Starting phenix.real_space_refine on Fri Feb 16 11:02:00 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o96_0652/02_2024/6o96_0652_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o96_0652/02_2024/6o96_0652.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o96_0652/02_2024/6o96_0652.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o96_0652/02_2024/6o96_0652.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o96_0652/02_2024/6o96_0652_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6o96_0652/02_2024/6o96_0652_updated.pdb" } resolution = 3.5 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= -0.007 sd= 0.345 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 292 5.49 5 S 28 5.16 5 C 8657 2.51 5 N 2794 2.21 5 O 3423 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C GLU 91": "OE1" <-> "OE2" Residue "C GLU 92": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D GLU 93": "OE1" <-> "OE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 97": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "G ARG 35": "NH1" <-> "NH2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "K GLU 6": "OE1" <-> "OE2" Residue "K GLU 16": "OE1" <-> "OE2" Residue "K TYR 20": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K GLU 39": "OE1" <-> "OE2" Residue "K GLU 56": "OE1" <-> "OE2" Residue "K GLU 69": "OE1" <-> "OE2" Residue "K GLU 138": "OE1" <-> "OE2" Residue "K GLU 150": "OE1" <-> "OE2" Residue "K GLU 201": "OE1" <-> "OE2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K GLU 227": "OE1" <-> "OE2" Residue "K GLU 230": "OE1" <-> "OE2" Residue "K GLU 255": "OE1" <-> "OE2" Residue "K GLU 262": "OE1" <-> "OE2" Residue "K GLU 323": "OE1" <-> "OE2" Residue "L GLU 18": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 15194 Number of models: 1 Model: "" Number of chains: 13 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 715 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 715 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 663 Classifications: {'peptide': 84} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 82} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'ARG:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 10 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 723 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 723 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 2596 Number of conformers: 1 Conformer: "" Number of residues, atoms: 321, 2596 Classifications: {'peptide': 321} Incomplete info: {'truncation_to_alanine': 8} Link IDs: {'PTRANS': 16, 'TRANS': 304} Chain breaks: 1 Unresolved chain link angles: 1 Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 17 Unresolved non-hydrogen chiralities: 3 Chain: "L" Number of atoms: 594 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 594 Classifications: {'peptide': 76} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 3, 'TRANS': 72} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 10 Unresolved non-hydrogen dihedrals: 8 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "K" Number of atoms: 26 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 26 Classifications: {'peptide': 1} Residues with excluded nonbonded symmetry interactions: 3 residue: pdb=" N LEU L 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU L 73 " occ=0.45 residue: pdb=" N ARG L 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG L 74 " occ=0.45 residue: pdb=" N GLY L 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY L 75 " occ=0.25 Time building chain proxies: 8.72, per 1000 atoms: 0.57 Number of scatterers: 15194 At special positions: 0 Unit cell: (134.55, 119.025, 143.865, 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 28 16.00 P 292 15.00 O 3423 8.00 N 2794 7.00 C 8657 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: 7.95 Conformation dependent library (CDL) restraints added in 1.9 seconds 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2190 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 3 sheets defined 53.8% alpha, 3.7% beta 144 base pairs and 261 stacking pairs defined. Time for finding SS restraints: 8.70 Creating SS restraints... Processing helix chain 'A' and resid 45 through 56 Processing helix chain 'A' and resid 64 through 77 removed outlier: 4.555A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 86 through 113 Processing helix chain 'A' and resid 121 through 131 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 50 through 76 removed outlier: 3.731A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'C' and resid 17 through 21 removed outlier: 3.774A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 17 through 21' Processing helix chain 'C' and resid 28 through 35 Processing helix chain 'C' and resid 45 through 71 removed outlier: 4.600A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.564A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 80 through 87 Processing helix chain 'C' and resid 91 through 96 Processing helix chain 'D' and resid 38 through 48 Processing helix chain 'D' and resid 56 through 83 Processing helix chain 'D' and resid 91 through 101 Processing helix chain 'D' and resid 105 through 122 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 64 through 77 removed outlier: 4.022A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 86 through 113 Processing helix chain 'E' and resid 121 through 130 Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 50 through 75 Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 17 through 20 No H-bonds generated for 'chain 'G' and resid 17 through 20' Processing helix chain 'G' and resid 27 through 36 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.594A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 80 through 89 Processing helix chain 'G' and resid 92 through 96 Processing helix chain 'H' and resid 38 through 48 Processing helix chain 'H' and resid 56 through 83 Processing helix chain 'H' and resid 91 through 101 Processing helix chain 'H' and resid 105 through 123 Processing helix chain 'K' and resid 33 through 47 Processing helix chain 'K' and resid 49 through 54 Processing helix chain 'K' and resid 68 through 89 Processing helix chain 'K' and resid 104 through 118 Processing helix chain 'K' and resid 123 through 126 Processing helix chain 'K' and resid 141 through 150 Processing helix chain 'K' and resid 168 through 176 Processing helix chain 'K' and resid 189 through 209 removed outlier: 4.114A pdb=" N THR K 197 " --> pdb=" O LYS K 193 " (cutoff:3.500A) Processing helix chain 'K' and resid 226 through 234 removed outlier: 4.144A pdb=" N GLU K 230 " --> pdb=" O GLU K 226 " (cutoff:3.500A) Processing helix chain 'K' and resid 247 through 259 removed outlier: 4.796A pdb=" N ASN K 259 " --> pdb=" O GLU K 255 " (cutoff:3.500A) Processing helix chain 'K' and resid 287 through 289 No H-bonds generated for 'chain 'K' and resid 287 through 289' Processing helix chain 'K' and resid 321 through 330 removed outlier: 4.617A pdb=" N LYS K 330 " --> pdb=" O PHE K 326 " (cutoff:3.500A) Processing helix chain 'L' and resid 23 through 34 Processing helix chain 'L' and resid 57 through 59 No H-bonds generated for 'chain 'L' and resid 57 through 59' Processing sheet with id= A, first strand: chain 'K' and resid 6 through 9 Processing sheet with id= B, first strand: chain 'K' and resid 291 through 294 removed outlier: 3.529A pdb=" N PHE K 159 " --> pdb=" O HIS K 181 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N ASP K 161 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N VAL K 185 " --> pdb=" O ASP K 161 " (cutoff:3.500A) removed outlier: 6.878A pdb=" N GLU K 215 " --> pdb=" O HIS K 182 " (cutoff:3.500A) removed outlier: 8.587A pdb=" N GLY K 184 " --> pdb=" O GLU K 215 " (cutoff:3.500A) removed outlier: 6.450A pdb=" N THR K 217 " --> pdb=" O GLY K 184 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'L' and resid 12 through 16 removed outlier: 6.313A pdb=" N SER L 65 " --> pdb=" O PHE L 4 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LYS L 6 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 6.341A pdb=" N LEU L 67 " --> pdb=" O LYS L 6 " (cutoff:3.500A) 452 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 367 hydrogen bonds 734 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 261 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 8.47 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: 2804 1.33 - 1.45: 5104 1.45 - 1.57: 7536 1.57 - 1.69: 582 1.69 - 1.81: 49 Bond restraints: 16075 Sorted by residual: bond pdb=" C4 SAH K 401 " pdb=" C5 SAH K 401 " ideal model delta sigma weight residual 1.386 1.470 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C5 SAH K 401 " pdb=" C6 SAH K 401 " ideal model delta sigma weight residual 1.407 1.489 -0.082 2.00e-02 2.50e+03 1.68e+01 bond pdb=" C TRP K 22 " pdb=" N PRO K 23 " ideal model delta sigma weight residual 1.332 1.382 -0.050 1.34e-02 5.57e+03 1.40e+01 bond pdb=" N ARG E 42 " pdb=" CA ARG E 42 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.16e-02 7.43e+03 9.10e+00 bond pdb=" N ARG E 40 " pdb=" CA ARG E 40 " ideal model delta sigma weight residual 1.455 1.488 -0.033 1.23e-02 6.61e+03 7.10e+00 ... (remaining 16070 not shown) Histogram of bond angle deviations from ideal: 95.80 - 103.96: 1039 103.96 - 112.12: 8855 112.12 - 120.28: 7365 120.28 - 128.44: 5413 128.44 - 136.60: 327 Bond angle restraints: 22999 Sorted by residual: angle pdb=" N ASN K 178 " pdb=" CA ASN K 178 " pdb=" C ASN K 178 " ideal model delta sigma weight residual 110.44 117.63 -7.19 1.20e+00 6.94e-01 3.59e+01 angle pdb=" C LEU K 60 " pdb=" N ILE K 61 " pdb=" CA ILE K 61 " ideal model delta sigma weight residual 120.62 128.00 -7.38 1.64e+00 3.72e-01 2.03e+01 angle pdb=" C TYR K 312 " pdb=" N TYR K 313 " pdb=" CA TYR K 313 " ideal model delta sigma weight residual 120.71 127.08 -6.37 1.42e+00 4.96e-01 2.01e+01 angle pdb=" C LYS K 10 " pdb=" N SER K 11 " pdb=" CA SER K 11 " ideal model delta sigma weight residual 120.86 127.51 -6.65 1.60e+00 3.91e-01 1.73e+01 angle pdb=" CA ARG F 95 " pdb=" C ARG F 95 " pdb=" N THR F 96 " ideal model delta sigma weight residual 114.76 119.32 -4.56 1.14e+00 7.69e-01 1.60e+01 ... (remaining 22994 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 7099 31.83 - 63.65: 1750 63.65 - 95.48: 51 95.48 - 127.30: 0 127.30 - 159.13: 3 Dihedral angle restraints: 8903 sinusoidal: 5517 harmonic: 3386 Sorted by residual: dihedral pdb=" CA ASN K 57 " pdb=" C ASN K 57 " pdb=" N TYR K 58 " pdb=" CA TYR K 58 " ideal model delta harmonic sigma weight residual 180.00 152.56 27.44 0 5.00e+00 4.00e-02 3.01e+01 dihedral pdb=" CA THR K 306 " pdb=" C THR K 306 " pdb=" N GLY K 307 " pdb=" CA GLY K 307 " ideal model delta harmonic sigma weight residual -180.00 -153.38 -26.62 0 5.00e+00 4.00e-02 2.84e+01 dihedral pdb=" CA THR K 177 " pdb=" C THR K 177 " pdb=" N ASN K 178 " pdb=" CA ASN K 178 " ideal model delta harmonic sigma weight residual -180.00 -154.98 -25.02 0 5.00e+00 4.00e-02 2.50e+01 ... (remaining 8900 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.067: 2117 0.067 - 0.134: 428 0.134 - 0.201: 59 0.201 - 0.268: 10 0.268 - 0.336: 1 Chirality restraints: 2615 Sorted by residual: chirality pdb=" CB ILE H 54 " pdb=" CA ILE H 54 " pdb=" CG1 ILE H 54 " pdb=" CG2 ILE H 54 " both_signs ideal model delta sigma weight residual False 2.64 2.31 0.34 2.00e-01 2.50e+01 2.82e+00 chirality pdb=" CB VAL C 100 " pdb=" CA VAL C 100 " pdb=" CG1 VAL C 100 " pdb=" CG2 VAL C 100 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.39 0.26 2.00e-01 2.50e+01 1.63e+00 ... (remaining 2612 not shown) Planarity restraints: 1909 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 142 " -0.045 2.00e-02 2.50e+03 2.26e-02 1.15e+01 pdb=" N1 DC J 142 " 0.042 2.00e-02 2.50e+03 pdb=" C2 DC J 142 " -0.006 2.00e-02 2.50e+03 pdb=" O2 DC J 142 " 0.016 2.00e-02 2.50e+03 pdb=" N3 DC J 142 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DC J 142 " -0.009 2.00e-02 2.50e+03 pdb=" N4 DC J 142 " -0.011 2.00e-02 2.50e+03 pdb=" C5 DC J 142 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DC J 142 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " 0.046 5.00e-02 4.00e+02 6.95e-02 7.72e+00 pdb=" N PRO G 80 " -0.120 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " 0.035 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " 0.039 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " -0.046 5.00e-02 4.00e+02 6.85e-02 7.51e+00 pdb=" N PRO C 80 " 0.118 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " -0.035 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " -0.038 5.00e-02 4.00e+02 ... (remaining 1906 not shown) Histogram of nonbonded interaction distances: 2.21 - 2.75: 2232 2.75 - 3.28: 12957 3.28 - 3.82: 29819 3.82 - 4.36: 34323 4.36 - 4.90: 50404 Nonbonded interactions: 129735 Sorted by model distance: nonbonded pdb=" NH2 ARG E 40 " pdb=" O2 DT J 83 " model vdw 2.207 2.520 nonbonded pdb=" OH TYR D 40 " pdb=" OP1 DG I 122 " model vdw 2.277 2.440 nonbonded pdb=" O THR C 16 " pdb=" OG SER C 19 " model vdw 2.303 2.440 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.305 2.440 nonbonded pdb=" O SER D 123 " pdb=" OG SER D 123 " model vdw 2.325 2.440 ... (remaining 129730 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 32 through 33 or (resid 34 and (name N or name CA or name \ C or name O or name CB )) or resid 35 through 56 or (resid 57 through 58 and (na \ me N or name CA or name C or name O or name CB )) or resid 59 through 124)) } 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=0.25 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.340 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: 7.760 Check model and map are aligned: 0.250 Set scattering table: 0.170 Process input model: 51.630 Find NCS groups from input model: 0.490 Set up NCS constraints: 0.060 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:2.830 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 64.540 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 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 : 0.011 0.090 16075 Z= 0.654 Angle : 1.027 11.260 22999 Z= 0.585 Chirality : 0.056 0.336 2615 Planarity : 0.008 0.069 1909 Dihedral : 27.276 159.131 6713 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 0.41 % Allowed : 9.21 % Favored : 90.37 % 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: -4.03 (0.18), residues: 1139 helix: -2.83 (0.13), residues: 686 sheet: -0.32 (0.63), residues: 62 loop : -2.40 (0.26), residues: 391 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 208 HIS 0.012 0.002 HIS K 109 PHE 0.029 0.003 PHE E 67 TYR 0.022 0.003 TYR K 183 ARG 0.012 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 614 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 610 time to evaluate : 1.309 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: A 93 GLN cc_start: 0.7279 (tt0) cc_final: 0.6695 (tt0) REVERT: A 116 ARG cc_start: 0.7277 (mtm110) cc_final: 0.6718 (mtp180) REVERT: A 120 MET cc_start: 0.6506 (mtp) cc_final: 0.5999 (mtm) REVERT: C 57 TYR cc_start: 0.7821 (t80) cc_final: 0.7313 (t80) REVERT: C 94 ASN cc_start: 0.8289 (t0) cc_final: 0.8027 (t0) REVERT: D 68 ASP cc_start: 0.7915 (t0) cc_final: 0.7626 (t0) REVERT: D 89 ILE cc_start: 0.8832 (mm) cc_final: 0.8618 (mm) REVERT: F 39 ARG cc_start: 0.8166 (mmt-90) cc_final: 0.7956 (mmt180) REVERT: G 50 TYR cc_start: 0.7895 (t80) cc_final: 0.7623 (t80) REVERT: G 57 TYR cc_start: 0.7629 (t80) cc_final: 0.7316 (t80) REVERT: G 100 VAL cc_start: 0.8659 (m) cc_final: 0.8378 (m) REVERT: K 241 ASN cc_start: 0.8129 (t0) cc_final: 0.7497 (t0) REVERT: K 312 TYR cc_start: 0.7937 (m-80) cc_final: 0.7686 (m-80) outliers start: 4 outliers final: 1 residues processed: 613 average time/residue: 0.3569 time to fit residues: 291.6072 Evaluate side-chains 493 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 492 time to evaluate : 1.234 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 316 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 8.9990 chunk 105 optimal weight: 30.0000 chunk 58 optimal weight: 0.9980 chunk 35 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 56 optimal weight: 0.6980 chunk 108 optimal weight: 7.9990 chunk 42 optimal weight: 0.6980 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 126 optimal weight: 0.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN C 89 ASN D 49 HIS D 63 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN G 31 HIS G 73 ASN G 89 ASN G 104 GLN H 95 GLN K 99 ASN K 113 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 315 HIS ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 60 ASN Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.2623 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16075 Z= 0.240 Angle : 0.661 7.991 22999 Z= 0.381 Chirality : 0.038 0.204 2615 Planarity : 0.005 0.057 1909 Dihedral : 29.615 168.739 4480 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 5.90 % Allowed : 25.05 % Favored : 69.05 % 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: -1.45 (0.23), residues: 1139 helix: -0.48 (0.18), residues: 673 sheet: -0.42 (0.55), residues: 76 loop : -1.74 (0.29), residues: 390 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 305 HIS 0.011 0.001 HIS K 109 PHE 0.032 0.003 PHE A 67 TYR 0.024 0.002 TYR B 88 ARG 0.008 0.001 ARG F 55 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 604 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 57 poor density : 547 time to evaluate : 1.393 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: A 93 GLN cc_start: 0.6938 (tt0) cc_final: 0.6310 (tt0) REVERT: C 24 GLN cc_start: 0.7843 (mm-40) cc_final: 0.7445 (mm-40) REVERT: C 68 ASN cc_start: 0.7708 (m-40) cc_final: 0.7126 (m-40) REVERT: C 73 ASN cc_start: 0.8141 (OUTLIER) cc_final: 0.7873 (t0) REVERT: C 94 ASN cc_start: 0.8318 (t0) cc_final: 0.7951 (t0) REVERT: D 47 GLN cc_start: 0.7316 (mt0) cc_final: 0.7050 (mt0) REVERT: G 50 TYR cc_start: 0.7954 (t80) cc_final: 0.7513 (t80) REVERT: L 36 ILE cc_start: 0.8899 (mp) cc_final: 0.8342 (tt) REVERT: L 41 GLN cc_start: 0.7583 (pt0) cc_final: 0.6678 (pt0) REVERT: L 48 LYS cc_start: 0.8333 (ttmt) cc_final: 0.7911 (mtpt) REVERT: L 50 LEU cc_start: 0.8790 (mm) cc_final: 0.8212 (tp) outliers start: 57 outliers final: 31 residues processed: 561 average time/residue: 0.3284 time to fit residues: 253.0199 Evaluate side-chains 540 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 508 time to evaluate : 1.366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 89 VAL Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 73 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 290 ILE Chi-restraints excluded: chain K residue 306 THR Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 4 PHE Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 3.9990 chunk 39 optimal weight: 0.8980 chunk 105 optimal weight: 9.9990 chunk 85 optimal weight: 7.9990 chunk 34 optimal weight: 10.0000 chunk 126 optimal weight: 0.0370 chunk 136 optimal weight: 8.9990 chunk 112 optimal weight: 7.9990 chunk 125 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 overall best weight: 0.7458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN E 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS F 93 GLN G 89 ASN G 104 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN L 31 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8020 moved from start: 0.3173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16075 Z= 0.217 Angle : 0.654 12.282 22999 Z= 0.371 Chirality : 0.038 0.175 2615 Planarity : 0.005 0.046 1909 Dihedral : 29.437 170.496 4480 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 16.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 5.69 % Allowed : 29.40 % Favored : 64.91 % 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: -0.34 (0.24), residues: 1139 helix: 0.56 (0.19), residues: 670 sheet: -0.44 (0.55), residues: 77 loop : -1.48 (0.31), residues: 392 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 305 HIS 0.009 0.001 HIS L 68 PHE 0.033 0.003 PHE A 67 TYR 0.028 0.002 TYR B 88 ARG 0.007 0.001 ARG F 45 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 580 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 55 poor density : 525 time to evaluate : 1.371 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: C 24 GLN cc_start: 0.7740 (mm-40) cc_final: 0.7378 (mm-40) REVERT: C 73 ASN cc_start: 0.8181 (t0) cc_final: 0.7907 (t0) REVERT: C 75 LYS cc_start: 0.8766 (mmtp) cc_final: 0.8393 (mttm) REVERT: C 94 ASN cc_start: 0.8387 (t0) cc_final: 0.8061 (t0) REVERT: D 47 GLN cc_start: 0.7330 (mt0) cc_final: 0.7072 (mt0) REVERT: F 51 TYR cc_start: 0.7881 (m-80) cc_final: 0.7534 (m-10) REVERT: F 55 ARG cc_start: 0.7902 (mtt90) cc_final: 0.7618 (mtt90) REVERT: G 50 TYR cc_start: 0.7754 (t80) cc_final: 0.7533 (t80) REVERT: K 55 MET cc_start: -0.0128 (mmt) cc_final: -0.0791 (tpp) REVERT: K 101 ARG cc_start: 0.7310 (mmt90) cc_final: 0.5492 (mmp80) REVERT: K 113 GLN cc_start: 0.8561 (OUTLIER) cc_final: 0.8262 (pt0) REVERT: L 36 ILE cc_start: 0.8946 (mp) cc_final: 0.8657 (tt) REVERT: L 41 GLN cc_start: 0.7755 (pt0) cc_final: 0.6625 (pt0) outliers start: 55 outliers final: 36 residues processed: 541 average time/residue: 0.2978 time to fit residues: 226.0959 Evaluate side-chains 536 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 499 time to evaluate : 1.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 71 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 3.9990 chunk 95 optimal weight: 3.9990 chunk 65 optimal weight: 0.9990 chunk 13 optimal weight: 0.1980 chunk 60 optimal weight: 2.9990 chunk 84 optimal weight: 4.9990 chunk 126 optimal weight: 0.0010 chunk 134 optimal weight: 8.9990 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 20.0000 chunk 36 optimal weight: 7.9990 overall best weight: 1.0190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN E 93 GLN G 104 GLN H 84 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8041 moved from start: 0.3615 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 16075 Z= 0.240 Angle : 0.655 10.114 22999 Z= 0.370 Chirality : 0.038 0.184 2615 Planarity : 0.004 0.040 1909 Dihedral : 29.333 172.688 4480 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 15.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 7.04 % Allowed : 30.12 % Favored : 62.84 % 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: 0.18 (0.25), residues: 1139 helix: 1.03 (0.20), residues: 672 sheet: -0.49 (0.56), residues: 80 loop : -1.32 (0.32), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 205 HIS 0.009 0.001 HIS K 109 PHE 0.015 0.002 PHE H 70 TYR 0.029 0.002 TYR G 57 ARG 0.007 0.001 ARG C 42 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 68 poor density : 508 time to evaluate : 1.311 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: C 73 ASN cc_start: 0.8354 (t0) cc_final: 0.8029 (t0) REVERT: C 94 ASN cc_start: 0.8432 (t0) cc_final: 0.8129 (t0) REVERT: D 47 GLN cc_start: 0.7377 (mt0) cc_final: 0.7015 (mt0) REVERT: F 51 TYR cc_start: 0.7896 (m-80) cc_final: 0.7637 (m-80) REVERT: F 55 ARG cc_start: 0.7954 (mtt90) cc_final: 0.7683 (mtt90) REVERT: G 42 ARG cc_start: 0.8038 (OUTLIER) cc_final: 0.7712 (ptm160) REVERT: H 80 LEU cc_start: 0.8027 (OUTLIER) cc_final: 0.7826 (mt) REVERT: K 55 MET cc_start: -0.0073 (mmt) cc_final: -0.0674 (tpp) REVERT: K 101 ARG cc_start: 0.7221 (mmt90) cc_final: 0.5445 (mmp80) REVERT: K 113 GLN cc_start: 0.8476 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: L 51 GLU cc_start: 0.9296 (mm-30) cc_final: 0.9085 (mm-30) outliers start: 68 outliers final: 49 residues processed: 530 average time/residue: 0.3208 time to fit residues: 241.6779 Evaluate side-chains 553 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 501 time to evaluate : 1.358 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 93 GLN Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 80 LEU Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 9 LEU Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 0.4980 chunk 76 optimal weight: 3.9990 chunk 1 optimal weight: 0.4980 chunk 100 optimal weight: 30.0000 chunk 55 optimal weight: 0.8980 chunk 114 optimal weight: 20.0000 chunk 92 optimal weight: 3.9990 chunk 0 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 120 optimal weight: 30.0000 chunk 33 optimal weight: 1.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 63 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** L 25 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.3808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 16075 Z= 0.299 Angle : 0.676 9.571 22999 Z= 0.380 Chirality : 0.039 0.217 2615 Planarity : 0.004 0.033 1909 Dihedral : 29.349 174.638 4480 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.94 % Allowed : 31.68 % Favored : 61.39 % 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: 0.23 (0.25), residues: 1139 helix: 1.07 (0.20), residues: 677 sheet: -0.48 (0.57), residues: 80 loop : -1.33 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 205 HIS 0.004 0.001 HIS K 109 PHE 0.031 0.002 PHE A 67 TYR 0.049 0.003 TYR D 83 ARG 0.008 0.001 ARG B 45 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 576 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 67 poor density : 509 time to evaluate : 1.198 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: C 73 ASN cc_start: 0.8407 (t0) cc_final: 0.8161 (t0) REVERT: C 94 ASN cc_start: 0.8512 (t0) cc_final: 0.8144 (t0) REVERT: D 63 ASN cc_start: 0.8360 (OUTLIER) cc_final: 0.8158 (t0) REVERT: E 76 GLN cc_start: 0.7393 (pp30) cc_final: 0.7163 (pp30) REVERT: F 51 TYR cc_start: 0.8095 (m-80) cc_final: 0.7828 (m-80) REVERT: F 55 ARG cc_start: 0.8114 (mtt90) cc_final: 0.7755 (mtt90) REVERT: G 42 ARG cc_start: 0.8011 (OUTLIER) cc_final: 0.7698 (ptm160) REVERT: H 95 GLN cc_start: 0.7907 (tp40) cc_final: 0.7538 (tp40) REVERT: K 55 MET cc_start: -0.0273 (mmt) cc_final: -0.0918 (tpp) REVERT: K 101 ARG cc_start: 0.7445 (mmt90) cc_final: 0.5682 (mmp80) REVERT: K 113 GLN cc_start: 0.8442 (OUTLIER) cc_final: 0.8053 (pt0) REVERT: K 159 PHE cc_start: 0.8750 (t80) cc_final: 0.8308 (m-10) REVERT: K 177 THR cc_start: 0.7377 (OUTLIER) cc_final: 0.6954 (p) REVERT: K 198 MET cc_start: 0.7958 (mmt) cc_final: 0.7693 (mmm) REVERT: K 239 PHE cc_start: 0.8482 (t80) cc_final: 0.8208 (m-80) REVERT: K 240 VAL cc_start: 0.8972 (m) cc_final: 0.8340 (m) REVERT: K 243 PHE cc_start: 0.8550 (m-10) cc_final: 0.8281 (m-80) REVERT: L 51 GLU cc_start: 0.9236 (mm-30) cc_final: 0.9029 (mm-30) outliers start: 67 outliers final: 50 residues processed: 528 average time/residue: 0.2923 time to fit residues: 216.7524 Evaluate side-chains 541 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 487 time to evaluate : 1.222 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 63 ASN Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 97 GLU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 42 ARG Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 1.9990 chunk 120 optimal weight: 8.9990 chunk 26 optimal weight: 2.9990 chunk 78 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 134 optimal weight: 5.9990 chunk 111 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 89 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 104 GLN H 63 ASN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.4071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 16075 Z= 0.278 Angle : 0.671 8.631 22999 Z= 0.376 Chirality : 0.039 0.194 2615 Planarity : 0.004 0.046 1909 Dihedral : 29.344 176.978 4480 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 17.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.13 % Favored : 95.87 % Rotamer: Outliers : 7.25 % Allowed : 32.82 % Favored : 59.94 % 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 (0.25), residues: 1139 helix: 1.07 (0.20), residues: 677 sheet: -0.33 (0.58), residues: 79 loop : -1.25 (0.31), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP K 205 HIS 0.004 0.001 HIS B 75 PHE 0.010 0.001 PHE K 277 TYR 0.034 0.003 TYR D 83 ARG 0.012 0.001 ARG B 36 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 571 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 70 poor density : 501 time to evaluate : 1.184 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: A 133 GLU cc_start: 0.7614 (mp0) cc_final: 0.7244 (mp0) REVERT: C 73 ASN cc_start: 0.8423 (t0) cc_final: 0.8111 (t0) REVERT: C 94 ASN cc_start: 0.8510 (t0) cc_final: 0.8152 (t0) REVERT: F 51 TYR cc_start: 0.8074 (m-80) cc_final: 0.7779 (m-80) REVERT: F 55 ARG cc_start: 0.8135 (mtt90) cc_final: 0.7735 (mtt90) REVERT: K 55 MET cc_start: 0.0020 (mmt) cc_final: -0.0606 (tpp) REVERT: K 101 ARG cc_start: 0.7304 (mmt90) cc_final: 0.5535 (mmp80) REVERT: K 113 GLN cc_start: 0.8432 (OUTLIER) cc_final: 0.8012 (pt0) REVERT: K 177 THR cc_start: 0.7183 (OUTLIER) cc_final: 0.6971 (p) REVERT: K 243 PHE cc_start: 0.8520 (m-10) cc_final: 0.8301 (m-80) REVERT: L 1 MET cc_start: 0.5645 (ptt) cc_final: 0.4888 (ptm) outliers start: 70 outliers final: 52 residues processed: 520 average time/residue: 0.2904 time to fit residues: 212.4468 Evaluate side-chains 532 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 478 time to evaluate : 1.205 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 63 ARG Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 96 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 177 THR Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 30.0000 chunk 15 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 98 optimal weight: 4.9990 chunk 113 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 133 optimal weight: 8.9990 chunk 83 optimal weight: 3.9990 chunk 81 optimal weight: 3.9990 chunk 61 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 104 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8171 moved from start: 0.4217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.068 16075 Z= 0.464 Angle : 0.751 8.989 22999 Z= 0.421 Chirality : 0.043 0.197 2615 Planarity : 0.005 0.049 1909 Dihedral : 29.421 178.406 4480 Min Nonbonded Distance : 2.024 Molprobity Statistics. All-atom Clashscore : 22.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 7.97 % Allowed : 33.23 % Favored : 58.80 % 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: 0.04 (0.25), residues: 1139 helix: 0.85 (0.19), residues: 683 sheet: -0.67 (0.56), residues: 80 loop : -1.26 (0.32), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP K 205 HIS 0.005 0.001 HIS K 181 PHE 0.037 0.002 PHE E 67 TYR 0.064 0.003 TYR D 83 ARG 0.012 0.001 ARG L 74 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 558 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 77 poor density : 481 time to evaluate : 1.337 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: A 133 GLU cc_start: 0.7835 (mp0) cc_final: 0.7377 (mp0) REVERT: C 73 ASN cc_start: 0.8522 (t0) cc_final: 0.8026 (t0) REVERT: C 94 ASN cc_start: 0.8674 (t0) cc_final: 0.8315 (t0) REVERT: D 46 LYS cc_start: 0.8752 (mmmt) cc_final: 0.8527 (mmmt) REVERT: K 101 ARG cc_start: 0.7447 (mmt90) cc_final: 0.5717 (mmp80) REVERT: K 113 GLN cc_start: 0.8473 (OUTLIER) cc_final: 0.8038 (pm20) REVERT: K 198 MET cc_start: 0.7934 (mmm) cc_final: 0.7549 (mmm) REVERT: L 1 MET cc_start: 0.5034 (ptt) cc_final: 0.3879 (ptm) REVERT: L 36 ILE cc_start: 0.8939 (mp) cc_final: 0.8626 (tt) outliers start: 77 outliers final: 65 residues processed: 501 average time/residue: 0.3042 time to fit residues: 214.7821 Evaluate side-chains 526 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 66 poor density : 460 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 39 HIS Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 118 THR Chi-restraints excluded: chain A residue 124 ILE Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 30 VAL Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 59 THR Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 64 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 54 THR Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 30 VAL Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 66 VAL Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 63 TYR Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 242 ASN Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 53 optimal weight: 6.9990 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 26 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 91 optimal weight: 3.9990 chunk 66 optimal weight: 0.5980 chunk 12 optimal weight: 0.8980 chunk 105 optimal weight: 0.9980 chunk 121 optimal weight: 3.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 38 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN G 73 ASN G 104 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8084 moved from start: 0.4389 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.068 16075 Z= 0.265 Angle : 0.714 9.042 22999 Z= 0.393 Chirality : 0.039 0.202 2615 Planarity : 0.004 0.044 1909 Dihedral : 29.448 177.384 4480 Min Nonbonded Distance : 2.027 Molprobity Statistics. All-atom Clashscore : 19.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 6.00 % Allowed : 35.92 % Favored : 58.07 % 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 (0.25), residues: 1139 helix: 0.91 (0.19), residues: 685 sheet: -0.68 (0.56), residues: 80 loop : -1.14 (0.33), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 205 HIS 0.003 0.001 HIS B 75 PHE 0.035 0.002 PHE E 67 TYR 0.068 0.004 TYR D 83 ARG 0.011 0.001 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 546 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 488 time to evaluate : 1.248 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: A 41 TYR cc_start: 0.8558 (m-80) cc_final: 0.8340 (m-80) REVERT: A 133 GLU cc_start: 0.7924 (mp0) cc_final: 0.7466 (mp0) REVERT: B 75 HIS cc_start: 0.7831 (t70) cc_final: 0.7543 (t-90) REVERT: C 73 ASN cc_start: 0.8446 (t0) cc_final: 0.8002 (t0) REVERT: C 94 ASN cc_start: 0.8539 (t0) cc_final: 0.8183 (t0) REVERT: H 95 GLN cc_start: 0.7887 (tp40) cc_final: 0.7427 (tp40) REVERT: K 55 MET cc_start: -0.0075 (mmt) cc_final: -0.0729 (tpp) REVERT: K 101 ARG cc_start: 0.7459 (mmt90) cc_final: 0.5746 (mmp80) REVERT: K 113 GLN cc_start: 0.8568 (OUTLIER) cc_final: 0.8097 (pt0) REVERT: K 198 MET cc_start: 0.8043 (mmm) cc_final: 0.7689 (mmm) REVERT: L 1 MET cc_start: 0.5116 (ptt) cc_final: 0.4007 (ptm) REVERT: L 51 GLU cc_start: 0.9203 (OUTLIER) cc_final: 0.8866 (mm-30) outliers start: 58 outliers final: 49 residues processed: 504 average time/residue: 0.2962 time to fit residues: 210.7116 Evaluate side-chains 531 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 480 time to evaluate : 1.445 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 65 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 13 VAL Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 51 GLU Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 128 optimal weight: 0.0980 chunk 117 optimal weight: 5.9990 chunk 124 optimal weight: 0.9980 chunk 75 optimal weight: 4.9990 chunk 54 optimal weight: 0.6980 chunk 98 optimal weight: 4.9990 chunk 38 optimal weight: 1.9990 chunk 112 optimal weight: 30.0000 chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 3.9990 chunk 132 optimal weight: 20.0000 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 93 GLN F 64 ASN G 104 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8100 moved from start: 0.4544 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.088 16075 Z= 0.313 Angle : 0.741 9.333 22999 Z= 0.405 Chirality : 0.041 0.264 2615 Planarity : 0.005 0.051 1909 Dihedral : 29.378 174.893 4480 Min Nonbonded Distance : 2.035 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.95 % Favored : 96.05 % Rotamer: Outliers : 6.42 % Allowed : 37.16 % Favored : 56.42 % 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: 0.13 (0.25), residues: 1139 helix: 0.91 (0.19), residues: 678 sheet: -0.77 (0.57), residues: 79 loop : -1.13 (0.32), residues: 382 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 89 HIS 0.011 0.001 HIS G 82 PHE 0.011 0.002 PHE K 159 TYR 0.061 0.003 TYR D 83 ARG 0.013 0.001 ARG L 42 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 544 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 62 poor density : 482 time to evaluate : 1.187 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: A 41 TYR cc_start: 0.8573 (m-80) cc_final: 0.8337 (m-80) REVERT: A 133 GLU cc_start: 0.7996 (mp0) cc_final: 0.7564 (mp0) REVERT: B 75 HIS cc_start: 0.7767 (t70) cc_final: 0.7560 (t-90) REVERT: C 73 ASN cc_start: 0.8493 (t0) cc_final: 0.8057 (t0) REVERT: C 94 ASN cc_start: 0.8576 (t0) cc_final: 0.8197 (t0) REVERT: K 55 MET cc_start: 0.0208 (mmt) cc_final: -0.0448 (tpp) REVERT: K 101 ARG cc_start: 0.7466 (mmt90) cc_final: 0.5779 (mmp80) REVERT: K 113 GLN cc_start: 0.8586 (OUTLIER) cc_final: 0.8135 (pt0) REVERT: K 198 MET cc_start: 0.8130 (mmm) cc_final: 0.7686 (mmm) REVERT: L 1 MET cc_start: 0.5223 (ptt) cc_final: 0.4043 (ptm) outliers start: 62 outliers final: 51 residues processed: 498 average time/residue: 0.2858 time to fit residues: 201.6836 Evaluate side-chains 517 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 52 poor density : 465 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 60 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 60 SER Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 106 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 80 optimal weight: 3.9990 chunk 62 optimal weight: 2.9990 chunk 91 optimal weight: 3.9990 chunk 138 optimal weight: 0.6980 chunk 127 optimal weight: 2.9990 chunk 110 optimal weight: 7.9990 chunk 11 optimal weight: 0.6980 chunk 85 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 87 optimal weight: 5.9990 chunk 117 optimal weight: 8.9990 overall best weight: 1.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 63 ASN ** D 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 64 ASN F 93 GLN G 89 ASN G 104 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.094 16075 Z= 0.321 Angle : 0.752 14.823 22999 Z= 0.409 Chirality : 0.041 0.267 2615 Planarity : 0.005 0.060 1909 Dihedral : 29.374 172.517 4480 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 20.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer: Outliers : 6.73 % Allowed : 36.96 % Favored : 56.31 % 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: 0.14 (0.25), residues: 1139 helix: 0.90 (0.20), residues: 679 sheet: -0.74 (0.57), residues: 80 loop : -1.10 (0.32), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 89 HIS 0.005 0.001 HIS F 75 PHE 0.012 0.002 PHE F 100 TYR 0.060 0.003 TYR D 83 ARG 0.013 0.001 ARG L 42 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2278 Ramachandran restraints generated. 1139 Oldfield, 0 Emsley, 1139 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 538 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 65 poor density : 473 time to evaluate : 1.370 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: A 133 GLU cc_start: 0.8003 (mp0) cc_final: 0.7637 (mp0) REVERT: C 73 ASN cc_start: 0.8501 (t0) cc_final: 0.8052 (t0) REVERT: C 94 ASN cc_start: 0.8610 (t0) cc_final: 0.8216 (t0) REVERT: F 49 LEU cc_start: 0.8735 (mm) cc_final: 0.8449 (mm) REVERT: K 55 MET cc_start: 0.0199 (mmt) cc_final: -0.0462 (tpp) REVERT: K 101 ARG cc_start: 0.7442 (mmt90) cc_final: 0.5790 (mmp80) REVERT: K 113 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8141 (pt0) REVERT: K 198 MET cc_start: 0.8180 (mmm) cc_final: 0.7739 (mmm) REVERT: L 1 MET cc_start: 0.5346 (ptt) cc_final: 0.3088 (ptm) outliers start: 65 outliers final: 55 residues processed: 494 average time/residue: 0.2803 time to fit residues: 199.4459 Evaluate side-chains 517 residues out of total 994 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 56 poor density : 461 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 65 LEU Chi-restraints excluded: chain A residue 74 ILE Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain A residue 107 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 65 VAL Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain B residue 92 ARG Chi-restraints excluded: chain B residue 96 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 62 ILE Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 102 ILE Chi-restraints excluded: chain D residue 56 SER Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain E residue 46 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 117 VAL Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 22 LEU Chi-restraints excluded: chain F residue 43 VAL Chi-restraints excluded: chain F residue 50 ILE Chi-restraints excluded: chain F residue 85 ASP Chi-restraints excluded: chain F residue 92 ARG Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 43 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 88 THR Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain H residue 101 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 40 THR Chi-restraints excluded: chain K residue 52 LYS Chi-restraints excluded: chain K residue 60 LEU Chi-restraints excluded: chain K residue 86 HIS Chi-restraints excluded: chain K residue 112 GLN Chi-restraints excluded: chain K residue 113 GLN Chi-restraints excluded: chain K residue 160 VAL Chi-restraints excluded: chain K residue 170 VAL Chi-restraints excluded: chain K residue 185 VAL Chi-restraints excluded: chain K residue 190 ILE Chi-restraints excluded: chain K residue 316 THR Chi-restraints excluded: chain K residue 317 ILE Chi-restraints excluded: chain L residue 67 LEU Chi-restraints excluded: chain L residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 33 optimal weight: 0.7980 chunk 101 optimal weight: 30.0000 chunk 16 optimal weight: 0.4980 chunk 30 optimal weight: 0.7980 chunk 110 optimal weight: 0.0270 chunk 46 optimal weight: 0.9980 chunk 113 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 20 optimal weight: 0.5980 chunk 96 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 overall best weight: 0.5438 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 84 ASN ** E 68 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 125 GLN F 64 ASN F 93 GLN ** K 182 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 324 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.107168 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3139 r_free = 0.3139 target = 0.069614 restraints weight = 42768.038| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.071795 restraints weight = 17314.674| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.3205 r_free = 0.3205 target = 0.073065 restraints weight = 10765.346| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.070 | | occupancies: max = 1.00 min = 0.27 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3123 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8292 moved from start: 0.4926 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.073 16075 Z= 0.227 Angle : 0.753 14.142 22999 Z= 0.402 Chirality : 0.040 0.322 2615 Planarity : 0.004 0.056 1909 Dihedral : 29.334 172.448 4480 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 17.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 4.87 % Allowed : 39.23 % Favored : 55.90 % 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: 0.05 (0.25), residues: 1139 helix: 0.84 (0.20), residues: 673 sheet: -0.75 (0.58), residues: 80 loop : -1.14 (0.31), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 89 HIS 0.007 0.001 HIS G 82 PHE 0.015 0.002 PHE K 239 TYR 0.040 0.003 TYR D 83 ARG 0.014 0.001 ARG L 42 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4261.34 seconds wall clock time: 76 minutes 57.33 seconds (4617.33 seconds total)