Starting phenix.real_space_refine on Sun Mar 10 22:56:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/03_2024/7n00_24095.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/03_2024/7n00_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_24095/03_2024/7n00_24095.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/03_2024/7n00_24095.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/03_2024/7n00_24095.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7n00_24095/03_2024/7n00_24095.pdb" } resolution = 2.27 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- 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 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. 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-5265/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: 3.43, per 1000 atoms: 0.59 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: 2.04 Conformation dependent library (CDL) restraints added in 1.2 seconds 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: 0.62 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: 1.51 Time building geometry restraints manager: 2.26 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 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: 0.730 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: 3.670 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 19.430 Find NCS groups from input model: 0.320 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.240 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.570 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7521 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 % Allowed : 5.16 % Favored : 91.39 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 726 HIS 0.007 0.001 HIS B 100 PHE 0.014 0.002 PHE C 828 TYR 0.009 0.001 TYR C 826 ARG 0.002 0.001 ARG C 918 *********************** 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 : 0.663 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 1007 PHE cc_start: 0.8763 (OUTLIER) cc_final: 0.8439 (p90) REVERT: B 136 ARG cc_start: 0.8061 (mtt90) cc_final: 0.7794 (mtm110) REVERT: D 113 LYS cc_start: 0.8516 (tttp) cc_final: 0.7876 (tptp) outliers start: 20 outliers final: 10 residues processed: 244 average time/residue: 1.0357 time to fit residues: 264.8665 Evaluate side-chains 218 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 207 time to evaluate : 0.642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 804 GLU Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain A residue 964 ILE Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 964 ILE Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 143 VAL Chi-restraints excluded: chain D residue 143 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 65 optimal weight: 0.8980 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: 0.6980 chunk 37 optimal weight: 2.9990 chunk 45 optimal weight: 0.9990 chunk 70 optimal weight: 0.8980 overall best weight: 0.6796 ------------------------------------------------------------------------------- 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: 0.7540 moved from start: 0.2049 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= 0.175 Angle : 0.557 7.636 8056 Z= 0.288 Chirality : 0.046 0.128 836 Planarity : 0.004 0.049 1077 Dihedral : 5.688 49.910 869 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 3.27 % Allowed : 19.45 % Favored : 77.28 % 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: -0.50 (0.27), residues: 798 helix: 0.55 (0.43), residues: 138 sheet: 0.21 (0.32), residues: 190 loop : -0.82 (0.26), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 726 HIS 0.007 0.001 HIS A 989 PHE 0.018 0.001 PHE D 115 TYR 0.009 0.001 TYR D 119 ARG 0.007 0.001 ARG C 806 *********************** 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 234 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 215 time to evaluate : 0.579 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 994 GLU cc_start: 0.7438 (mp0) cc_final: 0.6963 (mp0) outliers start: 19 outliers final: 7 residues processed: 224 average time/residue: 1.0295 time to fit residues: 241.8457 Evaluate side-chains 185 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 178 time to evaluate : 0.645 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain B residue 124 ASP 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: 9.9990 chunk 19 optimal weight: 1.9990 chunk 70 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 24 optimal weight: 6.9990 chunk 56 optimal weight: 0.8980 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: 0.7652 moved from start: 0.2552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.029 5953 Z= 0.405 Angle : 0.620 7.866 8056 Z= 0.323 Chirality : 0.048 0.142 836 Planarity : 0.004 0.036 1077 Dihedral : 4.832 34.304 858 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 5.51 % Allowed : 19.28 % Favored : 75.22 % 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: -0.72 (0.27), residues: 798 helix: 0.85 (0.45), residues: 138 sheet: -0.53 (0.33), residues: 200 loop : -0.84 (0.26), residues: 460 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 726 HIS 0.010 0.001 HIS D 100 PHE 0.022 0.002 PHE D 115 TYR 0.009 0.001 TYR C 739 ARG 0.008 0.001 ARG A 806 *********************** 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 204 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 172 time to evaluate : 0.619 Fit side-chains revert: symmetry clash REVERT: B 93 MET cc_start: 0.7920 (ppp) cc_final: 0.7719 (ppp) outliers start: 32 outliers final: 13 residues processed: 194 average time/residue: 1.0281 time to fit residues: 209.2651 Evaluate side-chains 184 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 171 time to evaluate : 0.678 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 752 MET Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain B residue 146 VAL Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 36 optimal weight: 0.8980 chunk 7 optimal weight: 5.9990 chunk 33 optimal weight: 9.9990 chunk 47 optimal weight: 2.9990 chunk 71 optimal weight: 2.9990 chunk 75 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 0.0670 chunk 20 optimal weight: 5.9990 chunk 62 optimal weight: 5.9990 chunk 42 optimal weight: 0.9990 overall best weight: 1.3924 ------------------------------------------------------------------------------- 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: 0.7611 moved from start: 0.2916 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 5953 Z= 0.240 Angle : 0.580 7.462 8056 Z= 0.300 Chirality : 0.047 0.156 836 Planarity : 0.004 0.037 1077 Dihedral : 4.674 32.104 858 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 2.58 % Allowed : 22.89 % Favored : 74.53 % 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: -0.63 (0.27), residues: 798 helix: 0.99 (0.44), residues: 138 sheet: -0.46 (0.30), residues: 218 loop : -0.81 (0.27), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 726 HIS 0.007 0.001 HIS A 996 PHE 0.017 0.001 PHE D 115 TYR 0.007 0.001 TYR A 739 ARG 0.008 0.001 ARG A 806 *********************** 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 208 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 193 time to evaluate : 0.634 Fit side-chains revert: symmetry clash REVERT: D 113 LYS cc_start: 0.8566 (tppp) cc_final: 0.8142 (tptp) outliers start: 15 outliers final: 12 residues processed: 205 average time/residue: 1.0648 time to fit residues: 228.9412 Evaluate side-chains 190 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 178 time to evaluate : 0.644 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 752 MET Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain B residue 124 ASP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 1 optimal weight: 0.0000 chunk 56 optimal weight: 6.9990 chunk 31 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 52 optimal weight: 0.7980 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 67 optimal weight: 20.0000 chunk 19 optimal weight: 3.9990 chunk 25 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- 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: 0.7633 moved from start: 0.3127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 5953 Z= 0.287 Angle : 0.624 8.285 8056 Z= 0.319 Chirality : 0.049 0.185 836 Planarity : 0.004 0.040 1077 Dihedral : 4.751 32.562 858 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 8.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Rotamer: Outliers : 3.61 % Allowed : 24.27 % Favored : 72.12 % 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: -0.59 (0.28), residues: 798 helix: 1.11 (0.44), residues: 138 sheet: -0.46 (0.30), residues: 218 loop : -0.81 (0.28), residues: 442 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 814 HIS 0.007 0.001 HIS A 996 PHE 0.024 0.001 PHE D 115 TYR 0.008 0.001 TYR C 739 ARG 0.009 0.001 ARG A 806 *********************** 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 209 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 188 time to evaluate : 0.660 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 946 ASN cc_start: 0.7552 (t0) cc_final: 0.7273 (t0) REVERT: C 1007 PHE cc_start: 0.8533 (OUTLIER) cc_final: 0.7975 (p90) outliers start: 21 outliers final: 15 residues processed: 202 average time/residue: 1.0594 time to fit residues: 224.4326 Evaluate side-chains 196 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 180 time to evaluate : 0.627 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 752 MET Chi-restraints excluded: chain C residue 766 GLU Chi-restraints excluded: chain C residue 832 ASP Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain C residue 1007 PHE Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain D residue 146 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 75 optimal weight: 4.9990 chunk 62 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 4.9990 chunk 72 optimal weight: 0.7980 chunk 8 optimal weight: 0.8980 chunk 42 optimal weight: 0.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.7598 moved from start: 0.3308 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= 0.196 Angle : 0.635 9.308 8056 Z= 0.319 Chirality : 0.049 0.193 836 Planarity : 0.004 0.042 1077 Dihedral : 4.647 32.107 858 Min Nonbonded Distance : 2.042 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.76 % Favored : 97.24 % Rotamer: Outliers : 3.10 % Allowed : 26.51 % Favored : 70.40 % 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: -0.55 (0.28), residues: 798 helix: 1.17 (0.45), residues: 138 sheet: -0.32 (0.31), residues: 208 loop : -0.86 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 891 HIS 0.007 0.001 HIS A 996 PHE 0.024 0.001 PHE D 115 TYR 0.007 0.001 TYR A 739 ARG 0.010 0.001 ARG A 806 *********************** 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 207 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 189 time to evaluate : 0.675 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 951 ASP cc_start: 0.7162 (m-30) cc_final: 0.6959 (m-30) REVERT: C 946 ASN cc_start: 0.7460 (t0) cc_final: 0.7168 (t0) outliers start: 18 outliers final: 12 residues processed: 203 average time/residue: 1.0271 time to fit residues: 218.7567 Evaluate side-chains 195 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 183 time to evaluate : 0.691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 771 LEU Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 985 LEU Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain D residue 146 VAL 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: 0.9990 chunk 47 optimal weight: 2.9990 chunk 45 optimal weight: 0.0670 chunk 34 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 1.9990 chunk 22 optimal weight: 10.0000 overall best weight: 1.6126 ------------------------------------------------------------------------------- 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** ** 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: 0.7630 moved from start: 0.3336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 5953 Z= 0.280 Angle : 0.650 8.366 8056 Z= 0.331 Chirality : 0.049 0.198 836 Planarity : 0.004 0.044 1077 Dihedral : 4.770 32.341 858 Min Nonbonded Distance : 2.020 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.01 % Favored : 96.99 % Rotamer: Outliers : 2.93 % Allowed : 27.37 % Favored : 69.71 % 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: -0.54 (0.28), residues: 798 helix: 1.14 (0.45), residues: 138 sheet: -0.29 (0.31), residues: 208 loop : -0.84 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 726 HIS 0.008 0.001 HIS A 996 PHE 0.023 0.001 PHE D 115 TYR 0.008 0.001 TYR C 739 ARG 0.010 0.001 ARG A 806 *********************** 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 206 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 189 time to evaluate : 0.691 Fit side-chains revert: symmetry clash REVERT: C 946 ASN cc_start: 0.7553 (t0) cc_final: 0.7271 (t0) outliers start: 17 outliers final: 13 residues processed: 201 average time/residue: 1.0836 time to fit residues: 228.2245 Evaluate side-chains 200 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 187 time to evaluate : 0.677 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 898 GLU Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain D residue 146 VAL 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: 4.9990 chunk 51 optimal weight: 8.9990 chunk 37 optimal weight: 0.7980 chunk 7 optimal weight: 6.9990 chunk 59 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 65 optimal weight: 7.9990 chunk 70 optimal weight: 0.8980 chunk 42 optimal weight: 4.9990 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 120 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 5953 Z= 0.347 Angle : 0.692 9.933 8056 Z= 0.352 Chirality : 0.050 0.203 836 Planarity : 0.004 0.048 1077 Dihedral : 4.941 33.374 858 Min Nonbonded Distance : 2.003 Molprobity Statistics. All-atom Clashscore : 9.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.79 % Allowed : 27.19 % Favored : 69.02 % 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: -0.63 (0.28), residues: 798 helix: 1.00 (0.45), residues: 138 sheet: -0.27 (0.31), residues: 208 loop : -0.92 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 814 HIS 0.010 0.001 HIS A 989 PHE 0.023 0.001 PHE D 115 TYR 0.012 0.001 TYR D 131 ARG 0.010 0.001 ARG A 806 *********************** 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 208 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 186 time to evaluate : 0.653 Fit side-chains revert: symmetry clash outliers start: 22 outliers final: 15 residues processed: 202 average time/residue: 1.0600 time to fit residues: 224.3930 Evaluate side-chains 197 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 182 time to evaluate : 0.630 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 855 THR Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 735 SER Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 805 ILE Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain C residue 992 VAL Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 111 CYS Chi-restraints excluded: chain B residue 124 ASP Chi-restraints excluded: chain D residue 146 VAL 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: 3.9990 chunk 63 optimal weight: 5.9990 chunk 66 optimal weight: 4.9990 chunk 69 optimal weight: 7.9990 chunk 46 optimal weight: 0.7980 chunk 74 optimal weight: 0.4980 chunk 45 optimal weight: 0.7980 chunk 35 optimal weight: 0.4980 chunk 51 optimal weight: 0.9980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7584 moved from start: 0.3647 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 5953 Z= 0.197 Angle : 0.727 12.485 8056 Z= 0.358 Chirality : 0.049 0.202 836 Planarity : 0.004 0.044 1077 Dihedral : 4.649 31.701 858 Min Nonbonded Distance : 2.036 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 2.24 % Allowed : 28.74 % Favored : 69.02 % 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: -0.52 (0.27), residues: 798 helix: 1.09 (0.45), residues: 136 sheet: 0.23 (0.32), residues: 186 loop : -1.03 (0.27), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP C 726 HIS 0.010 0.001 HIS A 989 PHE 0.023 0.001 PHE D 115 TYR 0.013 0.001 TYR B 131 ARG 0.011 0.001 ARG A 806 *********************** 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 207 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 194 time to evaluate : 0.630 Fit side-chains outliers start: 13 outliers final: 9 residues processed: 205 average time/residue: 1.0211 time to fit residues: 219.8690 Evaluate side-chains 201 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 192 time to evaluate : 0.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 111 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 78 random chunks: chunk 77 optimal weight: 4.9990 chunk 71 optimal weight: 3.9990 chunk 61 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 chunk 37 optimal weight: 5.9990 chunk 49 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 57 optimal weight: 0.0010 chunk 9 optimal weight: 1.9990 overall best weight: 0.9792 ------------------------------------------------------------------------------- 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: 0.7597 moved from start: 0.3755 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 5953 Z= 0.225 Angle : 0.747 12.422 8056 Z= 0.365 Chirality : 0.049 0.203 836 Planarity : 0.004 0.049 1077 Dihedral : 4.605 31.070 856 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 9.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.63 % Favored : 97.37 % Rotamer: Outliers : 1.55 % Allowed : 29.95 % Favored : 68.50 % 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: -0.52 (0.28), residues: 798 helix: 1.18 (0.45), residues: 138 sheet: -0.21 (0.31), residues: 208 loop : -0.88 (0.27), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 814 HIS 0.011 0.001 HIS A 989 PHE 0.022 0.001 PHE D 115 TYR 0.007 0.001 TYR D 131 ARG 0.011 0.001 ARG A 806 ********************** 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 202 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 193 time to evaluate : 0.662 Fit side-chains outliers start: 9 outliers final: 9 residues processed: 201 average time/residue: 1.0668 time to fit residues: 224.7460 Evaluate side-chains 197 residues out of total 620 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 188 time to evaluate : 0.674 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 735 SER Chi-restraints excluded: chain A residue 737 SER Chi-restraints excluded: chain A residue 913 TRP Chi-restraints excluded: chain C residue 737 SER Chi-restraints excluded: chain C residue 855 THR Chi-restraints excluded: chain C residue 911 LYS Chi-restraints excluded: chain C residue 913 TRP Chi-restraints excluded: chain B residue 98 LEU Chi-restraints excluded: chain B residue 111 CYS 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: 4.9990 chunk 25 optimal weight: 8.9990 chunk 63 optimal weight: 0.0870 chunk 7 optimal weight: 4.9990 chunk 11 optimal weight: 0.9980 chunk 54 optimal weight: 8.9990 chunk 3 optimal weight: 5.9990 chunk 44 optimal weight: 2.9990 chunk 70 optimal weight: 3.9990 chunk 41 optimal weight: 6.9990 overall best weight: 2.6164 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3407 r_free = 0.3407 target = 0.102874 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.074695 restraints weight = 10265.052| |-----------------------------------------------------------------------------| r_work (start): 0.2912 rms_B_bonded: 3.43 r_work: 0.2767 rms_B_bonded: 3.68 restraints_weight: 0.5000 r_work (final): 0.2767 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8623 moved from start: 0.3575 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= 0.423 Angle : 0.776 12.016 8056 Z= 0.389 Chirality : 0.051 0.212 836 Planarity : 0.004 0.053 1077 Dihedral : 4.968 34.053 856 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 10.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 1.38 % Allowed : 30.98 % Favored : 67.64 % 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: 0.97 (0.44), residues: 138 sheet: -0.19 (0.31), residues: 208 loop : -0.92 (0.28), residues: 452 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 814 HIS 0.011 0.002 HIS C 996 PHE 0.020 0.002 PHE D 115 TYR 0.025 0.002 TYR B 131 ARG 0.011 0.001 ARG C 806 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3689.43 seconds wall clock time: 65 minutes 34.49 seconds (3934.49 seconds total)