Starting phenix.real_space_refine on Mon Jul 22 13:02:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u14_41801/07_2024/8u14_41801_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u14_41801/07_2024/8u14_41801.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u14_41801/07_2024/8u14_41801.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u14_41801/07_2024/8u14_41801.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u14_41801/07_2024/8u14_41801_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u14_41801/07_2024/8u14_41801_neut.cif" } resolution = 3.9 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 293 5.49 5 S 32 5.16 5 C 7885 2.51 5 N 2608 2.21 5 O 3175 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "D GLU 35": "OE1" <-> "OE2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E GLU 133": "OE1" <-> "OE2" Residue "F GLU 53": "OE1" <-> "OE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F ASP 85": "OD1" <-> "OD2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H PHE 70": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 71": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "C GLU 56": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13995 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "H" Number of atoms: 731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "L" Number of atoms: 1176 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1176 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "C" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "G" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 843 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 10611 SG CYS K 31 77.501 68.587 45.284 1.00155.98 S ATOM 10761 SG CYS K 51 77.762 71.763 47.414 1.00157.25 S ATOM 10785 SG CYS K 54 76.542 71.999 43.785 1.00157.66 S ATOM 10502 SG CYS K 16 86.876 72.181 56.653 1.00201.51 S ATOM 10520 SG CYS K 19 87.004 73.675 59.834 1.00219.51 S ATOM 10650 SG CYS K 36 84.987 70.188 59.204 1.00192.64 S ATOM 10672 SG CYS K 39 83.453 73.315 58.539 1.00199.41 S Time building chain proxies: 8.28, per 1000 atoms: 0.59 Number of scatterers: 13995 At special positions: 0 Unit cell: (107.898, 126.395, 118.174, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 32 16.00 P 293 15.00 O 3175 8.00 N 2608 7.00 C 7885 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 8.07 Conformation dependent library (CDL) restraints added in 1.6 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " Number of angles added : 9 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1892 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 8 sheets defined 65.5% alpha, 3.3% beta 140 base pairs and 241 stacking pairs defined. Time for finding SS restraints: 6.27 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.702A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.768A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.639A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.799A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.653A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 removed outlier: 3.528A pdb=" N GLY F 41 " --> pdb=" O LEU F 37 " (cutoff:3.500A) Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.365A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.896A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.514A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 36 through 45 removed outlier: 3.664A pdb=" N GLU K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 67 removed outlier: 4.642A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 92 removed outlier: 3.935A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.983A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.535A pdb=" N ALA L 124 " --> pdb=" O VAL L 120 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 147 removed outlier: 3.700A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) removed outlier: 3.545A pdb=" N ALA L 146 " --> pdb=" O THR L 142 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N MET L 147 " --> pdb=" O GLN L 143 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.395A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.898A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 74 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 98 Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.634A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.214A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA4, first strand: chain 'E' and resid 118 through 119 removed outlier: 3.600A pdb=" N ILE E 119 " --> pdb=" O ARG F 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.393A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AA7, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.555A pdb=" N VAL K 27 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 3.528A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'L' and resid 21 through 25 486 hydrogen bonds defined for protein. 1442 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 358 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 140 basepair parallelities 241 stacking parallelities Total time for adding SS restraints: 5.05 Time building geometry restraints manager: 8.59 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: 3398 1.34 - 1.46: 4244 1.46 - 1.58: 6583 1.58 - 1.70: 584 1.70 - 1.82: 46 Bond restraints: 14855 Sorted by residual: bond pdb=" C HIS H 49 " pdb=" O HIS H 49 " ideal model delta sigma weight residual 1.249 1.237 0.012 8.50e-03 1.38e+04 1.91e+00 bond pdb=" CB LYS B 59 " pdb=" CG LYS B 59 " ideal model delta sigma weight residual 1.520 1.558 -0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.40e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.460 1.476 -0.017 1.42e-02 4.96e+03 1.35e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.32e+00 ... (remaining 14850 not shown) Histogram of bond angle deviations from ideal: 98.58 - 105.66: 1538 105.66 - 112.74: 8173 112.74 - 119.81: 5073 119.81 - 126.89: 5741 126.89 - 133.96: 809 Bond angle restraints: 21334 Sorted by residual: angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.53 108.56 4.97 9.80e-01 1.04e+00 2.57e+01 angle pdb=" N GLU F 63 " pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " ideal model delta sigma weight residual 110.39 116.07 -5.68 1.66e+00 3.63e-01 1.17e+01 angle pdb=" CA GLU F 63 " pdb=" CB GLU F 63 " pdb=" CG GLU F 63 " ideal model delta sigma weight residual 114.10 120.81 -6.71 2.00e+00 2.50e-01 1.13e+01 angle pdb=" CB LYS B 59 " pdb=" CG LYS B 59 " pdb=" CD LYS B 59 " ideal model delta sigma weight residual 111.30 118.47 -7.17 2.30e+00 1.89e-01 9.73e+00 angle pdb=" N ARG B 36 " pdb=" CA ARG B 36 " pdb=" CB ARG B 36 " ideal model delta sigma weight residual 110.28 114.90 -4.62 1.55e+00 4.16e-01 8.88e+00 ... (remaining 21329 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.61: 6641 31.61 - 63.22: 1528 63.22 - 94.84: 41 94.84 - 126.45: 0 126.45 - 158.06: 2 Dihedral angle restraints: 8212 sinusoidal: 5284 harmonic: 2928 Sorted by residual: dihedral pdb=" CA ASN B 25 " pdb=" C ASN B 25 " pdb=" N ILE B 26 " pdb=" CA ILE B 26 " ideal model delta harmonic sigma weight residual 180.00 -154.56 -25.44 0 5.00e+00 4.00e-02 2.59e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 61.94 158.06 1 3.50e+01 8.16e-04 1.51e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 65.92 154.08 1 3.50e+01 8.16e-04 1.49e+01 ... (remaining 8209 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 1787 0.034 - 0.069: 477 0.069 - 0.103: 120 0.103 - 0.138: 29 0.138 - 0.172: 5 Chirality restraints: 2418 Sorted by residual: chirality pdb=" CA GLU F 63 " pdb=" N GLU F 63 " pdb=" C GLU F 63 " pdb=" CB GLU F 63 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.39e-01 chirality pdb=" CA ASP B 24 " pdb=" N ASP B 24 " pdb=" C ASP B 24 " pdb=" CB ASP B 24 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.51e-01 chirality pdb=" CA GLN E 125 " pdb=" N GLN E 125 " pdb=" C GLN E 125 " pdb=" CB GLN E 125 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.10e-01 ... (remaining 2415 not shown) Planarity restraints: 1690 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.024 2.00e-02 2.50e+03 1.04e-02 2.98e+00 pdb=" N9 DA I -35 " -0.022 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.007 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS F 59 " -0.008 2.00e-02 2.50e+03 1.66e-02 2.77e+00 pdb=" C LYS F 59 " 0.029 2.00e-02 2.50e+03 pdb=" O LYS F 59 " -0.011 2.00e-02 2.50e+03 pdb=" N VAL F 60 " -0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU A 73 " -0.008 2.00e-02 2.50e+03 1.64e-02 2.68e+00 pdb=" CD GLU A 73 " 0.028 2.00e-02 2.50e+03 pdb=" OE1 GLU A 73 " -0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU A 73 " -0.010 2.00e-02 2.50e+03 ... (remaining 1687 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1967 2.76 - 3.47: 20767 3.47 - 4.19: 39250 4.19 - 4.90: 58379 Nonbonded interactions: 120365 Sorted by model distance: nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.330 3.350 nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.331 3.350 nonbonded pdb=" O ARG K 63 " pdb=" NH1 ARG K 67 " model vdw 2.124 2.520 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.150 2.496 nonbonded pdb=" OE1 GLN D 95 " pdb=" OH TYR C 50 " model vdw 2.160 2.440 ... (remaining 120360 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 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 119) } ncs_group { reference = (chain 'D' and resid 31 through 123) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.080 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.110 Construct map_model_manager: 0.010 Extract box with map and model: 0.470 Check model and map are aligned: 0.100 Set scattering table: 0.110 Process input model: 49.860 Find NCS groups from input model: 0.420 Set up NCS constraints: 0.070 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8264 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14855 Z= 0.190 Angle : 0.645 8.235 21334 Z= 0.371 Chirality : 0.035 0.172 2418 Planarity : 0.004 0.041 1690 Dihedral : 26.360 158.059 6320 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 0.00 % Allowed : 0.93 % Favored : 99.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.65 (0.27), residues: 987 helix: 1.25 (0.21), residues: 623 sheet: 0.72 (0.98), residues: 24 loop : -1.10 (0.32), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 PHE 0.017 0.001 PHE E 78 TYR 0.024 0.001 TYR F 88 ARG 0.016 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 354 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 354 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 106 ASP cc_start: 0.8750 (m-30) cc_final: 0.8495 (m-30) REVERT: A 125 GLN cc_start: 0.8605 (mp10) cc_final: 0.7989 (mp10) REVERT: D 59 MET cc_start: 0.8760 (tpt) cc_final: 0.8526 (tpt) REVERT: E 73 GLU cc_start: 0.8223 (mt-10) cc_final: 0.8008 (mt-10) REVERT: E 77 ASP cc_start: 0.8106 (m-30) cc_final: 0.7873 (m-30) REVERT: E 120 MET cc_start: 0.8851 (mmm) cc_final: 0.8432 (mmm) REVERT: F 31 LYS cc_start: 0.9471 (tttm) cc_final: 0.9057 (tptm) REVERT: F 64 ASN cc_start: 0.8753 (m-40) cc_final: 0.8430 (m110) REVERT: H 47 GLN cc_start: 0.8800 (tt0) cc_final: 0.8495 (tm-30) REVERT: H 48 VAL cc_start: 0.9346 (p) cc_final: 0.9145 (p) REVERT: H 71 GLU cc_start: 0.8552 (tm-30) cc_final: 0.8206 (tm-30) REVERT: H 85 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9034 (mtmm) REVERT: K 18 ILE cc_start: 0.8706 (mm) cc_final: 0.8483 (mm) REVERT: K 41 GLN cc_start: 0.9313 (mt0) cc_final: 0.8888 (mp10) REVERT: C 56 GLU cc_start: 0.9069 (tp30) cc_final: 0.8812 (tp30) REVERT: C 90 ASP cc_start: 0.8551 (t70) cc_final: 0.8319 (t0) REVERT: G 92 GLU cc_start: 0.7885 (pt0) cc_final: 0.7273 (pt0) REVERT: G 104 GLN cc_start: 0.8553 (tt0) cc_final: 0.7766 (tm-30) outliers start: 0 outliers final: 0 residues processed: 354 average time/residue: 0.3205 time to fit residues: 152.6188 Evaluate side-chains 279 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 279 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.8980 chunk 62 optimal weight: 7.9990 chunk 49 optimal weight: 0.9990 chunk 96 optimal weight: 20.0000 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 6.9990 chunk 71 optimal weight: 7.9990 chunk 111 optimal weight: 0.9980 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8318 moved from start: 0.1291 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 14855 Z= 0.240 Angle : 0.639 11.537 21334 Z= 0.364 Chirality : 0.037 0.182 2418 Planarity : 0.004 0.037 1690 Dihedral : 29.592 157.029 4321 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 16.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.45 % Allowed : 18.53 % Favored : 79.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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 (0.26), residues: 987 helix: 1.37 (0.21), residues: 630 sheet: 0.61 (1.00), residues: 24 loop : -1.20 (0.32), residues: 333 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 61 HIS 0.007 0.001 HIS K 65 PHE 0.019 0.002 PHE A 104 TYR 0.027 0.002 TYR B 88 ARG 0.014 0.001 ARG K 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 321 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 300 time to evaluate : 1.125 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 120 MET cc_start: 0.8077 (mmm) cc_final: 0.7867 (mmm) REVERT: A 125 GLN cc_start: 0.8448 (mp10) cc_final: 0.8110 (mp10) REVERT: B 84 MET cc_start: 0.9235 (tpp) cc_final: 0.8670 (tpp) REVERT: D 33 ARG cc_start: 0.8696 (ttm-80) cc_final: 0.8158 (tpp80) REVERT: E 77 ASP cc_start: 0.8213 (m-30) cc_final: 0.7955 (m-30) REVERT: E 120 MET cc_start: 0.8733 (mmm) cc_final: 0.8331 (mmm) REVERT: F 64 ASN cc_start: 0.8600 (m-40) cc_final: 0.8267 (m110) REVERT: F 84 MET cc_start: 0.8039 (tpp) cc_final: 0.7778 (tpp) REVERT: F 92 ARG cc_start: 0.8743 (ttp80) cc_final: 0.8201 (ttp80) REVERT: H 47 GLN cc_start: 0.8761 (tt0) cc_final: 0.8459 (tm-30) REVERT: H 71 GLU cc_start: 0.8599 (tm-30) cc_final: 0.8320 (tm-30) REVERT: K 18 ILE cc_start: 0.8707 (mm) cc_final: 0.8479 (mm) REVERT: K 86 ARG cc_start: 0.9419 (pmt170) cc_final: 0.9030 (pmt170) REVERT: L 63 LYS cc_start: 0.7644 (tptt) cc_final: 0.7333 (tppt) REVERT: C 73 ASN cc_start: 0.9466 (t0) cc_final: 0.9205 (t0) REVERT: C 90 ASP cc_start: 0.8410 (t70) cc_final: 0.8119 (t0) REVERT: G 38 ASN cc_start: 0.7879 (m110) cc_final: 0.7337 (m-40) REVERT: G 104 GLN cc_start: 0.8629 (tt0) cc_final: 0.7868 (tm-30) outliers start: 21 outliers final: 13 residues processed: 307 average time/residue: 0.3058 time to fit residues: 127.9586 Evaluate side-chains 300 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 287 time to evaluate : 1.105 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 92 optimal weight: 30.0000 chunk 76 optimal weight: 5.9990 chunk 30 optimal weight: 10.0000 chunk 111 optimal weight: 0.3980 chunk 120 optimal weight: 3.9990 chunk 99 optimal weight: 0.2980 chunk 110 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 89 optimal weight: 5.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 20 GLN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8307 moved from start: 0.1555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 14855 Z= 0.203 Angle : 0.624 10.437 21334 Z= 0.355 Chirality : 0.036 0.196 2418 Planarity : 0.004 0.038 1690 Dihedral : 29.609 156.325 4321 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 14.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.96 % Favored : 96.04 % Rotamer: Outliers : 2.91 % Allowed : 19.46 % Favored : 77.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.89 (0.26), residues: 987 helix: 1.51 (0.21), residues: 627 sheet: 0.76 (1.04), residues: 24 loop : -1.21 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP K 61 HIS 0.003 0.001 HIS G 31 PHE 0.014 0.001 PHE K 40 TYR 0.029 0.002 TYR B 88 ARG 0.009 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 323 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 298 time to evaluate : 1.188 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.8286 (mt0) cc_final: 0.8037 (mp10) REVERT: D 33 ARG cc_start: 0.8719 (ttm-80) cc_final: 0.8082 (tpp80) REVERT: E 73 GLU cc_start: 0.8770 (tt0) cc_final: 0.8465 (tt0) REVERT: E 77 ASP cc_start: 0.8223 (m-30) cc_final: 0.7980 (m-30) REVERT: E 90 MET cc_start: 0.8005 (mmt) cc_final: 0.7663 (mmp) REVERT: E 120 MET cc_start: 0.8831 (mmm) cc_final: 0.8307 (mmm) REVERT: E 126 LEU cc_start: 0.9566 (tt) cc_final: 0.9346 (tp) REVERT: F 39 ARG cc_start: 0.9311 (tpp80) cc_final: 0.8981 (mmt-90) REVERT: F 84 MET cc_start: 0.7981 (tpp) cc_final: 0.7725 (tpp) REVERT: F 92 ARG cc_start: 0.8696 (ttp80) cc_final: 0.8229 (ttp80) REVERT: H 47 GLN cc_start: 0.8732 (tt0) cc_final: 0.8450 (tm-30) REVERT: H 116 LYS cc_start: 0.9054 (mmtt) cc_final: 0.8716 (mmtp) REVERT: K 18 ILE cc_start: 0.8671 (mm) cc_final: 0.8449 (mm) REVERT: L 63 LYS cc_start: 0.7628 (tptt) cc_final: 0.7296 (tppt) REVERT: C 73 ASN cc_start: 0.9419 (t0) cc_final: 0.9130 (t0) REVERT: C 90 ASP cc_start: 0.8381 (t70) cc_final: 0.8089 (t0) REVERT: G 57 TYR cc_start: 0.8766 (t80) cc_final: 0.8523 (t80) REVERT: G 84 GLN cc_start: 0.8961 (tp-100) cc_final: 0.8275 (tp-100) REVERT: G 104 GLN cc_start: 0.8616 (tt0) cc_final: 0.7832 (tm-30) outliers start: 25 outliers final: 18 residues processed: 308 average time/residue: 0.3117 time to fit residues: 132.3713 Evaluate side-chains 300 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 282 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 2.9990 chunk 84 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 12 optimal weight: 0.7980 chunk 53 optimal weight: 10.0000 chunk 75 optimal weight: 6.9990 chunk 112 optimal weight: 7.9990 chunk 118 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 5.9990 chunk 99 optimal weight: 8.9990 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 14855 Z= 0.300 Angle : 0.655 10.340 21334 Z= 0.374 Chirality : 0.038 0.184 2418 Planarity : 0.004 0.039 1690 Dihedral : 29.827 154.377 4321 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 18.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 4.66 % Allowed : 22.26 % Favored : 73.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.82 (0.26), residues: 987 helix: 1.47 (0.21), residues: 628 sheet: 0.44 (1.03), residues: 24 loop : -1.24 (0.32), residues: 335 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 61 HIS 0.005 0.001 HIS C 31 PHE 0.013 0.002 PHE K 40 TYR 0.039 0.002 TYR B 88 ARG 0.008 0.001 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 337 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 297 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8439 (pp20) cc_final: 0.7790 (pp20) REVERT: A 53 ARG cc_start: 0.8696 (tmm-80) cc_final: 0.8165 (tmm-80) REVERT: A 108 ASN cc_start: 0.9293 (t0) cc_final: 0.9066 (t0) REVERT: D 33 ARG cc_start: 0.8758 (ttm-80) cc_final: 0.8092 (tpp80) REVERT: E 73 GLU cc_start: 0.8688 (tt0) cc_final: 0.8438 (tt0) REVERT: E 77 ASP cc_start: 0.8239 (m-30) cc_final: 0.8024 (m-30) REVERT: E 90 MET cc_start: 0.8089 (mmt) cc_final: 0.7764 (mmp) REVERT: E 120 MET cc_start: 0.8854 (mmm) cc_final: 0.8275 (mmm) REVERT: F 84 MET cc_start: 0.8073 (tpp) cc_final: 0.7826 (tpp) REVERT: F 92 ARG cc_start: 0.8769 (ttp80) cc_final: 0.8238 (ttp80) REVERT: H 47 GLN cc_start: 0.8757 (tt0) cc_final: 0.8491 (tm-30) REVERT: H 85 LYS cc_start: 0.9364 (mtmm) cc_final: 0.9131 (mtmm) REVERT: H 116 LYS cc_start: 0.9086 (mmtt) cc_final: 0.8714 (mmtp) REVERT: K 18 ILE cc_start: 0.8665 (mm) cc_final: 0.8418 (mm) REVERT: K 64 TYR cc_start: 0.8404 (t80) cc_final: 0.8194 (t80) REVERT: L 63 LYS cc_start: 0.7626 (tptt) cc_final: 0.7305 (tppt) REVERT: C 73 ASN cc_start: 0.9416 (t0) cc_final: 0.9124 (t0) REVERT: C 90 ASP cc_start: 0.8411 (t70) cc_final: 0.8101 (t0) REVERT: G 84 GLN cc_start: 0.8966 (tp-100) cc_final: 0.8227 (tp-100) REVERT: G 104 GLN cc_start: 0.8664 (tt0) cc_final: 0.7756 (tm-30) outliers start: 40 outliers final: 31 residues processed: 312 average time/residue: 0.2959 time to fit residues: 127.1000 Evaluate side-chains 313 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 282 time to evaluate : 1.155 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 98 VAL Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain L residue 54 ILE Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 55 LEU Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 8.9990 chunk 1 optimal weight: 1.9990 chunk 88 optimal weight: 0.9990 chunk 49 optimal weight: 0.8980 chunk 101 optimal weight: 20.0000 chunk 82 optimal weight: 0.0980 chunk 0 optimal weight: 20.0000 chunk 60 optimal weight: 5.9990 chunk 106 optimal weight: 0.6980 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 0.9980 overall best weight: 0.7382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN E 85 GLN ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 38 ASN G 68 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8316 moved from start: 0.2004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 14855 Z= 0.194 Angle : 0.634 11.022 21334 Z= 0.359 Chirality : 0.036 0.182 2418 Planarity : 0.004 0.034 1690 Dihedral : 29.740 154.698 4321 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 14.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 3.38 % Allowed : 26.22 % Favored : 70.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 1.00 (0.27), residues: 987 helix: 1.57 (0.21), residues: 627 sheet: 0.79 (1.09), residues: 24 loop : -1.09 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 77 HIS 0.003 0.001 HIS E 113 PHE 0.017 0.001 PHE K 40 TYR 0.049 0.002 TYR B 88 ARG 0.006 0.000 ARG F 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 298 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 59 LYS cc_start: 0.9130 (tppt) cc_final: 0.8908 (tppt) REVERT: D 33 ARG cc_start: 0.8710 (ttm-80) cc_final: 0.8171 (tpp80) REVERT: E 73 GLU cc_start: 0.8697 (tt0) cc_final: 0.8404 (tt0) REVERT: E 77 ASP cc_start: 0.8138 (m-30) cc_final: 0.7920 (m-30) REVERT: E 90 MET cc_start: 0.8094 (mmt) cc_final: 0.7755 (mmp) REVERT: E 120 MET cc_start: 0.8920 (mmm) cc_final: 0.8247 (mmm) REVERT: F 35 ARG cc_start: 0.9249 (ttm-80) cc_final: 0.8912 (ttm110) REVERT: F 84 MET cc_start: 0.8024 (tpp) cc_final: 0.7792 (tpp) REVERT: F 92 ARG cc_start: 0.8695 (ttp80) cc_final: 0.8244 (ttp80) REVERT: H 47 GLN cc_start: 0.8727 (tt0) cc_final: 0.8457 (tm-30) REVERT: H 71 GLU cc_start: 0.8536 (tm-30) cc_final: 0.8295 (tm-30) REVERT: H 116 LYS cc_start: 0.9041 (mmtt) cc_final: 0.8693 (mmtp) REVERT: L 32 HIS cc_start: 0.8717 (OUTLIER) cc_final: 0.8246 (m-70) REVERT: L 63 LYS cc_start: 0.7633 (tptt) cc_final: 0.7289 (tppt) REVERT: C 73 ASN cc_start: 0.9358 (t0) cc_final: 0.9064 (t0) REVERT: C 90 ASP cc_start: 0.8400 (t70) cc_final: 0.8106 (t0) REVERT: G 84 GLN cc_start: 0.8930 (tp-100) cc_final: 0.8084 (tp-100) outliers start: 29 outliers final: 18 residues processed: 306 average time/residue: 0.3008 time to fit residues: 126.6634 Evaluate side-chains 305 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 286 time to evaluate : 1.483 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 1.9990 chunk 23 optimal weight: 3.9990 chunk 69 optimal weight: 6.9990 chunk 29 optimal weight: 4.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 9 optimal weight: 6.9990 chunk 39 optimal weight: 0.7980 chunk 62 optimal weight: 7.9990 chunk 114 optimal weight: 4.9990 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8383 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.064 14855 Z= 0.330 Angle : 0.680 10.838 21334 Z= 0.385 Chirality : 0.039 0.193 2418 Planarity : 0.004 0.044 1690 Dihedral : 29.922 154.107 4321 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.01 % Allowed : 26.22 % Favored : 68.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.79 (0.26), residues: 987 helix: 1.40 (0.21), residues: 626 sheet: 0.83 (1.07), residues: 23 loop : -1.16 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP K 77 HIS 0.005 0.001 HIS F 75 PHE 0.017 0.002 PHE A 104 TYR 0.052 0.002 TYR B 88 ARG 0.010 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 289 time to evaluate : 1.111 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8532 (pp20) cc_final: 0.7759 (pp20) REVERT: A 53 ARG cc_start: 0.8757 (tmm-80) cc_final: 0.8263 (tmm-80) REVERT: A 64 LYS cc_start: 0.9250 (tppt) cc_final: 0.8986 (tppp) REVERT: B 88 TYR cc_start: 0.8889 (m-80) cc_final: 0.8493 (m-80) REVERT: D 83 TYR cc_start: 0.7970 (m-10) cc_final: 0.7417 (m-10) REVERT: D 105 GLU cc_start: 0.7867 (OUTLIER) cc_final: 0.7519 (mm-30) REVERT: E 73 GLU cc_start: 0.8730 (tt0) cc_final: 0.8428 (tt0) REVERT: E 77 ASP cc_start: 0.8113 (m-30) cc_final: 0.7902 (m-30) REVERT: E 90 MET cc_start: 0.8093 (mmt) cc_final: 0.7779 (mmp) REVERT: E 120 MET cc_start: 0.8909 (mmm) cc_final: 0.8228 (mmm) REVERT: E 125 GLN cc_start: 0.9335 (OUTLIER) cc_final: 0.9087 (mp10) REVERT: F 84 MET cc_start: 0.8087 (tpp) cc_final: 0.7878 (tpp) REVERT: F 92 ARG cc_start: 0.8774 (ttp80) cc_final: 0.8261 (ttp80) REVERT: H 47 GLN cc_start: 0.8760 (tt0) cc_final: 0.8474 (tm-30) REVERT: H 116 LYS cc_start: 0.9095 (mmtt) cc_final: 0.8685 (mmtp) REVERT: L 32 HIS cc_start: 0.8688 (OUTLIER) cc_final: 0.8122 (m-70) REVERT: C 90 ASP cc_start: 0.8396 (t70) cc_final: 0.8015 (t0) outliers start: 43 outliers final: 32 residues processed: 307 average time/residue: 0.3193 time to fit residues: 133.4296 Evaluate side-chains 315 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 280 time to evaluate : 1.824 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 107 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 1.9990 chunk 67 optimal weight: 8.9990 chunk 86 optimal weight: 5.9990 chunk 100 optimal weight: 0.0870 chunk 66 optimal weight: 10.0000 chunk 118 optimal weight: 4.9990 chunk 74 optimal weight: 6.9990 chunk 72 optimal weight: 5.9990 chunk 54 optimal weight: 7.9990 chunk 73 optimal weight: 5.9990 chunk 47 optimal weight: 0.9980 overall best weight: 2.8164 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8387 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 14855 Z= 0.310 Angle : 0.684 10.608 21334 Z= 0.385 Chirality : 0.039 0.173 2418 Planarity : 0.004 0.059 1690 Dihedral : 30.018 153.346 4321 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.24 % Allowed : 26.69 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.26), residues: 987 helix: 1.37 (0.21), residues: 626 sheet: 0.68 (1.07), residues: 23 loop : -1.14 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP K 77 HIS 0.004 0.001 HIS F 75 PHE 0.017 0.002 PHE E 78 TYR 0.038 0.002 TYR B 88 ARG 0.014 0.001 ARG F 67 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 340 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 295 time to evaluate : 1.101 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 105 GLU cc_start: 0.7930 (OUTLIER) cc_final: 0.7512 (tm-30) REVERT: D 109 HIS cc_start: 0.8210 (m-70) cc_final: 0.7753 (m170) REVERT: D 116 LYS cc_start: 0.9294 (OUTLIER) cc_final: 0.8900 (ptmt) REVERT: E 73 GLU cc_start: 0.8758 (OUTLIER) cc_final: 0.8438 (tt0) REVERT: E 120 MET cc_start: 0.8941 (mmm) cc_final: 0.8271 (mmm) REVERT: E 125 GLN cc_start: 0.9307 (OUTLIER) cc_final: 0.9096 (mp10) REVERT: F 84 MET cc_start: 0.8146 (tpp) cc_final: 0.7881 (tpp) REVERT: F 92 ARG cc_start: 0.8739 (ttp80) cc_final: 0.8397 (ttp80) REVERT: H 47 GLN cc_start: 0.8741 (tt0) cc_final: 0.8470 (tm-30) REVERT: L 32 HIS cc_start: 0.8755 (OUTLIER) cc_final: 0.8228 (m-70) REVERT: L 63 LYS cc_start: 0.7832 (tptt) cc_final: 0.7616 (tppt) REVERT: C 90 ASP cc_start: 0.8415 (t70) cc_final: 0.8109 (t0) outliers start: 45 outliers final: 34 residues processed: 315 average time/residue: 0.3189 time to fit residues: 137.3278 Evaluate side-chains 319 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 280 time to evaluate : 1.057 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain B residue 97 LEU Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 105 GLU Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 107 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 6.9990 chunk 35 optimal weight: 9.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 80 optimal weight: 7.9990 chunk 58 optimal weight: 6.9990 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 4.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 76 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8403 moved from start: 0.2734 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.048 14855 Z= 0.339 Angle : 0.707 10.737 21334 Z= 0.398 Chirality : 0.040 0.241 2418 Planarity : 0.004 0.039 1690 Dihedral : 30.148 153.371 4321 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 20.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.26 % Favored : 95.74 % Rotamer: Outliers : 5.24 % Allowed : 26.92 % Favored : 67.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.62 (0.26), residues: 987 helix: 1.27 (0.20), residues: 626 sheet: 0.61 (1.05), residues: 23 loop : -1.21 (0.32), residues: 338 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP K 77 HIS 0.010 0.002 HIS H 49 PHE 0.019 0.002 PHE A 104 TYR 0.031 0.003 TYR B 98 ARG 0.005 0.001 ARG F 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 326 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 281 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8767 (tmm-80) cc_final: 0.8276 (tmm-80) REVERT: B 59 LYS cc_start: 0.9287 (tppt) cc_final: 0.8536 (tptp) REVERT: B 88 TYR cc_start: 0.8820 (m-80) cc_final: 0.8341 (m-80) REVERT: D 83 TYR cc_start: 0.7857 (m-10) cc_final: 0.7297 (m-10) REVERT: D 116 LYS cc_start: 0.9306 (OUTLIER) cc_final: 0.8915 (ptmt) REVERT: E 120 MET cc_start: 0.8960 (mmm) cc_final: 0.8274 (mmm) REVERT: E 125 GLN cc_start: 0.9238 (OUTLIER) cc_final: 0.9027 (mp10) REVERT: F 84 MET cc_start: 0.8182 (tpp) cc_final: 0.7949 (tpp) REVERT: F 92 ARG cc_start: 0.8795 (ttp80) cc_final: 0.8362 (ttp80) REVERT: H 47 GLN cc_start: 0.8799 (tt0) cc_final: 0.8559 (tm-30) REVERT: L 63 LYS cc_start: 0.7744 (tptt) cc_final: 0.7541 (tppt) REVERT: C 63 LEU cc_start: 0.9488 (OUTLIER) cc_final: 0.9180 (mm) REVERT: C 90 ASP cc_start: 0.8377 (t70) cc_final: 0.8050 (t0) outliers start: 45 outliers final: 38 residues processed: 304 average time/residue: 0.3020 time to fit residues: 126.0812 Evaluate side-chains 318 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 277 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 51 ASP Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 70 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 98 VAL Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 107 CYS Chi-restraints excluded: chain C residue 13 SER Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 58 LEU Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 74 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.5980 chunk 110 optimal weight: 6.9990 chunk 113 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 48 optimal weight: 0.0970 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 0.8980 chunk 72 optimal weight: 5.9990 chunk 116 optimal weight: 0.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 49 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8344 moved from start: 0.2639 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14855 Z= 0.219 Angle : 0.686 10.722 21334 Z= 0.382 Chirality : 0.038 0.248 2418 Planarity : 0.004 0.044 1690 Dihedral : 30.006 154.697 4321 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 17.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.85 % Allowed : 29.02 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 987 helix: 1.35 (0.21), residues: 625 sheet: 0.75 (1.08), residues: 23 loop : -1.11 (0.33), residues: 339 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.043 0.003 TRP K 77 HIS 0.009 0.001 HIS H 49 PHE 0.015 0.001 PHE A 104 TYR 0.026 0.002 TYR B 88 ARG 0.007 0.001 ARG L 139 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 328 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 295 time to evaluate : 1.054 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 53 ARG cc_start: 0.8731 (tmm-80) cc_final: 0.8254 (tmm-80) REVERT: A 93 GLN cc_start: 0.8901 (tt0) cc_final: 0.8654 (tt0) REVERT: B 59 LYS cc_start: 0.9201 (tppt) cc_final: 0.8423 (tptt) REVERT: D 33 ARG cc_start: 0.8654 (ttm-80) cc_final: 0.8195 (tpp80) REVERT: D 116 LYS cc_start: 0.9249 (OUTLIER) cc_final: 0.8772 (ptmt) REVERT: E 120 MET cc_start: 0.8983 (mmm) cc_final: 0.8250 (mmm) REVERT: E 125 GLN cc_start: 0.9246 (OUTLIER) cc_final: 0.9011 (mp10) REVERT: F 84 MET cc_start: 0.8053 (tpp) cc_final: 0.7826 (tpp) REVERT: F 92 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8202 (ttp80) REVERT: H 47 GLN cc_start: 0.8778 (tt0) cc_final: 0.8456 (tm-30) REVERT: L 63 LYS cc_start: 0.7756 (tptt) cc_final: 0.7524 (tppt) REVERT: C 15 LYS cc_start: 0.6488 (pttt) cc_final: 0.6246 (pttm) REVERT: C 90 ASP cc_start: 0.8452 (t70) cc_final: 0.8130 (t0) outliers start: 33 outliers final: 29 residues processed: 308 average time/residue: 0.3052 time to fit residues: 128.7786 Evaluate side-chains 312 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 281 time to evaluate : 1.174 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 93 GLN Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 107 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 94 ASN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 7.9990 chunk 55 optimal weight: 7.9990 chunk 81 optimal weight: 7.9990 chunk 122 optimal weight: 3.9990 chunk 112 optimal weight: 0.0070 chunk 97 optimal weight: 2.9990 chunk 10 optimal weight: 0.6980 chunk 75 optimal weight: 5.9990 chunk 59 optimal weight: 6.9990 chunk 77 optimal weight: 6.9990 chunk 103 optimal weight: 0.9990 overall best weight: 1.7404 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8358 moved from start: 0.2745 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 14855 Z= 0.254 Angle : 0.711 20.162 21334 Z= 0.393 Chirality : 0.038 0.239 2418 Planarity : 0.004 0.042 1690 Dihedral : 30.017 155.374 4321 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 18.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer: Outliers : 4.31 % Allowed : 29.72 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 987 helix: 1.31 (0.21), residues: 623 sheet: 0.87 (0.96), residues: 28 loop : -1.16 (0.33), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 77 HIS 0.008 0.001 HIS H 49 PHE 0.013 0.001 PHE A 104 TYR 0.026 0.002 TYR B 88 ARG 0.006 0.000 ARG F 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1974 Ramachandran restraints generated. 987 Oldfield, 0 Emsley, 987 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 322 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 285 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.8080 (m-80) cc_final: 0.7740 (m-80) REVERT: A 93 GLN cc_start: 0.8950 (tt0) cc_final: 0.8651 (tt0) REVERT: B 59 LYS cc_start: 0.9195 (tppt) cc_final: 0.8431 (tptt) REVERT: D 33 ARG cc_start: 0.8653 (ttm-80) cc_final: 0.8179 (tpp80) REVERT: D 67 ASN cc_start: 0.8886 (OUTLIER) cc_final: 0.8670 (t0) REVERT: D 105 GLU cc_start: 0.7888 (tm-30) cc_final: 0.7443 (tm-30) REVERT: D 116 LYS cc_start: 0.9243 (OUTLIER) cc_final: 0.8764 (ptmt) REVERT: E 120 MET cc_start: 0.8986 (mmm) cc_final: 0.8242 (mmm) REVERT: F 67 ARG cc_start: 0.8094 (mmp-170) cc_final: 0.7738 (ttm-80) REVERT: F 84 MET cc_start: 0.8128 (tpp) cc_final: 0.7857 (tpp) REVERT: F 92 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8110 (ttp80) REVERT: H 47 GLN cc_start: 0.8785 (tt0) cc_final: 0.8507 (tm-30) REVERT: L 63 LYS cc_start: 0.7703 (tptt) cc_final: 0.7481 (tppt) REVERT: C 15 LYS cc_start: 0.6917 (pttt) cc_final: 0.6559 (pttm) REVERT: C 63 LEU cc_start: 0.9478 (OUTLIER) cc_final: 0.9206 (mm) REVERT: C 90 ASP cc_start: 0.8303 (t70) cc_final: 0.7997 (t0) outliers start: 37 outliers final: 31 residues processed: 302 average time/residue: 0.3033 time to fit residues: 125.4917 Evaluate side-chains 315 residues out of total 856 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 281 time to evaluate : 1.131 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 86 SER Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 54 THR Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 63 GLU Chi-restraints excluded: chain B residue 90 LEU Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain D residue 67 ASN Chi-restraints excluded: chain D residue 116 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 96 CYS Chi-restraints excluded: chain F residue 59 LYS Chi-restraints excluded: chain F residue 63 GLU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain L residue 86 LEU Chi-restraints excluded: chain L residue 107 CYS Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 63 LEU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 83 LEU Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 61 GLU Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 64 GLU Chi-restraints excluded: chain G residue 94 ASN Chi-restraints excluded: chain G residue 108 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 0.6980 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 97 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 12 optimal weight: 6.9990 chunk 18 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 5 optimal weight: 3.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 109 HIS ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 85 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 125 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 92 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.080951 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3107 r_free = 0.3107 target = 0.057540 restraints weight = 61807.238| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 59)----------------| | r_work = 0.3142 r_free = 0.3142 target = 0.059048 restraints weight = 32456.200| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 56)----------------| | r_work = 0.3165 r_free = 0.3165 target = 0.060077 restraints weight = 22359.264| |-----------------------------------------------------------------------------| r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 8 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8375 moved from start: 0.2773 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.065 14855 Z= 0.241 Angle : 0.712 19.247 21334 Z= 0.393 Chirality : 0.038 0.243 2418 Planarity : 0.004 0.042 1690 Dihedral : 30.010 155.127 4321 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 18.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 3.85 % Allowed : 30.19 % Favored : 65.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.22 % 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: 0.65 (0.27), residues: 987 helix: 1.27 (0.21), residues: 623 sheet: 0.97 (1.06), residues: 23 loop : -1.16 (0.33), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP K 77 HIS 0.007 0.001 HIS L 75 PHE 0.014 0.002 PHE A 104 TYR 0.058 0.003 TYR D 83 ARG 0.006 0.001 ARG H 79 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2986.30 seconds wall clock time: 56 minutes 8.89 seconds (3368.89 seconds total)