD2" Residue "A GLU 953": "OE1" <-> "OE2" Residue "A ASP 954": "OD1" <-> "OD2" Residue "A GLU 994": "OE1" <-> "OE2" Residue "A PHE 1007": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 739": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 803": "OE1" <-> "OE2" Residue "C ASP 854": "OD1" <-> "OD2" Residue "C GLU 862": "OE1" <-> "OE2" Residue "C ASP 885": "OD1" <-> "OD2" Residue "C ASP 951": "OD1" <-> "OD2" Residue "C GLU 953": "OE1" <-> "OE2" Residue "B PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 97": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D PHE 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 5817 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 2446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2446 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 331} Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 73 Unresolved non-hydrogen dihedrals: 43 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 37 Chain: "C" Number of atoms: 2450 Number of conformers: 1 Conformer: "" Number of residues, atoms: 346, 2450 Classifications: {'peptide': 346} Incomplete info: {'truncation_to_alanine': 15} Link IDs: {'PCIS': 1, 'PTRANS': 13, 'TRANS': 331} Unresolved non-hydrogen bonds: 52 Unresolved non-hydrogen angles: 68 Unresolved non-hydrogen dihedrals: 40 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLU:plan': 3, 'HIS:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 34 Chain: "B" Number of atoms: 462 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 462 Classifications: {'peptide': 57} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 459 Number of conformers: 1 Conformer: "" Number of residues, atoms: 57, 459 Classifications: {'peptide': 57} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PTRANS': 4, 'TRANS': 52} Unresolved non-hydrogen bonds: 15 Unresolved non-hydrogen angles: 17 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 3.85, per 1000 atoms: 0.66 Number of scatterers: 5817 At special positions: 0 Unit cell: (96.642, 93.338, 66.08, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 52 16.00 O 1113 8.00 N 1039 7.00 C 3613 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=16, symmetry=0 Simple disulfide: pdb=" SG CYS A 688 " - pdb=" SG CYS A 701 " distance=2.03 Simple disulfide: pdb=" SG CYS A 783 " - pdb=" SG CYS A 794 " distance=2.03 Simple disulfide: pdb=" SG CYS A 906 " - pdb=" SG CYS A 928 " distance=2.03 Simple disulfide: pdb=" SG CYS A 987 " - pdb=" SG CYS A 995 " distance=2.03 Simple disulfide: pdb=" SG CYS A 990 " - pdb=" SG CYS A1006 " distance=2.03 Simple disulfide: pdb=" SG CYS A1008 " - pdb=" SG CYS A1021 " distance=2.03 Simple disulfide: pdb=" SG CYS C 688 " - pdb=" SG CYS C 701 " distance=2.03 Simple disulfide: pdb=" SG CYS C 783 " - pdb=" SG CYS C 794 " distance=2.03 Simple disulfide: pdb=" SG CYS C 906 " - pdb=" SG CYS C 928 " distance=2.03 Simple disulfide: pdb=" SG CYS C 987 " - pdb=" SG CYS C 995 " distance=2.02 Simple disulfide: pdb=" SG CYS C 990 " - pdb=" SG CYS C1006 " distance=2.03 Simple disulfide: pdb=" SG CYS C1008 " - pdb=" SG CYS C1021 " distance=2.03 Simple disulfide: pdb=" SG CYS B 111 " - pdb=" SG CYS B 147 " distance=2.03 Simple disulfide: pdb=" SG CYS B 125 " - pdb=" SG CYS B 134 " distance=2.03 Simple disulfide: pdb=" SG CYS D 111 " - pdb=" SG CYS D 147 " distance=2.03 Simple disulfide: pdb=" SG CYS D 125 " - pdb=" SG CYS D 134 " 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=0, symmetry=0 Time building additional restraints: 1.99 Conformation dependent library (CDL) restraints added in 802.0 milliseconds 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1338 Finding SS restraints... Secondary structure from input PDB file: 20 helices and 8 sheets defined 22.7% alpha, 15.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 697 through 705 Processing helix chain 'A' and resid 787 through 795 Processing helix chain 'A' and resid 799 through 809 Processing helix chain 'A' and resid 895 through 899 Processing helix chain 'A' and resid 906 through 913 Processing helix chain 'C' and resid 697 through 705 Processing helix chain 'C' and resid 717 through 721 removed outlier: 4.241A pdb=" N LEU C 720 " --> pdb=" O GLU C 717 " (cutoff:3.500A) Processing helix chain 'C' and resid 787 through 795 Processing helix chain 'C' and resid 799 through 809 Processing helix chain 'C' and resid 895 through 899 Processing helix chain 'C' and resid 906 through 914 removed outlier: 3.533A pdb=" N MET C 910 " --> pdb=" O CYS C 906 " (cutoff:3.500A) Processing helix chain 'B' and resid 95 through 103 removed outlier: 3.826A pdb=" N LEU B 101 " --> pdb=" O PHE B 97 " (cutoff:3.500A) Processing helix chain 'B' and resid 108 through 121 removed outlier: 3.912A pdb=" N LYS B 113 " --> pdb=" O PRO B 109 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N HIS B 114 " --> pdb=" O LYS B 110 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 127 Processing helix chain 'B' and resid 130 through 144 Processing helix chain 'B' and resid 145 through 149 removed outlier: 3.899A pdb=" N GLU B 149 " --> pdb=" O VAL B 146 " (cutoff:3.500A) Processing helix chain 'D' and resid 95 through 103 removed outlier: 3.859A pdb=" N LEU D 101 " --> pdb=" O PHE D 97 " (cutoff:3.500A) Processing helix chain 'D' and resid 108 through 121 Processing helix chain 'D' and resid 122 through 127 Processing helix chain 'D' and resid 130 through 144 Processing sheet with id=AA1, first strand: chain 'A' and resid 682 through 685 removed outlier: 5.374A pdb=" N GLY A 756 " --> pdb=" O VAL A 972 " (cutoff:3.500A) removed outlier: 5.412A pdb=" N LEU A 760 " --> pdb=" O PRO A 968 " (cutoff:3.500A) removed outlier: 7.926A pdb=" N ILE A 762 " --> pdb=" O TYR A 966 " (cutoff:3.500A) removed outlier: 7.025A pdb=" N TYR A 966 " --> pdb=" O ILE A 762 " (cutoff:3.500A) removed outlier: 8.746A pdb=" N ASN A 764 " --> pdb=" O ILE A 964 " (cutoff:3.500A) removed outlier: 9.502A pdb=" N ILE A 964 " --> pdb=" O ASN A 764 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 713 through 714 removed outlier: 7.285A pdb=" N MET A 770 " --> pdb=" O MET A 830 " (cutoff:3.500A) removed outlier: 4.669A pdb=" N MET A 830 " --> pdb=" O MET A 770 " (cutoff:3.500A) removed outlier: 6.441A pdb=" N THR A 825 " --> pdb=" O ILE A 840 " (cutoff:3.500A) removed outlier: 4.234A pdb=" N ILE A 840 " --> pdb=" O THR A 825 " (cutoff:3.500A) removed outlier: 6.771A pdb=" N VAL A 827 " --> pdb=" O LEU A 838 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 995 through 997 Processing sheet with id=AA4, first strand: chain 'A' and resid 1013 through 1014 Processing sheet with id=AA5, first strand: chain 'C' and resid 682 through 685 removed outlier: 5.386A pdb=" N GLY C 756 " --> pdb=" O VAL C 972 " (cutoff:3.500A) removed outlier: 5.397A pdb=" N LEU C 760 " --> pdb=" O PRO C 968 " (cutoff:3.500A) removed outlier: 7.925A pdb=" N ILE C 762 " --> pdb=" O TYR C 966 " (cutoff:3.500A) removed outlier: 7.032A pdb=" N TYR C 966 " --> pdb=" O ILE C 762 " (cutoff:3.500A) removed outlier: 8.740A pdb=" N ASN C 764 " --> pdb=" O ILE C 964 " (cutoff:3.500A) removed outlier: 9.499A pdb=" N ILE C 964 " --> pdb=" O ASN C 764 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'C' and resid 713 through 714 removed outlier: 7.781A pdb=" N MET C 770 " --> pdb=" O MET C 830 " (cutoff:3.500A) removed outlier: 4.822A pdb=" N MET C 830 " --> pdb=" O MET C 770 " (cutoff:3.500A) removed outlier: 6.448A pdb=" N THR C 825 " --> pdb=" O ILE C 840 " (cutoff:3.500A) removed outlier: 4.241A pdb=" N ILE C 840 " --> pdb=" O THR C 825 " (cutoff:3.500A) removed outlier: 6.760A pdb=" N VAL C 827 " --> pdb=" O LEU C 838 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'C' and resid 995 through 997 Processing sheet with id=AA8, first strand: chain 'C' and resid 1013 through 1014 188 hydrogen bonds defined for protein. 510 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: 1.56 Time building geometry restraints manager: 2.11 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: 1984 1.34 - 1.46: 1344 1.46 - 1.58: 2553 1.58 - 1.69: 0 1.69 - 1.81: 72 Bond restraints: 5953 Sorted by residual: bond pdb=" CB VAL C 775 " pdb=" CG1 VAL C 775 " ideal model delta sigma weight residual 1.521 1.492 0.029 3.30e-02 9.18e+02 7.85e-01 bond pdb=" C GLY C 935 " pdb=" N GLY C 936 " ideal model delta sigma weight residual 1.327 1.319 0.008 9.60e-03 1.09e+04 7.75e-01 bond pdb=" CB PRO C 784 " pdb=" CG PRO C 784 " ideal model delta sigma weight residual 1.506 1.472 0.034 3.90e-02 6.57e+02 7.52e-01 bond pdb=" CB VAL A 775 " pdb=" CG1 VAL A 775 " ideal model delta sigma weight residual 1.521 1.493 0.028 3.30e-02 9.18e+02 7.45e-01 bond pdb=" C ASP A 947 " pdb=" N PRO A 948 " ideal model delta sigma weight residual 1.335 1.327 0.008 9.40e-03 1.13e+04 7.40e-01 ... (remaining 5948 not shown) Histogram of bond angle deviations from ideal: 100.29 - 107.03: 221 107.03 - 113.77: 3191 113.77 - 120.51: 2165 120.51 - 127.25: 2390 127.25 - 133.99: 89 Bond angle restraints: 8056 Sorted by residual: angle pdb=" N VAL A1019 " pdb=" CA VAL A1019 " pdb=" C VAL A1019 " ideal model delta sigma weight residual 113.71 109.25 4.46 9.50e-01 1.11e+00 2.21e+01 angle pdb=" N LEU B 138 " pdb=" CA LEU B 138 " pdb=" C LEU B 138 " ideal model delta sigma weight residual 111.07 108.43 2.64 1.07e+00 8.73e-01 6.08e+00 angle pdb=" CA VAL A1019 " pdb=" C VAL A1019 " pdb=" N SER A1020 " ideal model delta sigma weight residual 119.87 116.61 3.26 1.34e+00 5.57e-01 5.93e+00 angle pdb=" C HIS C1002 " pdb=" CA HIS C1002 " pdb=" CB HIS C1002 " ideal model delta sigma weight residual 110.42 114.91 -4.49 1.99e+00 2.53e-01 5.09e+00 angle pdb=" C ILE C 805 " pdb=" CA ILE C 805 " pdb=" CB ILE C 805 " ideal model delta sigma weight residual 112.22 109.37 2.85 1.38e+00 5.25e-01 4.27e+00 ... (remaining 8051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.27: 3226 17.27 - 34.55: 172 34.55 - 51.82: 37 51.82 - 69.09: 17 69.09 - 86.37: 6 Dihedral angle restraints: 3458 sinusoidal: 1292 harmonic: 2166 Sorted by residual: dihedral pdb=" CA VAL A 972 " pdb=" C VAL A 972 " pdb=" N MET A 973 " pdb=" CA MET A 973 " ideal model delta harmonic sigma weight residual -180.00 -162.33 -17.67 0 5.00e+00 4.00e-02 1.25e+01 dihedral pdb=" CA VAL C 972 " pdb=" C VAL C 972 " pdb=" N MET C 973 " pdb=" CA MET C 973 " ideal model delta harmonic sigma weight residual 180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 dihedral pdb=" CA ASP D 124 " pdb=" CB ASP D 124 " pdb=" CG ASP D 124 " pdb=" OD1 ASP D 124 " ideal model delta sinusoidal sigma weight residual -30.00 -88.97 58.97 1 2.00e+01 2.50e-03 1.16e+01 ... (remaining 3455 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 463 0.028 - 0.057: 200 0.057 - 0.085: 93 0.085 - 0.113: 64 0.113 - 0.141: 16 Chirality restraints: 836 Sorted by residual: chirality pdb=" CA ILE A 839 " pdb=" N ILE A 839 " pdb=" C ILE A 839 " pdb=" CB ILE A 839 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 5.00e-01 chirality pdb=" CA ILE C 839 " pdb=" N ILE C 839 " pdb=" C ILE C 839 " pdb=" CB ILE C 839 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.74e-01 chirality pdb=" CA ILE A 736 " pdb=" N ILE A 736 " pdb=" C ILE A 736 " pdb=" CB ILE A 736 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.03e-01 ... (remaining 833 not shown) Planarity restraints: 1077 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA D 135 " -0.008 2.00e-02 2.50e+03 1.53e-02 2.34e+00 pdb=" C ALA D 135 " 0.026 2.00e-02 2.50e+03 pdb=" O ALA D 135 " -0.010 2.00e-02 2.50e+03 pdb=" N ARG D 136 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU D 137 " 0.007 2.00e-02 2.50e+03 1.51e-02 2.27e+00 pdb=" C LEU D 137 " -0.026 2.00e-02 2.50e+03 pdb=" O LEU D 137 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU D 138 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 135 " 0.007 2.00e-02 2.50e+03 1.48e-02 2.20e+00 pdb=" C ALA B 135 " -0.026 2.00e-02 2.50e+03 pdb=" O ALA B 135 " 0.010 2.00e-02 2.50e+03 pdb=" N ARG B 136 " 0.009 2.00e-02 2.50e+03 ... (remaining 1074 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 141 2.69 - 3.24: 5586 3.24 - 3.80: 9695 3.80 - 4.35: 13179 4.35 - 4.90: 21219 Nonbonded interactions: 49820 Sorted by model distance: nonbonded pdb=" OD1 ASN A 864 " pdb=" OG SER A 866 " model vdw 2.138 2.440 nonbonded pdb=" OD1 ASN C 864 " pdb=" OG SER C 866 " model vdw 2.143 2.440 nonbonded pdb=" O MET A 752 " pdb=" NH1 ARG A 847 " model vdw 2.283 2.520 nonbonded pdb=" O PHE D 97 " pdb=" ND1 HIS D 100 " model vdw 2.286 2.520 nonbonded pdb=" OE1 GLU C 803 " pdb=" NH1 ARG C 806 " model vdw 2.313 2.520 ... (remaining 49815 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 'C' and (resid 677 through 985 or (resid 986 and (name N or name CA or na \ me C or name O or name CB )) or resid 987 through 1019 or (resid 1020 and (name \ N or name CA or name C or name O or name CB )) or resid 1021 through 1022)) } ncs_group { reference = (chain 'B' and (resid 93 through 101 or (resid 102 through 103 and (name N or na \ me CA or name C or name O )) or resid 104 through 149)) selection = chain 'D' } 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: 4 Type Number sf(0) Gaussians S 52 5.16 5 C 3613 2.51 5 N 1039 2.21 5 O 1113 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: 1.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 4.150 Check model and map are aligned: 0.080 Process input model: 18.950 Find NCS groups from input model: 0.330 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:14.360 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.520 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.004 0.034 5953 Z= 0.268 Angle : 0.554 5.479 8056 Z= 0.330 Chirality : 0.046 0.141 836 Planarity : 0.004 0.025 1077 Dihedral : 12.228 86.366 2072 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 5.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -1.01 (0.26), residues: 798 helix: -0.54 (0.43), residues: 134 sheet: 0.14 (0.36), residues: 128 loop : -0.93 (0.24), residues: 536 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 253 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 233 time to evaluate : 0.690 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 10 residues processed: 244 average time/residue: 1.1004 time to fit residues: 281.4192 Evaluate side-chains 216 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 206 time to evaluate : 0.589 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 7 residues processed: 5 average time/residue: 0.3769 time to fit residues: 2.8932 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 4.9990 chunk 59 optimal weight: 6.9990 chunk 32 optimal weight: 10.0000 chunk 20 optimal weight: 9.9990 chunk 39 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 chunk 61 optimal weight: 0.0060 chunk 23 optimal weight: 0.5980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 777 GLN A 791 GLN A 812 HIS C 777 GLN C 791 GLN B 120 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.2099 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 5953 Z= 0.173 Angle : 0.557 7.243 8056 Z= 0.288 Chirality : 0.046 0.153 836 Planarity : 0.004 0.048 1077 Dihedral : 4.115 17.971 850 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 3.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.27), residues: 798 helix: 0.56 (0.43), residues: 138 sheet: 0.22 (0.32), residues: 190 loop : -0.81 (0.26), residues: 470 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 233 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 213 time to evaluate : 0.691 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 20 outliers final: 7 residues processed: 223 average time/residue: 1.0315 time to fit residues: 241.6051 Evaluate side-chains 186 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 179 time to evaluate : 0.674 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 6 residues processed: 1 average time/residue: 0.1046 time to fit residues: 1.0530 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 39 optimal weight: 5.9990 chunk 21 optimal weight: 6.9990 chunk 58 optimal weight: 6.9990 chunk 48 optimal weight: 10.0000 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 1.9990 chunk 76 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 HIS C 946 ASN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7883 moved from start: 0.2603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.033 5953 Z= 0.409 Angle : 0.617 7.809 8056 Z= 0.322 Chirality : 0.049 0.143 836 Planarity : 0.004 0.035 1077 Dihedral : 4.296 17.400 850 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 9.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 5.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.75 (0.27), residues: 798 helix: 0.81 (0.45), residues: 138 sheet: -0.41 (0.33), residues: 180 loop : -0.93 (0.26), residues: 480 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 184 time to evaluate : 0.645 Fit side-chains outliers start: 33 outliers final: 13 residues processed: 204 average time/residue: 1.0906 time to fit residues: 233.0264 Evaluate side-chains 183 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 170 time to evaluate : 0.595 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.3677 time to fit residues: 2.0803 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 4.9990 chunk 7 optimal weight: 6.9990 chunk 33 optimal weight: 20.0000 chunk 47 optimal weight: 0.9980 chunk 71 optimal weight: 0.6980 chunk 75 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 67 optimal weight: 6.9990 chunk 20 optimal weight: 6.9990 chunk 62 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 overall best weight: 2.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7878 moved from start: 0.2919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.040 5953 Z= 0.339 Angle : 0.607 7.431 8056 Z= 0.316 Chirality : 0.048 0.158 836 Planarity : 0.004 0.039 1077 Dihedral : 4.347 18.026 850 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer Outliers : 3.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.70 (0.27), residues: 798 helix: 0.98 (0.44), residues: 138 sheet: -0.53 (0.32), residues: 200 loop : -0.86 (0.27), residues: 460 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 187 time to evaluate : 0.651 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 13 residues processed: 202 average time/residue: 1.0611 time to fit residues: 224.7947 Evaluate side-chains 184 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 0.709 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.0871 time to fit residues: 1.3070 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 2.9990 chunk 56 optimal weight: 8.9990 chunk 31 optimal weight: 7.9990 chunk 64 optimal weight: 0.9980 chunk 52 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 1.9990 chunk 67 optimal weight: 0.1980 chunk 19 optimal weight: 2.9990 chunk 25 optimal weight: 8.9990 chunk 14 optimal weight: 1.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 812 HIS ** B 100 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7847 moved from start: 0.3174 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5953 Z= 0.228 Angle : 0.620 8.476 8056 Z= 0.314 Chirality : 0.048 0.182 836 Planarity : 0.004 0.038 1077 Dihedral : 4.246 19.069 850 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.60 (0.27), residues: 798 helix: 1.04 (0.44), residues: 138 sheet: -0.46 (0.30), residues: 218 loop : -0.80 (0.28), residues: 442 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 194 time to evaluate : 0.819 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 210 average time/residue: 1.0761 time to fit residues: 237.0772 Evaluate side-chains 198 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 185 time to evaluate : 0.669 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 11 residues processed: 3 average time/residue: 0.6806 time to fit residues: 3.0425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 62 optimal weight: 0.7980 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 39 optimal weight: 0.9980 chunk 72 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 42 optimal weight: 0.7980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN B 100 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7824 moved from start: 0.3334 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5953 Z= 0.185 Angle : 0.623 9.406 8056 Z= 0.311 Chirality : 0.048 0.182 836 Planarity : 0.004 0.036 1077 Dihedral : 4.116 19.720 850 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 8.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 2.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.51 (0.28), residues: 798 helix: 1.15 (0.45), residues: 138 sheet: -0.25 (0.31), residues: 208 loop : -0.83 (0.28), residues: 452 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 198 time to evaluate : 0.532 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 12 residues processed: 209 average time/residue: 1.0913 time to fit residues: 239.0289 Evaluate side-chains 203 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 191 time to evaluate : 0.696 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 11 residues processed: 1 average time/residue: 0.0599 time to fit residues: 1.0138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 55 optimal weight: 6.9990 chunk 42 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 47 optimal weight: 3.9990 chunk 45 optimal weight: 0.9990 chunk 34 optimal weight: 5.9990 chunk 46 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 22 optimal weight: 5.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN B 100 HIS ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7862 moved from start: 0.3357 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 5953 Z= 0.274 Angle : 0.645 8.634 8056 Z= 0.326 Chirality : 0.050 0.199 836 Planarity : 0.004 0.043 1077 Dihedral : 4.264 20.039 850 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 9.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 3.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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 (0.28), residues: 798 helix: 1.22 (0.45), residues: 138 sheet: -0.26 (0.31), residues: 208 loop : -0.81 (0.28), residues: 452 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 188 time to evaluate : 0.660 Fit side-chains revert: symmetry clash outliers start: 19 outliers final: 13 residues processed: 205 average time/residue: 1.1406 time to fit residues: 244.7560 Evaluate side-chains 202 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 189 time to evaluate : 0.605 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 13 residues processed: 1 average time/residue: 0.0962 time to fit residues: 1.0984 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 14 optimal weight: 7.9990 chunk 47 optimal weight: 3.9990 chunk 51 optimal weight: 7.9990 chunk 37 optimal weight: 0.4980 chunk 7 optimal weight: 7.9990 chunk 59 optimal weight: 3.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 2.9990 chunk 42 optimal weight: 4.9990 overall best weight: 2.4786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.3392 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 5953 Z= 0.398 Angle : 0.711 9.642 8056 Z= 0.362 Chirality : 0.051 0.205 836 Planarity : 0.004 0.048 1077 Dihedral : 4.515 19.802 850 Min Nonbonded Distance : 1.973 Molprobity Statistics. All-atom Clashscore : 10.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer Outliers : 2.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.60 (0.28), residues: 798 helix: 1.03 (0.45), residues: 138 sheet: -0.24 (0.31), residues: 208 loop : -0.92 (0.28), residues: 452 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 184 time to evaluate : 0.618 Fit side-chains revert: symmetry clash outliers start: 17 outliers final: 12 residues processed: 198 average time/residue: 1.0371 time to fit residues: 215.4993 Evaluate side-chains 193 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 181 time to evaluate : 0.598 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.0536 time to fit residues: 1.0374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 30 optimal weight: 2.9990 chunk 55 optimal weight: 5.9990 chunk 21 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 66 optimal weight: 7.9990 chunk 69 optimal weight: 0.0980 chunk 46 optimal weight: 0.9990 chunk 74 optimal weight: 7.9990 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 51 optimal weight: 0.2980 overall best weight: 0.5380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.3631 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5953 Z= 0.188 Angle : 0.700 10.889 8056 Z= 0.348 Chirality : 0.049 0.202 836 Planarity : 0.004 0.044 1077 Dihedral : 4.223 20.659 850 Min Nonbonded Distance : 2.045 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer Outliers : 1.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.51 (0.27), residues: 798 helix: 1.11 (0.44), residues: 138 sheet: 0.23 (0.32), residues: 186 loop : -1.04 (0.27), residues: 474 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 214 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 203 time to evaluate : 0.643 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 10 residues processed: 213 average time/residue: 1.0227 time to fit residues: 228.7844 Evaluate side-chains 209 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 199 time to evaluate : 0.616 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 9 residues processed: 2 average time/residue: 0.0720 time to fit residues: 1.1384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 0.9980 chunk 71 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 6 optimal weight: 0.8980 chunk 47 optimal weight: 3.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 2.9990 chunk 65 optimal weight: 0.3980 chunk 18 optimal weight: 1.9990 chunk 57 optimal weight: 0.1980 chunk 9 optimal weight: 0.0020 overall best weight: 0.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7802 moved from start: 0.3744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.032 5953 Z= 0.187 Angle : 0.718 11.757 8056 Z= 0.354 Chirality : 0.049 0.203 836 Planarity : 0.004 0.054 1077 Dihedral : 4.141 21.513 850 Min Nonbonded Distance : 2.069 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer Outliers : 1.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.46 (0.27), residues: 798 helix: 1.19 (0.45), residues: 138 sheet: 0.26 (0.31), residues: 186 loop : -1.02 (0.27), residues: 474 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1596 Ramachandran restraints generated. 798 Oldfield, 0 Emsley, 798 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 198 time to evaluate : 0.679 Fit side-chains outliers start: 9 outliers final: 8 residues processed: 206 average time/residue: 1.1084 time to fit residues: 239.4568 Evaluate side-chains 196 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 188 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 8 residues processed: 0 time to fit residues: 0.8913 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 17 optimal weight: 6.9990 chunk 61 optimal weight: 0.7980 chunk 25 optimal weight: 9.9990 chunk 63 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 54 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 44 optimal weight: 1.9990 chunk 70 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 overall best weight: 1.1186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 791 GLN A 812 HIS C 791 GLN C 897 GLN ** B 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3462 r_free = 0.3462 target = 0.107040 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3016 r_free = 0.3016 target = 0.079044 restraints weight = 10092.220| |-----------------------------------------------------------------------------| r_work (start): 0.2982 rms_B_bonded: 3.47 r_work: 0.2836 rms_B_bonded: 3.74 restraints_weight: 0.5000 r_work (final): 0.2836 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8713 moved from start: 0.3740 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 5953 Z= 0.233 Angle : 0.747 11.749 8056 Z= 0.363 Chirality : 0.050 0.213 836 Planarity : 0.004 0.049 1077 Dihedral : 4.215 21.197 850 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 10.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer Outliers : 1.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 5.56 % 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: -0.51 (0.28), residues: 798 helix: 1.19 (0.45), residues: 138 sheet: -0.26 (0.31), residues: 208 loop : -0.84 (0.28), residues: 452 =============================================================================== Job complete usr+sys time: 3742.14 seconds wall clock time: 66 minutes 40.22 seconds (4000.22 seconds total)