Starting phenix.real_space_refine on Sun Jul 21 21:06:56 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/07_2024/8jhf_36264_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/07_2024/8jhf_36264.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.68 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/07_2024/8jhf_36264.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/07_2024/8jhf_36264.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/07_2024/8jhf_36264_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jhf_36264/07_2024/8jhf_36264_neut.cif" } resolution = 3.68 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1772 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 1 6.06 5 P 320 5.49 5 S 35 5.16 5 C 8219 2.51 5 N 2739 2.21 5 O 3389 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K GLU 76": "OE1" <-> "OE2" Residue "K GLU 225": "OE1" <-> "OE2" Residue "K GLU 247": "OE1" <-> "OE2" Residue "K GLU 325": "OE1" <-> "OE2" Residue "B GLU 74": "OE1" <-> "OE2" Residue "C GLU 64": "OE1" <-> "OE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E GLU 94": "OE1" <-> "OE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "G GLU 67": "OE1" <-> "OE2" Residue "H TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 102": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 14703 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2014 Number of conformers: 1 Conformer: "" Number of residues, atoms: 256, 2014 Classifications: {'peptide': 256} Incomplete info: {'truncation_to_alanine': 11} Link IDs: {'PTRANS': 7, 'TRANS': 248} Chain breaks: 2 Unresolved non-hydrogen bonds: 56 Unresolved non-hydrogen angles: 70 Unresolved non-hydrogen dihedrals: 51 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 4, 'ARG:plan': 2, 'TRP:plan': 1, 'HIS:plan': 1} Unresolved non-hydrogen planarities: 40 Chain: "A" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 776 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 84, 672 Classifications: {'peptide': 84} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 82} Chain: "C" Number of atoms: 850 Number of conformers: 1 Conformer: "" Number of residues, atoms: 112, 850 Classifications: {'peptide': 112} Link IDs: {'PTRANS': 3, 'TRANS': 108} Chain: "D" Number of atoms: 744 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 744 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 693 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 693 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 84} Chain: "G" Number of atoms: 825 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 825 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 3, 'TRANS': 105} Chain: "H" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 740 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "I" Number of atoms: 3253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3253 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "J" Number of atoms: 3307 Number of conformers: 1 Conformer: "" Number of residues, atoms: 160, 3307 Classifications: {'DNA': 160} Link IDs: {'rna3p': 159} Chain: "K" Number of atoms: 28 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 28 Unusual residues: {' ZN': 1} Classifications: {'peptide': 1, 'undetermined': 1} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 1726 SG CYS K 319 83.531 34.352 85.709 1.00145.38 S ATOM 1741 SG CYS K 321 84.756 36.893 84.198 1.00141.85 S ATOM 1766 SG CYS K 324 86.241 36.603 85.599 1.00143.31 S Time building chain proxies: 7.91, per 1000 atoms: 0.54 Number of scatterers: 14703 At special positions: 0 Unit cell: (110.4, 125.12, 142.6, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 1 29.99 S 35 16.00 P 320 15.00 O 3389 8.00 N 2739 7.00 C 8219 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: 6.96 Conformation dependent library (CDL) restraints added in 1.4 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 401 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 319 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 324 " pdb="ZN ZN K 401 " - pdb=" SG CYS K 321 " 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1916 Finding SS restraints... Secondary structure from input PDB file: 44 helices and 8 sheets defined 61.1% alpha, 2.3% beta 141 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 6.00 Creating SS restraints... Processing helix chain 'K' and resid 77 through 94 removed outlier: 3.560A pdb=" N ASP K 90 " --> pdb=" O SER K 86 " (cutoff:3.500A) Proline residue: K 91 - end of helix Processing helix chain 'K' and resid 149 through 159 Processing helix chain 'K' and resid 160 through 170 Processing helix chain 'K' and resid 174 through 191 removed outlier: 3.689A pdb=" N PHE K 189 " --> pdb=" O TYR K 185 " (cutoff:3.500A) Processing helix chain 'K' and resid 266 through 270 removed outlier: 3.583A pdb=" N PHE K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 327 Processing helix chain 'K' and resid 354 through 360 Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.511A pdb=" N SER A 57 " --> pdb=" O ARG A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 76 removed outlier: 3.790A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 113 removed outlier: 4.037A pdb=" N ALA A 98 " --> pdb=" O GLU A 94 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N TYR A 99 " --> pdb=" O ALA A 95 " (cutoff:3.500A) removed outlier: 3.682A pdb=" N GLY A 102 " --> pdb=" O ALA A 98 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.679A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.109A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 18 through 23 removed outlier: 3.705A pdb=" N ALA C 23 " --> pdb=" O ARG C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 28 through 38 Processing helix chain 'C' and resid 49 through 71 removed outlier: 3.793A pdb=" N ASN C 71 " --> pdb=" O GLU C 67 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.709A pdb=" N ASP C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 53 through 81 removed outlier: 3.558A pdb=" N GLY D 57 " --> pdb=" O SER D 53 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASN D 81 " --> pdb=" O LEU D 77 " (cutoff:3.500A) Processing helix chain 'D' and resid 87 through 99 removed outlier: 3.602A pdb=" N ILE D 91 " --> pdb=" O THR D 87 " (cutoff:3.500A) Processing helix chain 'D' and resid 100 through 120 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.597A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.653A pdb=" N ASP E 106 " --> pdb=" O GLY E 102 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N ALA E 114 " --> pdb=" O CYS E 110 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.667A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 23 through 29 removed outlier: 4.061A pdb=" N ILE F 26 " --> pdb=" O ARG F 23 " (cutoff:3.500A) removed outlier: 3.649A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.053A pdb=" N ARG F 55 " --> pdb=" O TYR F 51 " (cutoff:3.500A) removed outlier: 4.135A pdb=" N GLY F 56 " --> pdb=" O GLU F 52 " (cutoff:3.500A) removed outlier: 3.530A pdb=" N VAL F 57 " --> pdb=" O GLU F 53 " (cutoff:3.500A) removed outlier: 4.139A pdb=" N ARG F 67 " --> pdb=" O GLU F 63 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 28 through 37 removed outlier: 3.540A pdb=" N ILE G 32 " --> pdb=" O PRO G 28 " (cutoff:3.500A) Processing helix chain 'G' and resid 49 through 76 Processing helix chain 'G' and resid 82 through 93 removed outlier: 3.984A pdb=" N ASP G 93 " --> pdb=" O ALA G 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'G' and resid 114 through 119 removed outlier: 3.919A pdb=" N ILE G 118 " --> pdb=" O HIS G 114 " (cutoff:3.500A) Processing helix chain 'G' and resid 119 through 124 removed outlier: 3.837A pdb=" N GLN G 124 " --> pdb=" O LYS G 120 " (cutoff:3.500A) Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 53 through 81 removed outlier: 3.678A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 98 Processing helix chain 'H' and resid 100 through 121 removed outlier: 3.563A pdb=" N THR H 119 " --> pdb=" O VAL H 115 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N SER H 120 " --> pdb=" O THR H 116 " (cutoff:3.500A) removed outlier: 3.567A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 230 through 234 removed outlier: 4.324A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'K' and resid 281 through 282 Processing sheet with id=AA3, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.904A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.590A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 45 through 46 removed outlier: 6.556A pdb=" N ARG C 45 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.129A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'G' and resid 45 through 46 removed outlier: 7.060A pdb=" N ARG G 45 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 80 through 81 431 hydrogen bonds defined for protein. 1263 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 365 hydrogen bonds 730 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 5.56 Time building geometry restraints manager: 7.53 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: 3082 1.33 - 1.45: 4823 1.45 - 1.57: 7022 1.57 - 1.69: 638 1.69 - 1.81: 55 Bond restraints: 15620 Sorted by residual: bond pdb=" N ASP G 93 " pdb=" CA ASP G 93 " ideal model delta sigma weight residual 1.454 1.490 -0.036 1.19e-02 7.06e+03 9.17e+00 bond pdb=" C2 SAM K 402 " pdb=" N3 SAM K 402 " ideal model delta sigma weight residual 1.322 1.380 -0.058 2.00e-02 2.50e+03 8.43e+00 bond pdb=" N ASN K 221 " pdb=" CA ASN K 221 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.21e-02 6.83e+03 8.37e+00 bond pdb=" N LYS K 219 " pdb=" CA LYS K 219 " ideal model delta sigma weight residual 1.452 1.492 -0.040 1.41e-02 5.03e+03 8.14e+00 bond pdb=" N GLU K 233 " pdb=" CA GLU K 233 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.23e-02 6.61e+03 8.11e+00 ... (remaining 15615 not shown) Histogram of bond angle deviations from ideal: 98.41 - 105.51: 1495 105.51 - 112.61: 8701 112.61 - 119.71: 5053 119.71 - 126.82: 6270 126.82 - 133.92: 925 Bond angle restraints: 22444 Sorted by residual: angle pdb=" N LEU G 96 " pdb=" CA LEU G 96 " pdb=" C LEU G 96 " ideal model delta sigma weight residual 111.82 106.63 5.19 1.16e+00 7.43e-01 2.00e+01 angle pdb=" C LEU G 99 " pdb=" N ILE G 100 " pdb=" CA ILE G 100 " ideal model delta sigma weight residual 121.80 115.96 5.84 1.40e+00 5.10e-01 1.74e+01 angle pdb=" CA LEU D 98 " pdb=" CB LEU D 98 " pdb=" CG LEU D 98 " ideal model delta sigma weight residual 116.30 127.67 -11.37 3.50e+00 8.16e-02 1.06e+01 angle pdb=" O SAM K 402 " pdb=" C SAM K 402 " pdb=" OXT SAM K 402 " ideal model delta sigma weight residual 126.77 117.79 8.98 3.00e+00 1.11e-01 8.97e+00 angle pdb=" CA GLU G 95 " pdb=" C GLU G 95 " pdb=" O GLU G 95 " ideal model delta sigma weight residual 120.82 117.69 3.13 1.05e+00 9.07e-01 8.91e+00 ... (remaining 22439 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.97: 7087 35.97 - 71.94: 1452 71.94 - 107.90: 24 107.90 - 143.87: 1 143.87 - 179.84: 5 Dihedral angle restraints: 8569 sinusoidal: 5598 harmonic: 2971 Sorted by residual: dihedral pdb=" C4' DT J 138 " pdb=" C3' DT J 138 " pdb=" O3' DT J 138 " pdb=" P DC J 139 " ideal model delta sinusoidal sigma weight residual -140.00 39.84 -179.84 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DA I 145 " pdb=" C3' DA I 145 " pdb=" O3' DA I 145 " pdb=" P DT I 146 " ideal model delta sinusoidal sigma weight residual 220.00 45.07 174.93 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DT I 99 " pdb=" C3' DT I 99 " pdb=" O3' DT I 99 " pdb=" P DA I 100 " ideal model delta sinusoidal sigma weight residual 220.00 64.06 155.94 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 8566 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.035: 1879 0.035 - 0.069: 512 0.069 - 0.104: 103 0.104 - 0.138: 32 0.138 - 0.173: 7 Chirality restraints: 2533 Sorted by residual: chirality pdb=" C2' SAM K 402 " pdb=" C1' SAM K 402 " pdb=" C3' SAM K 402 " pdb=" O2' SAM K 402 " both_signs ideal model delta sigma weight residual False -2.76 -2.58 -0.17 2.00e-01 2.50e+01 7.48e-01 chirality pdb=" CA ASP D 48 " pdb=" N ASP D 48 " pdb=" C ASP D 48 " pdb=" CB ASP D 48 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.36e-01 chirality pdb=" CA ASP E 81 " pdb=" N ASP E 81 " pdb=" C ASP E 81 " pdb=" CB ASP E 81 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.11e-01 ... (remaining 2530 not shown) Planarity restraints: 1733 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE K 231 " 0.012 2.00e-02 2.50e+03 2.32e-02 5.40e+00 pdb=" C ILE K 231 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE K 231 " 0.015 2.00e-02 2.50e+03 pdb=" N ALA K 232 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP K 264 " 0.013 2.00e-02 2.50e+03 1.45e-02 5.28e+00 pdb=" CG TRP K 264 " -0.037 2.00e-02 2.50e+03 pdb=" CD1 TRP K 264 " 0.022 2.00e-02 2.50e+03 pdb=" CD2 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP K 264 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TRP K 264 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" CZ2 TRP K 264 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP K 264 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP K 264 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS F 31 " -0.030 5.00e-02 4.00e+02 4.53e-02 3.28e+00 pdb=" N PRO F 32 " 0.078 5.00e-02 4.00e+02 pdb=" CA PRO F 32 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO F 32 " -0.025 5.00e-02 4.00e+02 ... (remaining 1730 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 422 2.67 - 3.23: 12731 3.23 - 3.78: 25247 3.78 - 4.34: 31782 4.34 - 4.90: 46876 Nonbonded interactions: 117058 Sorted by model distance: nonbonded pdb=" O THR K 284 " pdb=" OG1 THR K 288 " model vdw 2.111 2.440 nonbonded pdb=" O MET K 188 " pdb=" OG SER K 193 " model vdw 2.169 2.440 nonbonded pdb=" O2 DT I 157 " pdb=" N6 DA J 11 " model vdw 2.210 2.520 nonbonded pdb=" OG1 THR K 97 " pdb=" OD1 ASN K 208 " model vdw 2.224 2.440 nonbonded pdb=" OG1 THR K 97 " pdb=" O ASN K 208 " model vdw 2.231 2.440 ... (remaining 117053 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and resid 41 through 134) selection = (chain 'E' and (resid 41 through 60 or (resid 61 and (name N or name CA or name \ C or name O or name CB )) or resid 62 through 134)) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 19 through 102) } ncs_group { reference = (chain 'C' and resid 16 through 124) selection = chain 'G' } ncs_group { reference = (chain 'D' and (resid 28 through 72 or (resid 73 through 74 and (name N or name \ CA or name C or name O or name CB )) or resid 75 through 122)) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 0.560 Check model and map are aligned: 0.110 Set scattering table: 0.130 Process input model: 46.370 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 15620 Z= 0.226 Angle : 0.613 11.372 22444 Z= 0.357 Chirality : 0.035 0.173 2533 Planarity : 0.004 0.045 1733 Dihedral : 27.225 179.840 6653 Min Nonbonded Distance : 2.111 Molprobity Statistics. All-atom Clashscore : 8.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.77 % Favored : 95.23 % Rotamer: Outliers : 0.70 % Allowed : 0.35 % Favored : 98.95 % 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: 0.59 (0.27), residues: 1007 helix: 1.90 (0.22), residues: 598 sheet: -0.18 (0.84), residues: 22 loop : -2.15 (0.27), residues: 387 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP K 264 HIS 0.004 0.001 HIS K 98 PHE 0.010 0.001 PHE K 281 TYR 0.025 0.001 TYR F 88 ARG 0.008 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 157 time to evaluate : 1.199 Fit side-chains REVERT: K 100 MET cc_start: 0.7208 (pmm) cc_final: 0.6878 (pmm) REVERT: E 76 GLN cc_start: 0.8591 (tm-30) cc_final: 0.8325 (tm-30) REVERT: G 95 GLU cc_start: 0.7085 (mm-30) cc_final: 0.6652 (mm-30) REVERT: G 115 LYS cc_start: 0.7753 (ttmm) cc_final: 0.7519 (tptp) outliers start: 6 outliers final: 0 residues processed: 161 average time/residue: 0.3368 time to fit residues: 75.9323 Evaluate side-chains 134 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 1.030 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 0.8980 chunk 66 optimal weight: 3.9990 chunk 52 optimal weight: 0.0010 chunk 101 optimal weight: 10.0000 chunk 39 optimal weight: 2.9990 chunk 61 optimal weight: 8.9990 chunk 75 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 overall best weight: 2.3792 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 181 HIS ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8043 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 15620 Z= 0.206 Angle : 0.564 8.082 22444 Z= 0.332 Chirality : 0.035 0.146 2533 Planarity : 0.004 0.040 1733 Dihedral : 29.995 178.645 4658 Min Nonbonded Distance : 2.113 Molprobity Statistics. All-atom Clashscore : 7.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer: Outliers : 1.41 % Allowed : 9.84 % Favored : 88.76 % 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: 0.96 (0.27), residues: 1007 helix: 2.23 (0.22), residues: 606 sheet: 0.10 (0.92), residues: 22 loop : -2.15 (0.28), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS F 75 PHE 0.008 0.001 PHE K 195 TYR 0.019 0.001 TYR F 88 ARG 0.003 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 1.103 Fit side-chains REVERT: K 100 MET cc_start: 0.7204 (pmm) cc_final: 0.6813 (pmm) REVERT: E 76 GLN cc_start: 0.8607 (tm-30) cc_final: 0.8389 (tm-30) outliers start: 12 outliers final: 7 residues processed: 150 average time/residue: 0.2925 time to fit residues: 61.9966 Evaluate side-chains 138 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 131 time to evaluate : 1.137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 65 optimal weight: 6.9990 chunk 36 optimal weight: 7.9990 chunk 98 optimal weight: 40.0000 chunk 80 optimal weight: 7.9990 chunk 32 optimal weight: 4.9990 chunk 118 optimal weight: 10.0000 chunk 127 optimal weight: 10.0000 chunk 105 optimal weight: 10.0000 chunk 117 optimal weight: 10.0000 chunk 40 optimal weight: 6.9990 chunk 94 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 60 ASN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8161 moved from start: 0.1689 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.048 15620 Z= 0.435 Angle : 0.680 8.047 22444 Z= 0.394 Chirality : 0.040 0.155 2533 Planarity : 0.005 0.044 1733 Dihedral : 30.286 179.514 4658 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 9.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.26 % Favored : 93.74 % Rotamer: Outliers : 2.69 % Allowed : 15.11 % Favored : 82.20 % 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: 0.44 (0.27), residues: 1007 helix: 1.82 (0.21), residues: 602 sheet: -0.10 (0.85), residues: 24 loop : -2.34 (0.28), residues: 381 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP K 264 HIS 0.007 0.002 HIS H 46 PHE 0.013 0.002 PHE K 281 TYR 0.027 0.002 TYR H 80 ARG 0.004 0.001 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 136 time to evaluate : 1.201 Fit side-chains REVERT: K 100 MET cc_start: 0.7508 (pmm) cc_final: 0.7037 (pmm) REVERT: E 76 GLN cc_start: 0.8788 (tm-30) cc_final: 0.8495 (tm-30) outliers start: 23 outliers final: 17 residues processed: 151 average time/residue: 0.2918 time to fit residues: 62.2047 Evaluate side-chains 142 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 125 time to evaluate : 1.150 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 20 SER Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain D residue 87 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 118 ILE Chi-restraints excluded: chain H residue 115 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 116 optimal weight: 10.0000 chunk 88 optimal weight: 7.9990 chunk 61 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 56 optimal weight: 0.8980 chunk 79 optimal weight: 3.9990 chunk 118 optimal weight: 10.0000 chunk 125 optimal weight: 10.0000 chunk 62 optimal weight: 9.9990 chunk 112 optimal weight: 20.0000 chunk 33 optimal weight: 3.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8064 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15620 Z= 0.207 Angle : 0.556 6.589 22444 Z= 0.330 Chirality : 0.034 0.151 2533 Planarity : 0.004 0.045 1733 Dihedral : 30.056 179.356 4658 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.27 % Favored : 95.63 % Rotamer: Outliers : 1.99 % Allowed : 17.45 % Favored : 80.56 % 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: 0.91 (0.27), residues: 1007 helix: 2.24 (0.22), residues: 606 sheet: -0.49 (0.85), residues: 25 loop : -2.25 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 264 HIS 0.004 0.001 HIS F 75 PHE 0.007 0.001 PHE H 62 TYR 0.028 0.001 TYR H 80 ARG 0.005 0.000 ARG D 83 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 144 time to evaluate : 1.072 Fit side-chains REVERT: K 100 MET cc_start: 0.7321 (pmm) cc_final: 0.6840 (pmm) REVERT: K 188 MET cc_start: 0.7934 (tmm) cc_final: 0.7732 (tmm) REVERT: K 241 MET cc_start: 0.7443 (tmm) cc_final: 0.6775 (tmm) REVERT: E 76 GLN cc_start: 0.8657 (tm-30) cc_final: 0.8408 (tm-30) outliers start: 17 outliers final: 10 residues processed: 157 average time/residue: 0.2867 time to fit residues: 64.0828 Evaluate side-chains 146 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 136 time to evaluate : 1.069 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 104 optimal weight: 10.0000 chunk 71 optimal weight: 6.9990 chunk 1 optimal weight: 5.9990 chunk 93 optimal weight: 0.5980 chunk 51 optimal weight: 0.0050 chunk 107 optimal weight: 10.0000 chunk 86 optimal weight: 8.9990 chunk 0 optimal weight: 30.0000 chunk 64 optimal weight: 5.9990 chunk 112 optimal weight: 20.0000 chunk 31 optimal weight: 0.9980 overall best weight: 2.7198 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 181 HIS ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15620 Z= 0.216 Angle : 0.556 7.567 22444 Z= 0.329 Chirality : 0.034 0.151 2533 Planarity : 0.004 0.042 1733 Dihedral : 30.081 179.729 4658 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.78 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.06 % Favored : 94.84 % Rotamer: Outliers : 2.58 % Allowed : 17.10 % Favored : 80.33 % 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: 0.98 (0.27), residues: 1007 helix: 2.34 (0.22), residues: 606 sheet: -0.53 (0.85), residues: 25 loop : -2.31 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP K 264 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 62 TYR 0.027 0.001 TYR H 80 ARG 0.006 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 138 time to evaluate : 1.072 Fit side-chains REVERT: K 100 MET cc_start: 0.7288 (pmm) cc_final: 0.6804 (pmm) REVERT: K 188 MET cc_start: 0.7957 (tmm) cc_final: 0.7748 (tmm) REVERT: K 241 MET cc_start: 0.7499 (tmm) cc_final: 0.6825 (tmm) REVERT: K 254 TYR cc_start: 0.6353 (t80) cc_final: 0.6086 (t80) REVERT: E 76 GLN cc_start: 0.8671 (tm-30) cc_final: 0.8394 (tm-30) outliers start: 22 outliers final: 17 residues processed: 155 average time/residue: 0.2757 time to fit residues: 61.3983 Evaluate side-chains 147 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 130 time to evaluate : 1.020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 42 optimal weight: 2.9990 chunk 113 optimal weight: 20.0000 chunk 24 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 125 optimal weight: 10.0000 chunk 104 optimal weight: 10.0000 chunk 58 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 41 optimal weight: 5.9990 chunk 66 optimal weight: 8.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8055 moved from start: 0.1792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 15620 Z= 0.198 Angle : 0.548 8.157 22444 Z= 0.325 Chirality : 0.034 0.153 2533 Planarity : 0.004 0.042 1733 Dihedral : 30.049 179.773 4658 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.67 % Favored : 95.23 % Rotamer: Outliers : 2.22 % Allowed : 18.15 % Favored : 79.63 % 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: 1.05 (0.27), residues: 1007 helix: 2.41 (0.22), residues: 606 sheet: -0.54 (0.85), residues: 25 loop : -2.31 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 264 HIS 0.003 0.001 HIS H 79 PHE 0.007 0.001 PHE H 62 TYR 0.030 0.001 TYR H 80 ARG 0.006 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 139 time to evaluate : 1.125 Fit side-chains REVERT: K 100 MET cc_start: 0.7293 (pmm) cc_final: 0.6802 (pmm) REVERT: K 188 MET cc_start: 0.7997 (tmm) cc_final: 0.7795 (tmm) REVERT: K 241 MET cc_start: 0.7485 (tmm) cc_final: 0.6770 (tmm) REVERT: K 254 TYR cc_start: 0.6296 (t80) cc_final: 0.6011 (t80) REVERT: E 76 GLN cc_start: 0.8654 (tm-30) cc_final: 0.8384 (tm-30) outliers start: 19 outliers final: 13 residues processed: 153 average time/residue: 0.2869 time to fit residues: 62.7991 Evaluate side-chains 147 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 134 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 121 optimal weight: 10.0000 chunk 14 optimal weight: 7.9990 chunk 71 optimal weight: 4.9990 chunk 91 optimal weight: 6.9990 chunk 105 optimal weight: 10.0000 chunk 70 optimal weight: 2.9990 chunk 125 optimal weight: 10.0000 chunk 78 optimal weight: 1.9990 chunk 76 optimal weight: 0.9980 chunk 57 optimal weight: 1.9990 chunk 77 optimal weight: 0.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 44 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8039 moved from start: 0.1883 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 15620 Z= 0.178 Angle : 0.534 5.642 22444 Z= 0.318 Chirality : 0.033 0.155 2533 Planarity : 0.004 0.043 1733 Dihedral : 30.032 178.897 4658 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 8.48 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.67 % Favored : 95.23 % Rotamer: Outliers : 2.93 % Allowed : 17.33 % Favored : 79.74 % 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: 1.11 (0.27), residues: 1007 helix: 2.48 (0.22), residues: 606 sheet: -0.53 (0.88), residues: 25 loop : -2.30 (0.27), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.008 0.001 HIS H 79 PHE 0.007 0.001 PHE H 62 TYR 0.030 0.001 TYR H 80 ARG 0.006 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 142 time to evaluate : 1.193 Fit side-chains REVERT: K 100 MET cc_start: 0.7277 (pmm) cc_final: 0.6783 (pmm) REVERT: K 254 TYR cc_start: 0.6216 (t80) cc_final: 0.5938 (t80) REVERT: E 76 GLN cc_start: 0.8634 (tm-30) cc_final: 0.8370 (tm-30) outliers start: 25 outliers final: 20 residues processed: 161 average time/residue: 0.2746 time to fit residues: 63.9101 Evaluate side-chains 155 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.100 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 76 LEU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 50 optimal weight: 4.9990 chunk 74 optimal weight: 2.9990 chunk 37 optimal weight: 7.9990 chunk 24 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 85 optimal weight: 0.0070 chunk 61 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 98 optimal weight: 40.0000 chunk 113 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 overall best weight: 4.8006 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.2006 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 15620 Z= 0.326 Angle : 0.619 9.294 22444 Z= 0.361 Chirality : 0.037 0.155 2533 Planarity : 0.004 0.040 1733 Dihedral : 30.195 179.390 4658 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.10 % Allowed : 6.45 % Favored : 93.45 % Rotamer: Outliers : 2.81 % Allowed : 18.62 % Favored : 78.57 % 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: 0.74 (0.27), residues: 1007 helix: 2.14 (0.21), residues: 605 sheet: -0.36 (0.89), residues: 25 loop : -2.40 (0.27), residues: 377 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 264 HIS 0.005 0.001 HIS D 79 PHE 0.010 0.001 PHE H 62 TYR 0.024 0.002 TYR H 80 ARG 0.006 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 140 time to evaluate : 1.142 Fit side-chains REVERT: K 100 MET cc_start: 0.7418 (pmm) cc_final: 0.6915 (pmm) REVERT: B 53 GLU cc_start: 0.7591 (tt0) cc_final: 0.7387 (tt0) REVERT: E 76 GLN cc_start: 0.8756 (tm-30) cc_final: 0.8408 (tm-30) outliers start: 24 outliers final: 18 residues processed: 157 average time/residue: 0.2839 time to fit residues: 63.7984 Evaluate side-chains 148 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 130 time to evaluate : 1.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 109 optimal weight: 10.0000 chunk 116 optimal weight: 20.0000 chunk 120 optimal weight: 10.0000 chunk 70 optimal weight: 0.7980 chunk 50 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 chunk 35 optimal weight: 4.9990 chunk 105 optimal weight: 10.0000 chunk 110 optimal weight: 10.0000 chunk 76 optimal weight: 3.9990 chunk 123 optimal weight: 10.0000 overall best weight: 3.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 169 ASN ** K 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8095 moved from start: 0.1995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15620 Z= 0.246 Angle : 0.580 6.947 22444 Z= 0.341 Chirality : 0.035 0.152 2533 Planarity : 0.004 0.051 1733 Dihedral : 30.142 179.019 4658 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.16 % Favored : 94.74 % Rotamer: Outliers : 2.93 % Allowed : 19.09 % Favored : 77.99 % 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: 0.79 (0.27), residues: 1007 helix: 2.21 (0.21), residues: 605 sheet: -0.52 (0.91), residues: 23 loop : -2.42 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP K 264 HIS 0.004 0.001 HIS D 46 PHE 0.008 0.001 PHE H 62 TYR 0.014 0.001 TYR F 88 ARG 0.006 0.000 ARG E 40 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 136 time to evaluate : 1.160 Fit side-chains REVERT: K 100 MET cc_start: 0.7367 (pmm) cc_final: 0.6853 (pmm) REVERT: E 76 GLN cc_start: 0.8713 (tm-30) cc_final: 0.8385 (tm-30) outliers start: 25 outliers final: 20 residues processed: 155 average time/residue: 0.2801 time to fit residues: 62.4619 Evaluate side-chains 155 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 135 time to evaluate : 1.199 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 95 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 75 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 129 optimal weight: 40.0000 chunk 119 optimal weight: 10.0000 chunk 103 optimal weight: 9.9990 chunk 10 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 63 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 10.0000 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8079 moved from start: 0.2023 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 15620 Z= 0.225 Angle : 0.578 11.311 22444 Z= 0.338 Chirality : 0.034 0.150 2533 Planarity : 0.004 0.051 1733 Dihedral : 30.134 178.587 4658 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.10 % Allowed : 5.36 % Favored : 94.54 % Rotamer: Outliers : 2.81 % Allowed : 19.20 % Favored : 77.99 % 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: 0.84 (0.27), residues: 1007 helix: 2.27 (0.21), residues: 605 sheet: -0.57 (0.91), residues: 23 loop : -2.42 (0.27), residues: 379 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 264 HIS 0.003 0.001 HIS D 46 PHE 0.007 0.001 PHE H 62 TYR 0.030 0.001 TYR F 88 ARG 0.006 0.000 ARG E 40 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 159 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.232 Fit side-chains revert: symmetry clash REVERT: K 100 MET cc_start: 0.7358 (pmm) cc_final: 0.6840 (pmm) REVERT: E 76 GLN cc_start: 0.8701 (tm-30) cc_final: 0.8380 (tm-30) outliers start: 24 outliers final: 21 residues processed: 153 average time/residue: 0.2771 time to fit residues: 61.0688 Evaluate side-chains 156 residues out of total 867 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 135 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 191 THR Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain K residue 262 GLN Chi-restraints excluded: chain K residue 278 ASN Chi-restraints excluded: chain K residue 282 VAL Chi-restraints excluded: chain K residue 291 VAL Chi-restraints excluded: chain K residue 345 ILE Chi-restraints excluded: chain A residue 41 TYR Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 96 LEU Chi-restraints excluded: chain D residue 45 VAL Chi-restraints excluded: chain E residue 118 THR Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 17 VAL Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 118 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 130 random chunks: chunk 31 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 15 optimal weight: 20.0000 chunk 28 optimal weight: 0.7980 chunk 103 optimal weight: 10.0000 chunk 43 optimal weight: 0.0170 chunk 106 optimal weight: 10.0000 chunk 13 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 90 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 overall best weight: 1.1622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN E 108 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4013 r_free = 0.4013 target = 0.136583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3256 r_free = 0.3256 target = 0.089962 restraints weight = 35252.452| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3257 r_free = 0.3257 target = 0.090121 restraints weight = 21788.642| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.090946 restraints weight = 15577.461| |-----------------------------------------------------------------------------| r_work (final): 0.3211 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8068 moved from start: 0.2219 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 15620 Z= 0.162 Angle : 0.536 6.672 22444 Z= 0.318 Chirality : 0.033 0.173 2533 Planarity : 0.004 0.051 1733 Dihedral : 30.068 177.529 4658 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.10 % Allowed : 4.17 % Favored : 95.73 % Rotamer: Outliers : 1.76 % Allowed : 20.14 % Favored : 78.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.09 (0.27), residues: 1007 helix: 2.47 (0.21), residues: 606 sheet: -0.93 (0.95), residues: 25 loop : -2.30 (0.28), residues: 376 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP K 264 HIS 0.002 0.001 HIS K 98 PHE 0.006 0.001 PHE B 61 TYR 0.013 0.001 TYR F 88 ARG 0.007 0.000 ARG E 40 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2189.33 seconds wall clock time: 40 minutes 9.66 seconds (2409.66 seconds total)