Starting phenix.real_space_refine on Fri Mar 15 22:15:28 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/03_2024/8cbq_16549_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/03_2024/8cbq_16549.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/03_2024/8cbq_16549.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/03_2024/8cbq_16549.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/03_2024/8cbq_16549_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8cbq_16549/03_2024/8cbq_16549_updated.pdb" } resolution = 4.0 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= 0.001 sd= 0.021 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: 5 Type Number sf(0) Gaussians P 300 5.49 5 S 13 5.16 5 C 7231 2.51 5 N 2421 2.21 5 O 2994 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ASP 24": "OD1" <-> "OD2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 110": "OE1" <-> "OE2" Residue "F ARG 17": "NH1" <-> "NH2" Residue "F ARG 19": "NH1" <-> "NH2" Residue "F ARG 23": "NH1" <-> "NH2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G GLU 64": "OE1" <-> "OE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 110": "OE1" <-> "OE2" Residue "K ARG 3": "NH1" <-> "NH2" Residue "K GLU 66": "OE1" <-> "OE2" Residue "K ARG 74": "NH1" <-> "NH2" Residue "A ARG 134": "NH1" <-> "NH2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "E ARG 134": "NH1" <-> "NH2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 12959 Number of models: 1 Model: "" Number of chains: 11 Chain: "B" Number of atoms: 657 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 657 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "C" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "F" Number of atoms: 694 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 694 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 823 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 823 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "H" Number of atoms: 736 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 736 Classifications: {'peptide': 94} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "I" Number of atoms: 3055 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3055 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "J" Number of atoms: 3095 Number of conformers: 1 Conformer: "" Number of residues, atoms: 150, 3095 Classifications: {'DNA': 150} Link IDs: {'rna3p': 149} Chain: "K" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 710 Classifications: {'peptide': 86} Link IDs: {'PTRANS': 11, 'TRANS': 74} Chain breaks: 1 Chain: "A" Number of atoms: 829 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 829 Classifications: {'peptide': 100} Link IDs: {'PTRANS': 4, 'TRANS': 95} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Planarities with less than four sites: {'ML3:plan-1': 1} Unresolved non-hydrogen planarities: 1 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Time building chain proxies: 6.99, per 1000 atoms: 0.54 Number of scatterers: 12959 At special positions: 0 Unit cell: (135.792, 81.144, 120.888, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 13 16.00 P 300 15.00 O 2994 8.00 N 2421 7.00 C 7231 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: 5.77 Conformation dependent library (CDL) restraints added in 1.2 seconds 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1598 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 35 helices and 2 sheets defined 55.2% alpha, 1.4% beta 125 base pairs and 274 stacking pairs defined. Time for finding SS restraints: 7.62 Creating SS restraints... Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 31 through 41 removed outlier: 3.520A pdb=" N GLY B 41 " --> pdb=" O LEU B 37 " (cutoff:3.500A) Processing helix chain 'B' and resid 51 through 75 removed outlier: 3.791A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N LYS B 59 " --> pdb=" O ARG B 55 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 91 Processing helix chain 'C' and resid 17 through 21 Processing helix chain 'C' and resid 27 through 36 Processing helix chain 'C' and resid 47 through 72 removed outlier: 3.541A pdb=" N TYR C 57 " --> pdb=" O ALA C 53 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N GLU C 64 " --> pdb=" O ALA C 60 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'C' and resid 93 through 96 No H-bonds generated for 'chain 'C' and resid 93 through 96' Processing helix chain 'D' and resid 35 through 45 removed outlier: 3.957A pdb=" N GLN D 44 " --> pdb=" O LYS D 40 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N VAL D 45 " --> pdb=" O VAL D 41 " (cutoff:3.500A) Processing helix chain 'D' and resid 53 through 80 removed outlier: 3.735A pdb=" N ILE D 58 " --> pdb=" O LYS D 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU D 68 " --> pdb=" O ASN D 64 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N ARG D 76 " --> pdb=" O GLY D 72 " (cutoff:3.500A) Processing helix chain 'D' and resid 88 through 98 Processing helix chain 'D' and resid 103 through 121 removed outlier: 3.965A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA D 114 " --> pdb=" O GLU D 110 " (cutoff:3.500A) removed outlier: 3.525A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 28 Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 removed outlier: 3.944A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 3.788A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.749A pdb=" N LYS F 59 " --> pdb=" O ARG F 55 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 removed outlier: 3.515A pdb=" N ALA F 89 " --> pdb=" O ASP F 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 17 through 21 Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 47 through 72 removed outlier: 3.542A pdb=" N TYR G 57 " --> pdb=" O ALA G 53 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N GLU G 64 " --> pdb=" O ALA G 60 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 87 Processing helix chain 'G' and resid 93 through 96 No H-bonds generated for 'chain 'G' and resid 93 through 96' Processing helix chain 'H' and resid 35 through 45 removed outlier: 3.957A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) removed outlier: 3.551A pdb=" N VAL H 45 " --> pdb=" O VAL H 41 " (cutoff:3.500A) Processing helix chain 'H' and resid 53 through 80 removed outlier: 3.733A pdb=" N ILE H 58 " --> pdb=" O LYS H 54 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N GLU H 68 " --> pdb=" O ASN H 64 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N ARG H 76 " --> pdb=" O GLY H 72 " (cutoff:3.500A) Processing helix chain 'H' and resid 88 through 98 Processing helix chain 'H' and resid 103 through 121 removed outlier: 3.966A pdb=" N SER H 109 " --> pdb=" O LYS H 105 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ALA H 114 " --> pdb=" O GLU H 110 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) Processing helix chain 'K' and resid 80 through 86 removed outlier: 5.136A pdb=" N ASP K 85 " --> pdb=" O LEU K 81 " (cutoff:3.500A) removed outlier: 3.675A pdb=" N ASN K 86 " --> pdb=" O TRP K 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 45 through 54 Processing helix chain 'A' and resid 64 through 74 Processing helix chain 'A' and resid 86 through 113 removed outlier: 3.505A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N ASP A 106 " --> pdb=" O ALA A 102 " (cutoff:3.500A) Processing helix chain 'A' and resid 121 through 130 Processing helix chain 'E' and resid 45 through 54 removed outlier: 3.622A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.683A pdb=" N ALA E 98 " --> pdb=" O GLU E 94 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N ALA E 102 " --> pdb=" O ALA E 98 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.544A pdb=" N LEU E 126 " --> pdb=" O LYS E 122 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'K' and resid 10 through 14 removed outlier: 3.685A pdb=" N ILE K 11 " --> pdb=" O ALA K 23 " (cutoff:3.500A) removed outlier: 4.098A pdb=" N ALA K 23 " --> pdb=" O ILE K 11 " (cutoff:3.500A) removed outlier: 3.763A pdb=" N ALA K 13 " --> pdb=" O TRP K 21 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'K' and resid 42 through 44 removed outlier: 3.539A pdb=" N PHE K 44 " --> pdb=" O GLU K 49 " (cutoff:3.500A) removed outlier: 4.529A pdb=" N GLU K 49 " --> pdb=" O PHE K 44 " (cutoff:3.500A) 295 hydrogen bonds defined for protein. 879 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 307 hydrogen bonds 602 hydrogen bond angles 0 basepair planarities 125 basepair parallelities 274 stacking parallelities Total time for adding SS restraints: 4.44 Time building geometry restraints manager: 6.17 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2280 1.33 - 1.45: 4689 1.45 - 1.57: 6221 1.57 - 1.69: 598 1.69 - 1.81: 26 Bond restraints: 13814 Sorted by residual: bond pdb=" SG ML3 A 36 " pdb=" CD ML3 A 36 " ideal model delta sigma weight residual 1.815 1.757 0.058 2.00e-02 2.50e+03 8.32e+00 bond pdb=" CB ML3 A 36 " pdb=" SG ML3 A 36 " ideal model delta sigma weight residual 1.817 1.761 0.056 2.00e-02 2.50e+03 7.73e+00 bond pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " ideal model delta sigma weight residual 1.422 1.499 -0.077 3.00e-02 1.11e+03 6.55e+00 bond pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.15e+00 bond pdb=" CB ARG F 78 " pdb=" CG ARG F 78 " ideal model delta sigma weight residual 1.520 1.474 0.046 3.00e-02 1.11e+03 2.40e+00 ... (remaining 13809 not shown) Histogram of bond angle deviations from ideal: 98.53 - 105.61: 1537 105.61 - 112.69: 7638 112.69 - 119.77: 4646 119.77 - 126.85: 5280 126.85 - 133.93: 842 Bond angle restraints: 19943 Sorted by residual: angle pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sigma weight residual 120.20 125.91 -5.71 1.50e+00 4.44e-01 1.45e+01 angle pdb=" C SER K 62 " pdb=" N GLU K 63 " pdb=" CA GLU K 63 " ideal model delta sigma weight residual 122.61 128.15 -5.54 1.56e+00 4.11e-01 1.26e+01 angle pdb=" C3' DT J 54 " pdb=" O3' DT J 54 " pdb=" P DC J 55 " ideal model delta sigma weight residual 120.20 125.03 -4.83 1.50e+00 4.44e-01 1.04e+01 angle pdb=" C3' DT I 34 " pdb=" O3' DT I 34 " pdb=" P DC I 35 " ideal model delta sigma weight residual 120.20 125.00 -4.80 1.50e+00 4.44e-01 1.03e+01 angle pdb=" CA GLU K 63 " pdb=" CB GLU K 63 " pdb=" CG GLU K 63 " ideal model delta sigma weight residual 114.10 119.63 -5.53 2.00e+00 2.50e-01 7.64e+00 ... (remaining 19938 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.28: 6151 34.28 - 68.56: 1376 68.56 - 102.84: 15 102.84 - 137.12: 2 137.12 - 171.39: 1 Dihedral angle restraints: 7545 sinusoidal: 5071 harmonic: 2474 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 160.06 19.94 0 5.00e+00 4.00e-02 1.59e+01 dihedral pdb=" C4' DG I 20 " pdb=" C3' DG I 20 " pdb=" O3' DG I 20 " pdb=" P DC I 21 " ideal model delta sinusoidal sigma weight residual 220.00 48.61 171.39 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" CA LEU K 53 " pdb=" C LEU K 53 " pdb=" N GLY K 54 " pdb=" CA GLY K 54 " ideal model delta harmonic sigma weight residual 180.00 161.70 18.30 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 7542 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1240 0.035 - 0.070: 801 0.070 - 0.105: 162 0.105 - 0.140: 41 0.140 - 0.175: 9 Chirality restraints: 2253 Sorted by residual: chirality pdb=" P DC I 21 " pdb=" OP1 DC I 21 " pdb=" OP2 DC I 21 " pdb=" O5' DC I 21 " both_signs ideal model delta sigma weight residual True 2.35 -2.52 -0.18 2.00e-01 2.50e+01 7.68e-01 chirality pdb=" CA LEU A 65 " pdb=" N LEU A 65 " pdb=" C LEU A 65 " pdb=" CB LEU A 65 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.06e-01 chirality pdb=" CB VAL K 90 " pdb=" CA VAL K 90 " pdb=" CG1 VAL K 90 " pdb=" CG2 VAL K 90 " both_signs ideal model delta sigma weight residual False -2.63 -2.48 -0.15 2.00e-01 2.50e+01 5.87e-01 ... (remaining 2250 not shown) Planarity restraints: 1485 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LEU E 65 " -0.046 5.00e-02 4.00e+02 6.91e-02 7.63e+00 pdb=" N PRO E 66 " 0.119 5.00e-02 4.00e+02 pdb=" CA PRO E 66 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO E 66 " -0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.045 5.00e-02 4.00e+02 6.72e-02 7.22e+00 pdb=" N PRO C 80 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.045 5.00e-02 4.00e+02 6.68e-02 7.15e+00 pdb=" N PRO G 80 " 0.116 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.037 5.00e-02 4.00e+02 ... (remaining 1482 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 3129 2.81 - 3.33: 10190 3.33 - 3.85: 23981 3.85 - 4.38: 31450 4.38 - 4.90: 43650 Nonbonded interactions: 112400 Sorted by model distance: nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.284 2.440 nonbonded pdb=" NH2 ARG H 83 " pdb=" OP2 DG J -33 " model vdw 2.330 2.520 nonbonded pdb=" O2 DC I -38 " pdb=" N2 DG J 38 " model vdw 2.359 2.520 nonbonded pdb=" NH2 ARG D 83 " pdb=" OP2 DA I -33 " model vdw 2.361 2.520 nonbonded pdb=" ND2 ASN B 25 " pdb=" OE1 GLU A 73 " model vdw 2.364 2.520 ... (remaining 112395 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' and resid 38 through 134) selection = chain 'E' } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' 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: 0.490 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: 2.770 Check model and map are aligned: 0.190 Set scattering table: 0.120 Process input model: 41.200 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 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:2.550 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 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 : 0.008 0.077 13814 Z= 0.479 Angle : 0.724 7.992 19943 Z= 0.428 Chirality : 0.044 0.175 2253 Planarity : 0.006 0.069 1485 Dihedral : 26.198 171.394 5947 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 3.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 1.82 % Allowed : 7.99 % Favored : 90.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.85 (0.18), residues: 831 helix: -4.46 (0.09), residues: 530 sheet: -4.09 (0.99), residues: 17 loop : -2.11 (0.29), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.002 TRP K 82 HIS 0.004 0.001 HIS K 20 PHE 0.013 0.002 PHE G 25 TYR 0.012 0.002 TYR B 72 ARG 0.004 0.001 ARG B 55 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 473 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 460 time to evaluate : 0.971 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 22 LEU cc_start: 0.8026 (mt) cc_final: 0.7415 (mt) REVERT: B 44 LYS cc_start: 0.8631 (tttt) cc_final: 0.8380 (mtmt) REVERT: B 53 GLU cc_start: 0.8302 (tp30) cc_final: 0.7386 (tp30) REVERT: C 32 ARG cc_start: 0.6931 (ttp80) cc_final: 0.6706 (ttp80) REVERT: C 62 ILE cc_start: 0.9381 (mt) cc_final: 0.9068 (mm) REVERT: C 68 ASN cc_start: 0.8832 (m-40) cc_final: 0.8231 (m-40) REVERT: C 83 LEU cc_start: 0.9336 (mt) cc_final: 0.8972 (mt) REVERT: C 87 VAL cc_start: 0.9403 (m) cc_final: 0.9124 (m) REVERT: C 110 ASN cc_start: 0.7942 (t0) cc_final: 0.7375 (t0) REVERT: D 49 THR cc_start: 0.8903 (m) cc_final: 0.8702 (m) REVERT: D 59 MET cc_start: 0.8965 (mmm) cc_final: 0.8372 (tpp) REVERT: D 110 GLU cc_start: 0.7508 (mt-10) cc_final: 0.7295 (mt-10) REVERT: F 25 ASN cc_start: 0.8290 (m-40) cc_final: 0.7814 (m110) REVERT: F 34 ILE cc_start: 0.8857 (mt) cc_final: 0.8633 (mm) REVERT: F 39 ARG cc_start: 0.9036 (mmt-90) cc_final: 0.8787 (mmt180) REVERT: F 75 HIS cc_start: 0.7838 (t70) cc_final: 0.7611 (t70) REVERT: F 88 TYR cc_start: 0.8657 (m-10) cc_final: 0.8428 (m-80) REVERT: G 20 ARG cc_start: 0.7759 (mtt90) cc_final: 0.7420 (mtt90) REVERT: G 57 TYR cc_start: 0.8128 (t80) cc_final: 0.7804 (t80) REVERT: G 110 ASN cc_start: 0.8643 (t0) cc_final: 0.8246 (t0) REVERT: H 110 GLU cc_start: 0.8610 (mt-10) cc_final: 0.8303 (mt-10) REVERT: H 113 LYS cc_start: 0.8742 (mtmt) cc_final: 0.8240 (tppt) REVERT: K 40 LEU cc_start: 0.2756 (OUTLIER) cc_final: 0.2391 (tp) REVERT: A 46 VAL cc_start: 0.9040 (OUTLIER) cc_final: 0.8817 (t) REVERT: A 49 ARG cc_start: 0.7748 (ttp-170) cc_final: 0.7531 (mtp-110) REVERT: A 51 ILE cc_start: 0.8963 (mt) cc_final: 0.8737 (mt) REVERT: A 55 GLN cc_start: 0.8344 (mt0) cc_final: 0.7895 (mt0) REVERT: A 62 ILE cc_start: 0.8573 (mt) cc_final: 0.8240 (mt) REVERT: A 76 GLN cc_start: 0.8258 (mm110) cc_final: 0.7928 (mm-40) REVERT: A 84 PHE cc_start: 0.8420 (m-80) cc_final: 0.7629 (m-80) REVERT: A 99 TYR cc_start: 0.8300 (t80) cc_final: 0.8097 (t80) REVERT: A 120 MET cc_start: 0.7238 (mtp) cc_final: 0.6922 (mmm) REVERT: E 60 LEU cc_start: 0.8200 (mt) cc_final: 0.7431 (mp) REVERT: E 71 VAL cc_start: 0.9446 (t) cc_final: 0.9191 (t) REVERT: E 74 ILE cc_start: 0.9177 (mt) cc_final: 0.8909 (tt) REVERT: E 117 VAL cc_start: 0.9086 (t) cc_final: 0.8853 (p) REVERT: E 118 THR cc_start: 0.8515 (m) cc_final: 0.7808 (p) REVERT: E 119 ILE cc_start: 0.8810 (pt) cc_final: 0.7799 (pt) REVERT: E 120 MET cc_start: 0.7605 (mtt) cc_final: 0.6556 (mpp) outliers start: 13 outliers final: 6 residues processed: 468 average time/residue: 0.3688 time to fit residues: 221.4911 Evaluate side-chains 374 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 366 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 93 optimal weight: 0.6980 chunk 84 optimal weight: 8.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 0.4980 chunk 56 optimal weight: 2.9990 chunk 44 optimal weight: 0.1980 chunk 87 optimal weight: 3.9990 chunk 33 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 64 optimal weight: 1.9990 chunk 100 optimal weight: 0.0470 overall best weight: 0.4278 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN B 64 ASN ** D 46 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 18 HIS ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 89 ASN H 46 HIS H 92 GLN K 64 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 108 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7610 moved from start: 0.3893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 13814 Z= 0.232 Angle : 0.687 6.886 19943 Z= 0.394 Chirality : 0.038 0.206 2253 Planarity : 0.007 0.068 1485 Dihedral : 29.785 156.620 4250 Min Nonbonded Distance : 2.031 Molprobity Statistics. All-atom Clashscore : 15.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 5.05 % Allowed : 22.44 % Favored : 72.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.82 (0.24), residues: 831 helix: -1.99 (0.18), residues: 522 sheet: -4.44 (1.25), residues: 10 loop : -1.18 (0.32), residues: 299 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 82 HIS 0.004 0.001 HIS E 113 PHE 0.020 0.002 PHE H 62 TYR 0.025 0.002 TYR B 88 ARG 0.017 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 396 time to evaluate : 0.959 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.9081 (m110) cc_final: 0.8752 (m110) REVERT: B 44 LYS cc_start: 0.9039 (tttt) cc_final: 0.8633 (mttp) REVERT: B 79 LYS cc_start: 0.8801 (mmtp) cc_final: 0.8478 (mmtm) REVERT: C 32 ARG cc_start: 0.7210 (ttp80) cc_final: 0.6959 (ttp80) REVERT: C 110 ASN cc_start: 0.8544 (t0) cc_final: 0.8051 (t0) REVERT: D 59 MET cc_start: 0.9473 (mmm) cc_final: 0.9026 (tpp) REVERT: D 64 ASN cc_start: 0.8638 (m110) cc_final: 0.8046 (m110) REVERT: D 110 GLU cc_start: 0.7674 (mt-10) cc_final: 0.7338 (mt-10) REVERT: F 25 ASN cc_start: 0.8646 (m-40) cc_final: 0.8196 (m-40) REVERT: F 39 ARG cc_start: 0.8865 (mmt-90) cc_final: 0.8431 (mmt180) REVERT: F 53 GLU cc_start: 0.7836 (tp30) cc_final: 0.7575 (tp30) REVERT: F 75 HIS cc_start: 0.8352 (t70) cc_final: 0.8014 (t70) REVERT: F 88 TYR cc_start: 0.9089 (m-10) cc_final: 0.8615 (m-80) REVERT: F 95 ARG cc_start: 0.8311 (mpp80) cc_final: 0.7971 (mtt90) REVERT: G 17 ARG cc_start: 0.7876 (mtm180) cc_final: 0.7489 (ptp-170) REVERT: G 32 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8498 (tmm-80) REVERT: G 68 ASN cc_start: 0.8138 (p0) cc_final: 0.7880 (p0) REVERT: G 81 ARG cc_start: 0.8285 (tpt90) cc_final: 0.8040 (tpt90) REVERT: G 92 GLU cc_start: 0.8015 (pm20) cc_final: 0.7277 (mp0) REVERT: G 110 ASN cc_start: 0.8699 (t0) cc_final: 0.8268 (t0) REVERT: G 112 GLN cc_start: 0.8565 (mm-40) cc_final: 0.8032 (mm110) REVERT: H 34 TYR cc_start: 0.8017 (m-80) cc_final: 0.7369 (m-10) REVERT: H 39 TYR cc_start: 0.8095 (t80) cc_final: 0.7843 (t80) REVERT: H 40 LYS cc_start: 0.8927 (tppt) cc_final: 0.8674 (tppt) REVERT: H 102 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8000 (mm-30) REVERT: K 40 LEU cc_start: 0.3879 (OUTLIER) cc_final: 0.3484 (tp) REVERT: A 55 GLN cc_start: 0.8886 (mt0) cc_final: 0.8412 (tt0) REVERT: A 56 LYS cc_start: 0.7942 (pttp) cc_final: 0.7476 (ptpp) REVERT: A 72 ARG cc_start: 0.8468 (mtt-85) cc_final: 0.8066 (mtt-85) REVERT: A 76 GLN cc_start: 0.8281 (mm110) cc_final: 0.7938 (mm-40) REVERT: A 79 LYS cc_start: 0.8888 (tptp) cc_final: 0.8489 (tptp) REVERT: A 129 ARG cc_start: 0.8491 (mmm-85) cc_final: 0.8194 (mmp80) REVERT: E 50 GLU cc_start: 0.7718 (pt0) cc_final: 0.7254 (pt0) REVERT: E 68 GLN cc_start: 0.7987 (tm-30) cc_final: 0.7606 (pp30) REVERT: E 71 VAL cc_start: 0.9239 (t) cc_final: 0.8941 (t) REVERT: E 117 VAL cc_start: 0.9264 (t) cc_final: 0.9063 (p) REVERT: E 119 ILE cc_start: 0.8877 (pt) cc_final: 0.7886 (pt) REVERT: E 120 MET cc_start: 0.6570 (mtt) cc_final: 0.6321 (mpp) outliers start: 36 outliers final: 24 residues processed: 415 average time/residue: 0.3399 time to fit residues: 182.6710 Evaluate side-chains 390 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 365 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 41 VAL Chi-restraints excluded: chain D residue 58 ILE Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 92 GLN Chi-restraints excluded: chain H residue 93 THR Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 40 LEU Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 56 optimal weight: 3.9990 chunk 31 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 68 optimal weight: 5.9990 chunk 27 optimal weight: 10.0000 chunk 100 optimal weight: 0.9980 chunk 109 optimal weight: 0.9990 chunk 89 optimal weight: 10.0000 chunk 34 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS G 73 ASN G 89 ASN H 106 HIS ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 85 GLN A 108 ASN ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.5023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13814 Z= 0.267 Angle : 0.681 13.631 19943 Z= 0.384 Chirality : 0.037 0.186 2253 Planarity : 0.006 0.057 1485 Dihedral : 29.627 152.027 4247 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.53 % Favored : 97.47 % Rotamer: Outliers : 7.57 % Allowed : 26.09 % Favored : 66.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.27), residues: 831 helix: -0.31 (0.21), residues: 513 sheet: -4.42 (1.20), residues: 10 loop : -0.86 (0.32), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.005 0.001 HIS G 31 PHE 0.013 0.002 PHE F 61 TYR 0.021 0.002 TYR F 51 ARG 0.010 0.001 ARG E 53 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 452 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 398 time to evaluate : 1.058 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: symmetry clash 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: symmetry clash 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: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8994 (m110) cc_final: 0.8726 (m-40) REVERT: B 39 ARG cc_start: 0.8948 (mmt-90) cc_final: 0.8650 (tpp-160) REVERT: B 63 GLU cc_start: 0.7854 (mt-10) cc_final: 0.7532 (mt-10) REVERT: B 79 LYS cc_start: 0.9111 (mmtp) cc_final: 0.8737 (mmmm) REVERT: B 82 THR cc_start: 0.8437 (p) cc_final: 0.8145 (t) REVERT: C 32 ARG cc_start: 0.7515 (ttp80) cc_final: 0.6900 (ttp-110) REVERT: C 89 ASN cc_start: 0.8714 (m110) cc_final: 0.8497 (m110) REVERT: C 95 LYS cc_start: 0.8641 (pttt) cc_final: 0.8269 (pttp) REVERT: C 110 ASN cc_start: 0.8847 (t0) cc_final: 0.8509 (t0) REVERT: D 59 MET cc_start: 0.9467 (mmm) cc_final: 0.9236 (tpp) REVERT: D 69 ARG cc_start: 0.8773 (mmm-85) cc_final: 0.8494 (mtp180) REVERT: D 110 GLU cc_start: 0.7734 (mt-10) cc_final: 0.7498 (mt-10) REVERT: F 75 HIS cc_start: 0.8424 (t70) cc_final: 0.7773 (t70) REVERT: F 79 LYS cc_start: 0.9060 (mmtm) cc_final: 0.8763 (mmtm) REVERT: F 88 TYR cc_start: 0.9203 (m-10) cc_final: 0.8639 (m-80) REVERT: F 95 ARG cc_start: 0.8396 (mpp80) cc_final: 0.8065 (mtt90) REVERT: G 58 LEU cc_start: 0.8820 (mt) cc_final: 0.8412 (mp) REVERT: G 68 ASN cc_start: 0.8257 (p0) cc_final: 0.8036 (p0) REVERT: G 78 ILE cc_start: 0.8798 (mt) cc_final: 0.8349 (mt) REVERT: G 81 ARG cc_start: 0.8631 (tpt90) cc_final: 0.8426 (tpt90) REVERT: H 34 TYR cc_start: 0.8187 (m-80) cc_final: 0.7833 (m-10) REVERT: H 40 LYS cc_start: 0.9326 (tppt) cc_final: 0.8840 (tppt) REVERT: H 102 GLU cc_start: 0.8336 (mm-30) cc_final: 0.7554 (mm-30) REVERT: A 70 LEU cc_start: 0.9224 (tt) cc_final: 0.8993 (tt) REVERT: A 79 LYS cc_start: 0.9058 (tptp) cc_final: 0.8738 (tptt) REVERT: E 39 HIS cc_start: 0.5213 (p-80) cc_final: 0.4984 (p-80) REVERT: E 52 ARG cc_start: 0.9044 (ttm110) cc_final: 0.8840 (ttm-80) REVERT: E 56 LYS cc_start: 0.7871 (mmtm) cc_final: 0.7647 (mmtm) REVERT: E 67 PHE cc_start: 0.8890 (t80) cc_final: 0.7934 (t80) REVERT: E 71 VAL cc_start: 0.9302 (t) cc_final: 0.8944 (t) REVERT: E 120 MET cc_start: 0.7286 (mtt) cc_final: 0.6888 (mpp) outliers start: 54 outliers final: 37 residues processed: 416 average time/residue: 0.3635 time to fit residues: 195.3150 Evaluate side-chains 403 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 366 time to evaluate : 0.790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 65 LEU Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 120 SER Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 42 LEU Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 75 SER Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 58 ILE Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 71 VAL Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 75 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 67 optimal weight: 4.9990 chunk 101 optimal weight: 0.9980 chunk 107 optimal weight: 0.9990 chunk 96 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 89 optimal weight: 0.0870 chunk 60 optimal weight: 3.9990 overall best weight: 0.6560 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN G 73 ASN H 92 GLN K 78 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7812 moved from start: 0.5627 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13814 Z= 0.223 Angle : 0.646 12.895 19943 Z= 0.365 Chirality : 0.036 0.208 2253 Planarity : 0.005 0.054 1485 Dihedral : 29.565 151.870 4243 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 16.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.31 % Allowed : 30.72 % Favored : 62.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.29 (0.28), residues: 831 helix: 0.37 (0.22), residues: 526 sheet: -3.99 (1.47), residues: 10 loop : -0.94 (0.33), residues: 295 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP K 82 HIS 0.003 0.001 HIS E 113 PHE 0.024 0.002 PHE B 61 TYR 0.019 0.002 TYR D 37 ARG 0.009 0.001 ARG H 89 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 390 time to evaluate : 0.980 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8949 (m110) cc_final: 0.8560 (m-40) REVERT: B 45 ARG cc_start: 0.8537 (ttp80) cc_final: 0.8332 (ttt90) REVERT: B 63 GLU cc_start: 0.7968 (mt-10) cc_final: 0.7552 (mt-10) REVERT: B 73 THR cc_start: 0.9302 (t) cc_final: 0.9080 (t) REVERT: B 79 LYS cc_start: 0.8995 (mmtp) cc_final: 0.8661 (mmmm) REVERT: B 85 ASP cc_start: 0.8125 (OUTLIER) cc_final: 0.7887 (m-30) REVERT: C 36 LYS cc_start: 0.8401 (pttm) cc_final: 0.8152 (pttm) REVERT: C 73 ASN cc_start: 0.8649 (m110) cc_final: 0.8422 (t0) REVERT: C 95 LYS cc_start: 0.8471 (pttt) cc_final: 0.8114 (pttm) REVERT: C 110 ASN cc_start: 0.8825 (t0) cc_final: 0.8525 (t0) REVERT: C 115 LEU cc_start: 0.8728 (mp) cc_final: 0.8082 (mp) REVERT: D 31 LYS cc_start: 0.8672 (mppt) cc_final: 0.8444 (mppt) REVERT: D 59 MET cc_start: 0.9508 (mmm) cc_final: 0.9268 (tpp) REVERT: D 108 VAL cc_start: 0.8774 (p) cc_final: 0.8561 (p) REVERT: D 109 SER cc_start: 0.8908 (t) cc_final: 0.8626 (p) REVERT: D 110 GLU cc_start: 0.7976 (mt-10) cc_final: 0.7728 (mt-10) REVERT: F 31 LYS cc_start: 0.9070 (OUTLIER) cc_final: 0.8049 (tppp) REVERT: F 70 VAL cc_start: 0.9390 (t) cc_final: 0.9174 (p) REVERT: F 75 HIS cc_start: 0.8532 (t70) cc_final: 0.8018 (t70) REVERT: F 78 ARG cc_start: 0.8228 (tpp80) cc_final: 0.8018 (tpp80) REVERT: F 88 TYR cc_start: 0.9157 (m-10) cc_final: 0.8643 (m-80) REVERT: F 95 ARG cc_start: 0.8331 (mpp80) cc_final: 0.7970 (mtt90) REVERT: G 17 ARG cc_start: 0.8245 (mtm180) cc_final: 0.8020 (mtt90) REVERT: G 39 TYR cc_start: 0.8835 (m-80) cc_final: 0.8603 (m-80) REVERT: G 78 ILE cc_start: 0.8890 (mt) cc_final: 0.8480 (mt) REVERT: G 81 ARG cc_start: 0.8669 (tpt90) cc_final: 0.8429 (tpt90) REVERT: G 82 HIS cc_start: 0.8824 (m170) cc_final: 0.8343 (m-70) REVERT: G 112 GLN cc_start: 0.8518 (mm-40) cc_final: 0.8241 (mm110) REVERT: H 34 TYR cc_start: 0.8187 (m-80) cc_final: 0.7896 (m-10) REVERT: H 40 LYS cc_start: 0.9061 (tppt) cc_final: 0.8834 (tppt) REVERT: H 43 LYS cc_start: 0.8519 (OUTLIER) cc_final: 0.7961 (tmtt) REVERT: H 44 GLN cc_start: 0.8214 (mm-40) cc_final: 0.7190 (mm-40) REVERT: A 56 LYS cc_start: 0.8095 (pttp) cc_final: 0.7612 (pttp) REVERT: A 79 LYS cc_start: 0.9113 (tptp) cc_final: 0.8893 (tptt) REVERT: A 83 ARG cc_start: 0.7356 (mmp80) cc_final: 0.6929 (mmp80) REVERT: E 39 HIS cc_start: 0.5145 (p-80) cc_final: 0.4889 (p-80) REVERT: E 53 ARG cc_start: 0.7660 (tpt90) cc_final: 0.7039 (tpt90) REVERT: E 56 LYS cc_start: 0.7979 (mmtm) cc_final: 0.7763 (mmtm) REVERT: E 68 GLN cc_start: 0.7967 (pp30) cc_final: 0.7569 (pp30) REVERT: E 76 GLN cc_start: 0.8955 (tm-30) cc_final: 0.8649 (tm-30) REVERT: E 93 GLN cc_start: 0.7279 (tm-30) cc_final: 0.6941 (tm-30) REVERT: E 99 TYR cc_start: 0.8958 (t80) cc_final: 0.8722 (t80) REVERT: E 120 MET cc_start: 0.7253 (mtt) cc_final: 0.6928 (mpp) outliers start: 45 outliers final: 34 residues processed: 405 average time/residue: 0.3299 time to fit residues: 175.2638 Evaluate side-chains 417 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 380 time to evaluate : 0.953 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 26 ILE Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 85 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 31 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 33 SER Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 84 SER Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 119 ILE Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 123 ASP Chi-restraints excluded: chain E residue 125 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 1 optimal weight: 0.8980 chunk 79 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 74 optimal weight: 3.9990 chunk 0 optimal weight: 5.9990 chunk 54 optimal weight: 6.9990 chunk 96 optimal weight: 0.8980 chunk 27 optimal weight: 8.9990 chunk 36 optimal weight: 0.9990 chunk 21 optimal weight: 0.8980 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN G 73 ASN ** G 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 125 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.6420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13814 Z= 0.316 Angle : 0.694 15.062 19943 Z= 0.389 Chirality : 0.038 0.199 2253 Planarity : 0.005 0.051 1485 Dihedral : 29.630 150.001 4243 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 21.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.73 % Favored : 96.27 % Rotamer: Outliers : 8.56 % Allowed : 30.72 % Favored : 60.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.28), residues: 831 helix: 0.45 (0.22), residues: 518 sheet: -3.81 (1.55), residues: 10 loop : -0.76 (0.33), residues: 303 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.005 0.001 HIS E 113 PHE 0.021 0.002 PHE B 61 TYR 0.043 0.002 TYR D 80 ARG 0.009 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 444 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 61 poor density : 383 time to evaluate : 0.919 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.9088 (m110) cc_final: 0.8802 (m-40) REVERT: B 55 ARG cc_start: 0.8419 (mtt90) cc_final: 0.8123 (mtm-85) REVERT: B 63 GLU cc_start: 0.8317 (mt-10) cc_final: 0.7822 (mt-10) REVERT: B 75 HIS cc_start: 0.8797 (t70) cc_final: 0.8321 (t-90) REVERT: B 79 LYS cc_start: 0.9012 (mmtp) cc_final: 0.8745 (mmmm) REVERT: C 29 ARG cc_start: 0.7741 (tpp80) cc_final: 0.5226 (tpp80) REVERT: C 32 ARG cc_start: 0.7641 (ttp80) cc_final: 0.7139 (ttp-110) REVERT: C 34 LEU cc_start: 0.8786 (mt) cc_final: 0.8558 (mt) REVERT: C 89 ASN cc_start: 0.8812 (m110) cc_final: 0.8579 (m110) REVERT: C 95 LYS cc_start: 0.8639 (pttt) cc_final: 0.8229 (pttm) REVERT: C 110 ASN cc_start: 0.9093 (t0) cc_final: 0.8834 (t0) REVERT: C 115 LEU cc_start: 0.8755 (mp) cc_final: 0.8500 (mp) REVERT: D 31 LYS cc_start: 0.8706 (mppt) cc_final: 0.8406 (mppt) REVERT: D 39 TYR cc_start: 0.7903 (t80) cc_final: 0.7419 (t80) REVERT: D 59 MET cc_start: 0.9511 (mmm) cc_final: 0.9211 (tpp) REVERT: D 64 ASN cc_start: 0.8356 (m110) cc_final: 0.8081 (m110) REVERT: D 83 ARG cc_start: 0.8035 (tpp-160) cc_final: 0.7798 (tpp80) REVERT: D 110 GLU cc_start: 0.8223 (mt-10) cc_final: 0.7955 (mt-10) REVERT: F 70 VAL cc_start: 0.9398 (t) cc_final: 0.9180 (p) REVERT: F 74 GLU cc_start: 0.7675 (tp30) cc_final: 0.7431 (tp30) REVERT: F 88 TYR cc_start: 0.9316 (m-10) cc_final: 0.8677 (m-80) REVERT: F 90 LEU cc_start: 0.9434 (OUTLIER) cc_final: 0.9182 (mp) REVERT: F 95 ARG cc_start: 0.8614 (mpp80) cc_final: 0.8201 (mtt90) REVERT: G 17 ARG cc_start: 0.8331 (mtm180) cc_final: 0.8075 (mtt90) REVERT: G 18 SER cc_start: 0.8707 (m) cc_final: 0.8291 (t) REVERT: G 42 ARG cc_start: 0.8697 (mtm180) cc_final: 0.8206 (mtm180) REVERT: G 78 ILE cc_start: 0.9088 (mt) cc_final: 0.8660 (mm) REVERT: G 84 GLN cc_start: 0.9229 (tp-100) cc_final: 0.8860 (tp-100) REVERT: G 112 GLN cc_start: 0.8557 (mm-40) cc_final: 0.8177 (mm-40) REVERT: H 34 TYR cc_start: 0.8341 (m-80) cc_final: 0.8129 (m-10) REVERT: H 40 LYS cc_start: 0.9061 (tppt) cc_final: 0.8772 (tppt) REVERT: H 43 LYS cc_start: 0.8560 (OUTLIER) cc_final: 0.8055 (tmtt) REVERT: H 44 GLN cc_start: 0.8158 (mm-40) cc_final: 0.7196 (mm-40) REVERT: H 73 GLU cc_start: 0.8374 (OUTLIER) cc_final: 0.8071 (mm-30) REVERT: A 49 ARG cc_start: 0.8223 (mtp-110) cc_final: 0.7494 (ttt180) REVERT: A 76 GLN cc_start: 0.7896 (mm-40) cc_final: 0.7513 (mt0) REVERT: A 79 LYS cc_start: 0.9098 (tptp) cc_final: 0.8514 (tptp) REVERT: E 39 HIS cc_start: 0.5548 (p-80) cc_final: 0.5296 (p-80) REVERT: E 53 ARG cc_start: 0.7999 (tpt90) cc_final: 0.7498 (tpt90) REVERT: E 55 GLN cc_start: 0.8768 (pt0) cc_final: 0.8362 (pt0) REVERT: E 56 LYS cc_start: 0.8255 (mmtm) cc_final: 0.7766 (mmtm) REVERT: E 63 ARG cc_start: 0.7546 (mmp80) cc_final: 0.7123 (tpp-160) REVERT: E 67 PHE cc_start: 0.8970 (t80) cc_final: 0.8631 (t80) REVERT: E 68 GLN cc_start: 0.8130 (pp30) cc_final: 0.7795 (pp30) REVERT: E 70 LEU cc_start: 0.8729 (tp) cc_final: 0.8461 (tt) REVERT: E 76 GLN cc_start: 0.9137 (tm-30) cc_final: 0.8745 (tm-30) REVERT: E 99 TYR cc_start: 0.9047 (t80) cc_final: 0.8793 (t80) REVERT: E 120 MET cc_start: 0.7570 (mtt) cc_final: 0.7317 (mtp) outliers start: 61 outliers final: 48 residues processed: 405 average time/residue: 0.3323 time to fit residues: 174.7363 Evaluate side-chains 419 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 368 time to evaluate : 0.919 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 38 VAL Chi-restraints excluded: chain D residue 48 ASP Chi-restraints excluded: chain D residue 49 THR Chi-restraints excluded: chain D residue 51 ILE Chi-restraints excluded: chain D residue 52 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain F residue 91 LYS Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 90 ASP Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 95 VAL Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 68 GLN Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.8980 chunk 107 optimal weight: 0.8980 chunk 89 optimal weight: 30.0000 chunk 49 optimal weight: 0.9990 chunk 8 optimal weight: 10.0000 chunk 35 optimal weight: 0.2980 chunk 56 optimal weight: 3.9990 chunk 103 optimal weight: 0.3980 chunk 12 optimal weight: 0.6980 chunk 61 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7885 moved from start: 0.6729 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 13814 Z= 0.227 Angle : 0.663 13.106 19943 Z= 0.370 Chirality : 0.036 0.197 2253 Planarity : 0.005 0.048 1485 Dihedral : 29.613 149.977 4241 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 18.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.87 % Allowed : 34.36 % Favored : 58.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.28 (0.28), residues: 831 helix: 0.96 (0.23), residues: 505 sheet: -3.84 (1.52), residues: 10 loop : -0.86 (0.31), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.003 0.001 HIS E 113 PHE 0.025 0.002 PHE B 61 TYR 0.024 0.002 TYR D 80 ARG 0.012 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 435 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 386 time to evaluate : 1.081 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: symmetry clash 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: symmetry clash 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: symmetry clash REVERT: B 25 ASN cc_start: 0.8945 (m110) cc_final: 0.8538 (m-40) REVERT: B 45 ARG cc_start: 0.8657 (ttt90) cc_final: 0.8380 (ttt90) REVERT: B 55 ARG cc_start: 0.8431 (mtt90) cc_final: 0.8035 (mtm-85) REVERT: B 63 GLU cc_start: 0.8343 (mt-10) cc_final: 0.7775 (mt-10) REVERT: B 73 THR cc_start: 0.9218 (t) cc_final: 0.8993 (t) REVERT: B 79 LYS cc_start: 0.9185 (mmtp) cc_final: 0.8695 (mmmm) REVERT: C 17 ARG cc_start: 0.8716 (mtm180) cc_final: 0.8316 (mtt90) REVERT: C 29 ARG cc_start: 0.7562 (tpp80) cc_final: 0.4906 (tpp80) REVERT: C 32 ARG cc_start: 0.7562 (ttp80) cc_final: 0.7255 (ttp-110) REVERT: C 34 LEU cc_start: 0.8756 (mt) cc_final: 0.8555 (mt) REVERT: C 73 ASN cc_start: 0.8783 (t0) cc_final: 0.8426 (t0) REVERT: C 89 ASN cc_start: 0.8786 (m110) cc_final: 0.8516 (m110) REVERT: D 31 LYS cc_start: 0.8723 (mppt) cc_final: 0.8434 (mppt) REVERT: D 39 TYR cc_start: 0.7839 (t80) cc_final: 0.7352 (t80) REVERT: D 59 MET cc_start: 0.9478 (mmm) cc_final: 0.9253 (tpp) REVERT: D 64 ASN cc_start: 0.8190 (m110) cc_final: 0.7959 (m110) REVERT: D 110 GLU cc_start: 0.8216 (mt-10) cc_final: 0.7957 (mt-10) REVERT: F 63 GLU cc_start: 0.7711 (pp20) cc_final: 0.7170 (pp20) REVERT: F 70 VAL cc_start: 0.9342 (t) cc_final: 0.9124 (p) REVERT: F 74 GLU cc_start: 0.7679 (tp30) cc_final: 0.7305 (tp30) REVERT: F 88 TYR cc_start: 0.9204 (m-10) cc_final: 0.8556 (m-80) REVERT: F 90 LEU cc_start: 0.9470 (OUTLIER) cc_final: 0.9178 (mp) REVERT: F 95 ARG cc_start: 0.8521 (mpp80) cc_final: 0.8073 (mtt90) REVERT: G 17 ARG cc_start: 0.8194 (mtm180) cc_final: 0.7940 (mtt90) REVERT: G 18 SER cc_start: 0.8667 (m) cc_final: 0.8231 (t) REVERT: G 42 ARG cc_start: 0.8523 (mtm180) cc_final: 0.8073 (mtm180) REVERT: G 78 ILE cc_start: 0.9023 (mt) cc_final: 0.8770 (mm) REVERT: G 82 HIS cc_start: 0.8517 (m-70) cc_final: 0.7851 (m170) REVERT: G 84 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8814 (tp-100) REVERT: G 93 LEU cc_start: 0.9384 (mm) cc_final: 0.9120 (mt) REVERT: G 112 GLN cc_start: 0.8495 (mm-40) cc_final: 0.8093 (mm-40) REVERT: H 40 LYS cc_start: 0.9036 (tppt) cc_final: 0.8786 (tppt) REVERT: H 43 LYS cc_start: 0.8552 (OUTLIER) cc_final: 0.7972 (tmtt) REVERT: H 44 GLN cc_start: 0.8168 (mm-40) cc_final: 0.7187 (mm-40) REVERT: H 49 THR cc_start: 0.8993 (p) cc_final: 0.8791 (p) REVERT: H 73 GLU cc_start: 0.8273 (OUTLIER) cc_final: 0.7911 (mm-30) REVERT: A 49 ARG cc_start: 0.8203 (mtp-110) cc_final: 0.7537 (ttt180) REVERT: A 76 GLN cc_start: 0.7784 (mm-40) cc_final: 0.7345 (mp10) REVERT: E 39 HIS cc_start: 0.5512 (p-80) cc_final: 0.5278 (p-80) REVERT: E 53 ARG cc_start: 0.7974 (tpt90) cc_final: 0.7573 (tpt90) REVERT: E 56 LYS cc_start: 0.8289 (mmtm) cc_final: 0.7950 (mmtm) REVERT: E 67 PHE cc_start: 0.9003 (t80) cc_final: 0.8685 (t80) REVERT: E 68 GLN cc_start: 0.8210 (pp30) cc_final: 0.7878 (pp30) REVERT: E 76 GLN cc_start: 0.9145 (tm-30) cc_final: 0.8765 (tm-30) REVERT: E 94 GLU cc_start: 0.8282 (mt-10) cc_final: 0.8066 (mt-10) REVERT: E 99 TYR cc_start: 0.8917 (t80) cc_final: 0.8680 (t80) outliers start: 49 outliers final: 39 residues processed: 407 average time/residue: 0.3217 time to fit residues: 170.9822 Evaluate side-chains 421 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 379 time to evaluate : 0.978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 34 ILE Chi-restraints excluded: chain B residue 46 ILE Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 78 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 89 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 78 optimal weight: 2.9990 chunk 60 optimal weight: 3.9990 chunk 90 optimal weight: 8.9990 chunk 59 optimal weight: 2.9990 chunk 106 optimal weight: 0.0470 chunk 66 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 49 optimal weight: 0.7980 chunk 42 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 32 optimal weight: 0.7980 overall best weight: 1.0480 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.7095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 13814 Z= 0.272 Angle : 0.681 14.352 19943 Z= 0.381 Chirality : 0.037 0.212 2253 Planarity : 0.005 0.052 1485 Dihedral : 29.629 149.123 4241 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 19.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 7.57 % Allowed : 35.06 % Favored : 57.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.24 (0.28), residues: 831 helix: 0.81 (0.23), residues: 513 sheet: -3.81 (1.48), residues: 10 loop : -0.69 (0.33), residues: 308 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.004 0.001 HIS F 75 PHE 0.020 0.001 PHE B 61 TYR 0.050 0.003 TYR D 80 ARG 0.013 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 433 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 379 time to evaluate : 1.037 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.9021 (m110) cc_final: 0.8695 (m-40) REVERT: B 63 GLU cc_start: 0.8363 (mt-10) cc_final: 0.7844 (mt-10) REVERT: B 79 LYS cc_start: 0.9052 (mmtp) cc_final: 0.8654 (mmmm) REVERT: C 17 ARG cc_start: 0.8872 (mtm180) cc_final: 0.8390 (mtt90) REVERT: C 29 ARG cc_start: 0.7561 (tpp80) cc_final: 0.4918 (tpp80) REVERT: C 32 ARG cc_start: 0.7654 (ttp80) cc_final: 0.7359 (ttp-170) REVERT: C 34 LEU cc_start: 0.8816 (mt) cc_final: 0.8566 (mt) REVERT: C 56 GLU cc_start: 0.8250 (tt0) cc_final: 0.7877 (mm-30) REVERT: C 89 ASN cc_start: 0.8767 (m110) cc_final: 0.8467 (m110) REVERT: C 95 LYS cc_start: 0.8591 (pttt) cc_final: 0.8244 (pttm) REVERT: D 31 LYS cc_start: 0.8653 (mppt) cc_final: 0.8352 (mppt) REVERT: D 39 TYR cc_start: 0.7858 (t80) cc_final: 0.7307 (t80) REVERT: D 41 VAL cc_start: 0.9465 (t) cc_final: 0.8962 (p) REVERT: D 59 MET cc_start: 0.9487 (mmm) cc_final: 0.9272 (tpp) REVERT: D 64 ASN cc_start: 0.8219 (m110) cc_final: 0.7990 (m110) REVERT: D 73 GLU cc_start: 0.8794 (mm-30) cc_final: 0.8253 (mm-30) REVERT: D 110 GLU cc_start: 0.8319 (mt-10) cc_final: 0.8051 (mt-10) REVERT: F 50 ILE cc_start: 0.8788 (mm) cc_final: 0.8548 (mt) REVERT: F 63 GLU cc_start: 0.7794 (pp20) cc_final: 0.7300 (pp20) REVERT: F 74 GLU cc_start: 0.7571 (tp30) cc_final: 0.7174 (tp30) REVERT: F 88 TYR cc_start: 0.9247 (m-10) cc_final: 0.8535 (m-80) REVERT: F 90 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9187 (mp) REVERT: F 95 ARG cc_start: 0.8580 (mpp80) cc_final: 0.8106 (mtt90) REVERT: F 98 TYR cc_start: 0.8707 (m-10) cc_final: 0.8459 (m-10) REVERT: G 18 SER cc_start: 0.8834 (m) cc_final: 0.8410 (t) REVERT: G 35 ARG cc_start: 0.8057 (tpp-160) cc_final: 0.7839 (mmm160) REVERT: G 42 ARG cc_start: 0.8835 (mtm180) cc_final: 0.8348 (mtm180) REVERT: G 78 ILE cc_start: 0.9055 (mt) cc_final: 0.8831 (mm) REVERT: G 82 HIS cc_start: 0.8498 (m-70) cc_final: 0.7872 (m90) REVERT: G 84 GLN cc_start: 0.9126 (tp-100) cc_final: 0.8808 (tp-100) REVERT: G 112 GLN cc_start: 0.8505 (mm-40) cc_final: 0.8125 (mm-40) REVERT: H 40 LYS cc_start: 0.9042 (tppt) cc_final: 0.8772 (tppt) REVERT: H 43 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8026 (tmtt) REVERT: H 44 GLN cc_start: 0.8224 (mm-40) cc_final: 0.7279 (mm-40) REVERT: H 49 THR cc_start: 0.8906 (p) cc_final: 0.8654 (p) REVERT: H 73 GLU cc_start: 0.8450 (OUTLIER) cc_final: 0.8074 (mm-30) REVERT: H 112 THR cc_start: 0.9061 (m) cc_final: 0.8829 (p) REVERT: A 49 ARG cc_start: 0.8256 (mtp-110) cc_final: 0.7648 (ttt180) REVERT: A 123 ASP cc_start: 0.9028 (m-30) cc_final: 0.8776 (m-30) REVERT: E 53 ARG cc_start: 0.8274 (tpt90) cc_final: 0.7853 (tpt90) REVERT: E 67 PHE cc_start: 0.9030 (t80) cc_final: 0.8682 (t80) REVERT: E 68 GLN cc_start: 0.8252 (pp30) cc_final: 0.7871 (pp30) REVERT: E 73 GLU cc_start: 0.8443 (OUTLIER) cc_final: 0.8235 (tp30) REVERT: E 76 GLN cc_start: 0.9253 (tm-30) cc_final: 0.8855 (tm-30) REVERT: E 87 SER cc_start: 0.9212 (m) cc_final: 0.8983 (p) REVERT: E 99 TYR cc_start: 0.8957 (t80) cc_final: 0.8684 (t80) outliers start: 54 outliers final: 45 residues processed: 399 average time/residue: 0.3391 time to fit residues: 176.1571 Evaluate side-chains 424 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 375 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 77 LYS Chi-restraints excluded: chain B residue 86 VAL Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 19 ARG Chi-restraints excluded: chain F residue 25 ASN Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 73 GLU Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 chunk 68 optimal weight: 5.9990 chunk 72 optimal weight: 3.9990 chunk 52 optimal weight: 0.4980 chunk 9 optimal weight: 1.9990 chunk 84 optimal weight: 20.0000 chunk 97 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 99 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 76 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.7381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13814 Z= 0.235 Angle : 0.689 15.255 19943 Z= 0.381 Chirality : 0.036 0.203 2253 Planarity : 0.005 0.054 1485 Dihedral : 29.627 148.664 4241 Min Nonbonded Distance : 2.071 Molprobity Statistics. All-atom Clashscore : 19.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.59 % Allowed : 36.33 % Favored : 57.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.28), residues: 831 helix: 1.05 (0.23), residues: 506 sheet: -3.83 (1.42), residues: 10 loop : -0.62 (0.32), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.005 0.001 HIS E 113 PHE 0.026 0.001 PHE B 61 TYR 0.055 0.003 TYR D 80 ARG 0.013 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 432 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 385 time to evaluate : 1.011 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8937 (m110) cc_final: 0.8606 (m-40) REVERT: B 39 ARG cc_start: 0.9279 (tpp80) cc_final: 0.9035 (tpp80) REVERT: B 63 GLU cc_start: 0.8365 (mt-10) cc_final: 0.7769 (mt-10) REVERT: B 79 LYS cc_start: 0.9004 (mmtp) cc_final: 0.8592 (mmmm) REVERT: C 17 ARG cc_start: 0.8917 (mtm180) cc_final: 0.8460 (mtt90) REVERT: C 34 LEU cc_start: 0.8745 (mt) cc_final: 0.8498 (mt) REVERT: C 42 ARG cc_start: 0.8880 (mtm-85) cc_final: 0.8614 (mtm-85) REVERT: C 74 LYS cc_start: 0.8698 (mmmt) cc_final: 0.8385 (ptpp) REVERT: C 75 LYS cc_start: 0.8686 (mmmm) cc_final: 0.8287 (tppt) REVERT: C 93 LEU cc_start: 0.9073 (tp) cc_final: 0.8856 (tp) REVERT: C 95 LYS cc_start: 0.8661 (pttt) cc_final: 0.7879 (ptpp) REVERT: C 108 LEU cc_start: 0.8794 (mt) cc_final: 0.8355 (tt) REVERT: D 31 LYS cc_start: 0.8720 (mppt) cc_final: 0.8507 (mppt) REVERT: D 39 TYR cc_start: 0.7833 (t80) cc_final: 0.7363 (t80) REVERT: D 41 VAL cc_start: 0.9428 (t) cc_final: 0.8952 (p) REVERT: D 73 GLU cc_start: 0.8725 (mm-30) cc_final: 0.7810 (mm-30) REVERT: D 76 ARG cc_start: 0.7639 (ttp80) cc_final: 0.7062 (ttp-110) REVERT: D 85 THR cc_start: 0.8584 (p) cc_final: 0.8331 (p) REVERT: D 110 GLU cc_start: 0.8221 (mt-10) cc_final: 0.7954 (mt-10) REVERT: F 50 ILE cc_start: 0.8681 (mm) cc_final: 0.8452 (mt) REVERT: F 88 TYR cc_start: 0.9171 (m-10) cc_final: 0.8516 (m-80) REVERT: F 90 LEU cc_start: 0.9467 (OUTLIER) cc_final: 0.9188 (mp) REVERT: F 95 ARG cc_start: 0.8518 (mpp80) cc_final: 0.8098 (mtt90) REVERT: F 98 TYR cc_start: 0.8645 (m-10) cc_final: 0.8354 (m-10) REVERT: G 18 SER cc_start: 0.8737 (m) cc_final: 0.8322 (t) REVERT: G 29 ARG cc_start: 0.7363 (tpp80) cc_final: 0.7136 (tpp80) REVERT: G 38 ASN cc_start: 0.8659 (OUTLIER) cc_final: 0.7705 (t0) REVERT: G 42 ARG cc_start: 0.8802 (mtm180) cc_final: 0.8348 (mtm180) REVERT: G 78 ILE cc_start: 0.9082 (mt) cc_final: 0.8833 (mm) REVERT: G 84 GLN cc_start: 0.9092 (tp-100) cc_final: 0.8731 (tp-100) REVERT: G 92 GLU cc_start: 0.7633 (mm-30) cc_final: 0.7430 (tm-30) REVERT: G 112 GLN cc_start: 0.8472 (mm-40) cc_final: 0.8208 (mm-40) REVERT: H 30 ARG cc_start: 0.7200 (ttp80) cc_final: 0.6739 (ttp80) REVERT: H 40 LYS cc_start: 0.9047 (tppt) cc_final: 0.8799 (tppt) REVERT: H 43 LYS cc_start: 0.8630 (OUTLIER) cc_final: 0.7981 (tmtt) REVERT: H 44 GLN cc_start: 0.8213 (mm-40) cc_final: 0.7384 (mm-40) REVERT: H 49 THR cc_start: 0.8929 (p) cc_final: 0.8713 (p) REVERT: H 73 GLU cc_start: 0.8407 (OUTLIER) cc_final: 0.8058 (mm-30) REVERT: H 102 GLU cc_start: 0.8434 (mm-30) cc_final: 0.7708 (mm-30) REVERT: H 105 LYS cc_start: 0.8249 (ptpp) cc_final: 0.7488 (ptpp) REVERT: H 112 THR cc_start: 0.9022 (m) cc_final: 0.8784 (p) REVERT: A 49 ARG cc_start: 0.8222 (mtp-110) cc_final: 0.7632 (ttt180) REVERT: A 76 GLN cc_start: 0.7018 (mt0) cc_final: 0.6589 (mt0) REVERT: A 97 GLU cc_start: 0.7889 (mm-30) cc_final: 0.7686 (mm-30) REVERT: E 52 ARG cc_start: 0.8975 (ttm110) cc_final: 0.8630 (ttm-80) REVERT: E 53 ARG cc_start: 0.8388 (tpt90) cc_final: 0.7861 (tpt90) REVERT: E 56 LYS cc_start: 0.8442 (mmtm) cc_final: 0.7939 (mmtm) REVERT: E 63 ARG cc_start: 0.7632 (mmp80) cc_final: 0.7242 (tpp-160) REVERT: E 67 PHE cc_start: 0.9055 (t80) cc_final: 0.8814 (t80) REVERT: E 68 GLN cc_start: 0.8242 (pp30) cc_final: 0.7790 (pp30) REVERT: E 76 GLN cc_start: 0.9198 (tm-30) cc_final: 0.8815 (tm-30) REVERT: E 99 TYR cc_start: 0.8935 (t80) cc_final: 0.8601 (t80) outliers start: 47 outliers final: 39 residues processed: 404 average time/residue: 0.3413 time to fit residues: 178.6369 Evaluate side-chains 419 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 376 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain B residue 91 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 89 VAL Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 102 optimal weight: 1.9990 chunk 60 optimal weight: 3.9990 chunk 43 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 30 optimal weight: 0.6980 chunk 90 optimal weight: 7.9990 chunk 94 optimal weight: 0.0570 chunk 99 optimal weight: 0.9990 chunk 65 optimal weight: 3.9990 chunk 105 optimal weight: 0.7980 chunk 64 optimal weight: 3.9990 overall best weight: 0.7100 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7890 moved from start: 0.7636 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13814 Z= 0.239 Angle : 0.704 16.569 19943 Z= 0.387 Chirality : 0.037 0.203 2253 Planarity : 0.005 0.053 1485 Dihedral : 29.622 147.843 4241 Min Nonbonded Distance : 2.061 Molprobity Statistics. All-atom Clashscore : 19.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 6.73 % Allowed : 37.17 % Favored : 56.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 831 helix: 0.95 (0.23), residues: 501 sheet: -3.77 (1.38), residues: 10 loop : -0.55 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 82 HIS 0.003 0.001 HIS F 75 PHE 0.024 0.001 PHE B 61 TYR 0.023 0.002 TYR A 99 ARG 0.009 0.001 ARG D 76 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 422 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 374 time to evaluate : 0.932 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8943 (m110) cc_final: 0.8527 (m-40) REVERT: B 39 ARG cc_start: 0.9279 (tpp80) cc_final: 0.8597 (tpp-160) REVERT: B 63 GLU cc_start: 0.8321 (mt-10) cc_final: 0.7780 (mt-10) REVERT: B 79 LYS cc_start: 0.8953 (mmtp) cc_final: 0.8574 (mmmm) REVERT: C 24 GLN cc_start: 0.8173 (mm-40) cc_final: 0.7787 (mm-40) REVERT: C 35 ARG cc_start: 0.7955 (tpp-160) cc_final: 0.7526 (mmp-170) REVERT: C 74 LYS cc_start: 0.8717 (mmmt) cc_final: 0.8450 (ptpp) REVERT: C 75 LYS cc_start: 0.8734 (mmmm) cc_final: 0.8426 (tppt) REVERT: D 31 LYS cc_start: 0.8719 (mppt) cc_final: 0.8513 (mppt) REVERT: D 39 TYR cc_start: 0.7841 (t80) cc_final: 0.7413 (t80) REVERT: D 73 GLU cc_start: 0.8540 (mm-30) cc_final: 0.7817 (mm-30) REVERT: D 103 LEU cc_start: 0.9172 (mm) cc_final: 0.8900 (mt) REVERT: F 50 ILE cc_start: 0.8563 (mm) cc_final: 0.8336 (mt) REVERT: F 88 TYR cc_start: 0.9174 (m-10) cc_final: 0.8500 (m-80) REVERT: F 90 LEU cc_start: 0.9471 (OUTLIER) cc_final: 0.9173 (mp) REVERT: F 95 ARG cc_start: 0.8470 (mpp80) cc_final: 0.8123 (mtt90) REVERT: F 98 TYR cc_start: 0.8672 (m-10) cc_final: 0.8402 (m-10) REVERT: G 18 SER cc_start: 0.8739 (m) cc_final: 0.8396 (t) REVERT: G 35 ARG cc_start: 0.7801 (tpp-160) cc_final: 0.7164 (mmt180) REVERT: G 38 ASN cc_start: 0.8735 (OUTLIER) cc_final: 0.7754 (t0) REVERT: G 42 ARG cc_start: 0.8704 (mtm180) cc_final: 0.8304 (mtm180) REVERT: G 78 ILE cc_start: 0.9101 (mt) cc_final: 0.8846 (mm) REVERT: G 79 ILE cc_start: 0.9131 (OUTLIER) cc_final: 0.8793 (mm) REVERT: G 82 HIS cc_start: 0.8268 (m170) cc_final: 0.7802 (m170) REVERT: G 84 GLN cc_start: 0.9077 (tp-100) cc_final: 0.8749 (tp-100) REVERT: G 92 GLU cc_start: 0.7598 (mm-30) cc_final: 0.7339 (tm-30) REVERT: H 40 LYS cc_start: 0.9045 (tppt) cc_final: 0.8643 (tppt) REVERT: H 49 THR cc_start: 0.8948 (p) cc_final: 0.8735 (p) REVERT: H 73 GLU cc_start: 0.8368 (OUTLIER) cc_final: 0.8057 (mm-30) REVERT: H 102 GLU cc_start: 0.8413 (mm-30) cc_final: 0.7728 (mm-30) REVERT: H 105 LYS cc_start: 0.8323 (ptpp) cc_final: 0.7128 (ptpp) REVERT: H 112 THR cc_start: 0.9054 (m) cc_final: 0.8807 (p) REVERT: A 76 GLN cc_start: 0.7189 (mt0) cc_final: 0.6762 (mt0) REVERT: A 109 LEU cc_start: 0.9086 (mt) cc_final: 0.8876 (mt) REVERT: E 53 ARG cc_start: 0.8392 (tpt90) cc_final: 0.7841 (tpt90) REVERT: E 56 LYS cc_start: 0.8491 (mmtm) cc_final: 0.7829 (mmtm) REVERT: E 63 ARG cc_start: 0.7649 (mmp80) cc_final: 0.7278 (tpp-160) REVERT: E 67 PHE cc_start: 0.9049 (t80) cc_final: 0.8752 (t80) REVERT: E 68 GLN cc_start: 0.8107 (pp30) cc_final: 0.7730 (pp30) REVERT: E 76 GLN cc_start: 0.9099 (tm-30) cc_final: 0.8696 (tm-30) REVERT: E 99 TYR cc_start: 0.8904 (t80) cc_final: 0.8600 (t80) outliers start: 48 outliers final: 39 residues processed: 395 average time/residue: 0.3432 time to fit residues: 175.6569 Evaluate side-chains 411 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 368 time to evaluate : 0.924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 71 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 89 ARG Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 45 THR Chi-restraints excluded: chain E residue 103 LEU Chi-restraints excluded: chain E residue 123 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 50 optimal weight: 0.6980 chunk 73 optimal weight: 3.9990 chunk 110 optimal weight: 0.6980 chunk 101 optimal weight: 0.1980 chunk 88 optimal weight: 7.9990 chunk 9 optimal weight: 0.4980 chunk 68 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 69 optimal weight: 6.9990 chunk 93 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.7881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 13814 Z= 0.233 Angle : 0.726 18.089 19943 Z= 0.396 Chirality : 0.037 0.201 2253 Planarity : 0.005 0.060 1485 Dihedral : 29.611 147.159 4241 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 19.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 6.17 % Allowed : 39.69 % Favored : 54.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.46 (0.28), residues: 831 helix: 0.96 (0.23), residues: 501 sheet: -3.71 (1.34), residues: 10 loop : -0.51 (0.32), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP K 21 HIS 0.006 0.001 HIS D 106 PHE 0.025 0.001 PHE B 61 TYR 0.036 0.002 TYR C 57 ARG 0.012 0.001 ARG E 52 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1662 Ramachandran restraints generated. 831 Oldfield, 0 Emsley, 831 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 418 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 374 time to evaluate : 1.081 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: symmetry clash 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: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8914 (m110) cc_final: 0.8528 (m-40) REVERT: B 31 LYS cc_start: 0.9174 (OUTLIER) cc_final: 0.8797 (tptp) REVERT: B 63 GLU cc_start: 0.8298 (mt-10) cc_final: 0.7778 (mt-10) REVERT: B 79 LYS cc_start: 0.8917 (mmtp) cc_final: 0.8522 (mmmm) REVERT: C 24 GLN cc_start: 0.8305 (mm-40) cc_final: 0.8045 (mm-40) REVERT: C 25 PHE cc_start: 0.8520 (m-10) cc_final: 0.8234 (m-10) REVERT: C 35 ARG cc_start: 0.7870 (tpp-160) cc_final: 0.7497 (mmp-170) REVERT: C 56 GLU cc_start: 0.8866 (mm-30) cc_final: 0.8657 (mm-30) REVERT: C 74 LYS cc_start: 0.8593 (mmmt) cc_final: 0.8291 (ptpp) REVERT: C 75 LYS cc_start: 0.8716 (mmmm) cc_final: 0.8332 (tppt) REVERT: C 95 LYS cc_start: 0.8608 (pttt) cc_final: 0.8088 (pttm) REVERT: D 31 LYS cc_start: 0.8713 (mppt) cc_final: 0.8499 (mppt) REVERT: D 39 TYR cc_start: 0.7810 (t80) cc_final: 0.7349 (t80) REVERT: D 73 GLU cc_start: 0.8533 (mm-30) cc_final: 0.7457 (mm-30) REVERT: D 76 ARG cc_start: 0.7871 (ttp80) cc_final: 0.6904 (ttp-110) REVERT: F 88 TYR cc_start: 0.9146 (m-10) cc_final: 0.8514 (m-80) REVERT: F 90 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9166 (mp) REVERT: F 95 ARG cc_start: 0.8439 (mpp80) cc_final: 0.8092 (mtt90) REVERT: F 98 TYR cc_start: 0.8633 (m-10) cc_final: 0.8314 (m-10) REVERT: G 18 SER cc_start: 0.8727 (m) cc_final: 0.8397 (t) REVERT: G 38 ASN cc_start: 0.8696 (OUTLIER) cc_final: 0.7729 (t0) REVERT: G 78 ILE cc_start: 0.9071 (mt) cc_final: 0.8854 (mm) REVERT: G 79 ILE cc_start: 0.9103 (OUTLIER) cc_final: 0.8661 (mm) REVERT: G 81 ARG cc_start: 0.8503 (tpt90) cc_final: 0.8125 (tpt90) REVERT: G 82 HIS cc_start: 0.8247 (m170) cc_final: 0.7686 (m170) REVERT: G 84 GLN cc_start: 0.9052 (tp-100) cc_final: 0.8680 (tp-100) REVERT: G 92 GLU cc_start: 0.7782 (mm-30) cc_final: 0.7462 (tm-30) REVERT: H 40 LYS cc_start: 0.9115 (tppt) cc_final: 0.8604 (tppt) REVERT: H 43 LYS cc_start: 0.8731 (OUTLIER) cc_final: 0.8082 (tmtt) REVERT: H 49 THR cc_start: 0.9005 (p) cc_final: 0.8750 (p) REVERT: H 73 GLU cc_start: 0.8350 (OUTLIER) cc_final: 0.8019 (mm-30) REVERT: H 102 GLU cc_start: 0.8410 (mm-30) cc_final: 0.7995 (mm-30) REVERT: H 105 LYS cc_start: 0.8321 (ptpp) cc_final: 0.8000 (ptpp) REVERT: H 112 THR cc_start: 0.9034 (m) cc_final: 0.8781 (p) REVERT: H 113 LYS cc_start: 0.8716 (tptt) cc_final: 0.8417 (tppt) REVERT: H 117 LYS cc_start: 0.8700 (tppt) cc_final: 0.8497 (tptp) REVERT: A 42 ARG cc_start: 0.7660 (mmm-85) cc_final: 0.7446 (mmm-85) REVERT: A 56 LYS cc_start: 0.8071 (pttp) cc_final: 0.7725 (pttp) REVERT: A 76 GLN cc_start: 0.7247 (mt0) cc_final: 0.6926 (mt0) REVERT: E 53 ARG cc_start: 0.8412 (tpt90) cc_final: 0.7831 (tpt90) REVERT: E 55 GLN cc_start: 0.9174 (tt0) cc_final: 0.8840 (tt0) REVERT: E 56 LYS cc_start: 0.8566 (mmtm) cc_final: 0.8027 (mmtm) REVERT: E 60 LEU cc_start: 0.8796 (mm) cc_final: 0.8575 (tt) REVERT: E 63 ARG cc_start: 0.7600 (mmp80) cc_final: 0.7250 (tpp-160) REVERT: E 68 GLN cc_start: 0.8136 (pp30) cc_final: 0.7716 (pp30) REVERT: E 76 GLN cc_start: 0.9080 (tm-30) cc_final: 0.8700 (tm-30) REVERT: E 99 TYR cc_start: 0.8880 (t80) cc_final: 0.8548 (t80) outliers start: 44 outliers final: 36 residues processed: 390 average time/residue: 0.3430 time to fit residues: 173.6537 Evaluate side-chains 412 residues out of total 713 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 370 time to evaluate : 0.979 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 31 LYS Chi-restraints excluded: chain B residue 60 VAL Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 97 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 33 SER Chi-restraints excluded: chain D residue 77 LEU Chi-restraints excluded: chain D residue 97 LEU Chi-restraints excluded: chain D residue 122 LYS Chi-restraints excluded: chain F residue 29 ILE Chi-restraints excluded: chain F residue 44 LYS Chi-restraints excluded: chain F residue 46 ILE Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain F residue 84 MET Chi-restraints excluded: chain F residue 90 LEU Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 34 LEU Chi-restraints excluded: chain G residue 38 ASN Chi-restraints excluded: chain G residue 79 ILE Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain H residue 41 VAL Chi-restraints excluded: chain H residue 43 LYS Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 51 ILE Chi-restraints excluded: chain H residue 73 GLU Chi-restraints excluded: chain H residue 90 GLU Chi-restraints excluded: chain H residue 110 GLU Chi-restraints excluded: chain H residue 122 LYS Chi-restraints excluded: chain K residue 65 LYS Chi-restraints excluded: chain A residue 51 ILE Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 117 VAL Chi-restraints excluded: chain E residue 103 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 111 random chunks: chunk 81 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 24 optimal weight: 0.6980 chunk 88 optimal weight: 7.9990 chunk 36 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.8980 chunk 77 optimal weight: 2.9990 chunk 5 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 73 ASN ** C 84 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 89 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 64 ASN ** K 86 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 108 ASN ** E 55 GLN ** 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 = 0.4001 r_free = 0.4001 target = 0.138169 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.095397 restraints weight = 31150.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 58)----------------| | r_work = 0.3417 r_free = 0.3417 target = 0.098502 restraints weight = 17913.989| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3451 r_free = 0.3451 target = 0.100538 restraints weight = 12599.340| |-----------------------------------------------------------------------------| r_work (final): 0.3418 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.8091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 13814 Z= 0.251 Angle : 0.728 17.239 19943 Z= 0.399 Chirality : 0.037 0.205 2253 Planarity : 0.005 0.057 1485 Dihedral : 29.639 146.574 4241 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 20.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.89 % Favored : 97.11 % Rotamer: Outliers : 6.45 % Allowed : 39.69 % Favored : 53.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.28), residues: 831 helix: 0.86 (0.23), residues: 500 sheet: -3.58 (1.38), residues: 10 loop : -0.48 (0.32), residues: 321 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP K 82 HIS 0.008 0.001 HIS D 106 PHE 0.024 0.001 PHE B 61 TYR 0.024 0.002 TYR D 80 ARG 0.012 0.001 ARG E 52 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3418.30 seconds wall clock time: 61 minutes 31.85 seconds (3691.85 seconds total)