Starting phenix.real_space_refine on Sat Feb 17 10:46:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.59 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7afh_11765/02_2024/7afh_11765_neut_updated.pdb" } resolution = 3.59 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 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: 7 Type Number sf(0) Gaussians Zn 1 6.06 5 P 456 5.49 5 Mg 11 5.21 5 S 28 5.16 5 C 9820 2.51 5 N 3442 2.21 5 O 4724 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 193": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J TYR 65": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N PHE 77": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 18482 Number of models: 1 Model: "" Number of chains: 11 Chain: "1" Number of atoms: 9758 Number of conformers: 1 Conformer: "" Number of residues, atoms: 456, 9758 Classifications: {'RNA': 456} Modifications used: {'rna2p_pur': 37, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 211, 'rna3p_pyr': 171} Link IDs: {'rna2p': 71, 'rna3p': 384} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 9 Unresolved non-hydrogen dihedrals: 3 Chain: "B" Number of atoms: 1753 Number of conformers: 1 Conformer: "" Number of residues, atoms: 224, 1753 Classifications: {'peptide': 224} Link IDs: {'PTRANS': 7, 'TRANS': 216} Chain: "C" Number of atoms: 1653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1653 Classifications: {'peptide': 211} Link IDs: {'PTRANS': 7, 'TRANS': 203} Chain: "G" Number of atoms: 1143 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 1143 Classifications: {'peptide': 146} Link IDs: {'PTRANS': 5, 'TRANS': 140} Chain: "I" Number of atoms: 1022 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1022 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 123} Chain: "J" Number of atoms: 795 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 795 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 5, 'TRANS': 93} Chain: "M" Number of atoms: 883 Number of conformers: 1 Conformer: "" Number of residues, atoms: 114, 883 Classifications: {'peptide': 114} Link IDs: {'PTRANS': 4, 'TRANS': 109} Chain: "N" Number of atoms: 805 Number of conformers: 1 Conformer: "" Number of residues, atoms: 100, 805 Classifications: {'peptide': 100} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 4, 'TRANS': 95} Chain: "S" Number of atoms: 658 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 658 Classifications: {'peptide': 82} Link IDs: {'PTRANS': 5, 'TRANS': 76} Chain: "1" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Unusual residues: {' MG': 11} Classifications: {'undetermined': 11} Link IDs: {None: 10} Chain: "B" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' ZN': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.51, per 1000 atoms: 0.51 Number of scatterers: 18482 At special positions: 0 Unit cell: (116.095, 116.095, 158.41, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) Zn 1 29.99 S 28 16.00 P 456 15.00 Mg 11 11.99 O 4724 8.00 N 3442 7.00 C 9820 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: 12.49 Conformation dependent library (CDL) restraints added in 1.7 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2042 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 9 sheets defined 43.0% alpha, 11.7% beta 130 base pairs and 210 stacking pairs defined. Time for finding SS restraints: 9.96 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.707A pdb=" N ALA B 12 " --> pdb=" O ASP B 8 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 30 Proline residue: B 29 - end of helix Processing helix chain 'B' and resid 43 through 63 Proline residue: B 48 - end of helix Processing helix chain 'B' and resid 77 through 87 removed outlier: 3.674A pdb=" N CYS B 87 " --> pdb=" O ALA B 83 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 123 Processing helix chain 'B' and resid 131 through 148 Processing helix chain 'B' and resid 170 through 179 Processing helix chain 'B' and resid 193 through 195 No H-bonds generated for 'chain 'B' and resid 193 through 195' Processing helix chain 'B' and resid 207 through 226 Processing helix chain 'C' and resid 7 through 11 removed outlier: 3.781A pdb=" N ARG C 11 " --> pdb=" O PRO C 7 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 7 through 11' Processing helix chain 'C' and resid 29 through 49 removed outlier: 5.627A pdb=" N LYS C 49 " --> pdb=" O LYS C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 82 through 94 Processing helix chain 'C' and resid 109 through 111 No H-bonds generated for 'chain 'C' and resid 109 through 111' Processing helix chain 'C' and resid 114 through 125 Processing helix chain 'C' and resid 130 through 144 Processing helix chain 'C' and resid 157 through 159 No H-bonds generated for 'chain 'C' and resid 157 through 159' Processing helix chain 'G' and resid 21 through 30 Processing helix chain 'G' and resid 36 through 53 removed outlier: 4.003A pdb=" N ILE G 42 " --> pdb=" O THR G 38 " (cutoff:3.500A) removed outlier: 3.655A pdb=" N THR G 49 " --> pdb=" O SER G 45 " (cutoff:3.500A) removed outlier: 3.572A pdb=" N GLN G 52 " --> pdb=" O GLU G 48 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 69 removed outlier: 4.294A pdb=" N GLU G 63 " --> pdb=" O LEU G 59 " (cutoff:3.500A) removed outlier: 4.195A pdb=" N ASN G 68 " --> pdb=" O VAL G 64 " (cutoff:3.500A) Processing helix chain 'G' and resid 93 through 110 Processing helix chain 'G' and resid 116 through 128 Processing helix chain 'G' and resid 134 through 146 Processing helix chain 'I' and resid 35 through 38 No H-bonds generated for 'chain 'I' and resid 35 through 38' Processing helix chain 'I' and resid 42 through 55 Proline residue: I 51 - end of helix Processing helix chain 'I' and resid 72 through 91 Processing helix chain 'I' and resid 95 through 100 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 89 removed outlier: 3.872A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 21 Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 61 removed outlier: 4.497A pdb=" N THR M 55 " --> pdb=" O GLY M 51 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 82 Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 107 through 110 No H-bonds generated for 'chain 'M' and resid 107 through 110' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 32 Processing helix chain 'N' and resid 40 through 50 Processing helix chain 'N' and resid 53 through 55 No H-bonds generated for 'chain 'N' and resid 53 through 55' Processing helix chain 'N' and resid 83 through 89 Processing helix chain 'S' and resid 13 through 24 Processing helix chain 'S' and resid 64 through 66 No H-bonds generated for 'chain 'S' and resid 64 through 66' Processing helix chain 'S' and resid 71 through 74 Processing sheet with id= A, first strand: chain 'B' and resid 90 through 92 removed outlier: 6.697A pdb=" N ALA B 160 " --> pdb=" O LEU B 68 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N VAL B 70 " --> pdb=" O ALA B 160 " (cutoff:3.500A) removed outlier: 6.245A pdb=" N PHE B 162 " --> pdb=" O VAL B 70 " (cutoff:3.500A) removed outlier: 7.070A pdb=" N PHE B 198 " --> pdb=" O ALA B 185 " (cutoff:3.500A) removed outlier: 7.610A pdb=" N VAL B 187 " --> pdb=" O PHE B 198 " (cutoff:3.500A) removed outlier: 6.318A pdb=" N ILE B 200 " --> pdb=" O VAL B 187 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'B' and resid 31 through 35 removed outlier: 6.928A pdb=" N ILE B 40 " --> pdb=" O PHE B 32 " (cutoff:3.500A) removed outlier: 4.430A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.124A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 99 through 103 removed outlier: 6.745A pdb=" N ILE C 64 " --> pdb=" O GLN C 100 " (cutoff:3.500A) removed outlier: 7.567A pdb=" N ASN C 102 " --> pdb=" O ILE C 64 " (cutoff:3.500A) removed outlier: 5.807A pdb=" N VAL C 66 " --> pdb=" O ASN C 102 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'C' and resid 166 through 170 Processing sheet with id= E, first strand: chain 'G' and resid 73 through 75 Processing sheet with id= F, first strand: chain 'I' and resid 6 through 11 removed outlier: 3.738A pdb=" N GLY I 10 " --> pdb=" O ALA I 17 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'J' and resid 98 through 101 removed outlier: 4.678A pdb=" N LEU J 71 " --> pdb=" O LEU J 42 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'J' and resid 45 through 51 Processing sheet with id= I, first strand: chain 'S' and resid 31 through 33 removed outlier: 3.985A pdb=" N LEU S 31 " --> pdb=" O THR S 48 " (cutoff:3.500A) 372 hydrogen bonds defined for protein. 1080 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 299 hydrogen bonds 378 hydrogen bond angles 0 basepair planarities 130 basepair parallelities 210 stacking parallelities Total time for adding SS restraints: 9.14 Time building geometry restraints manager: 12.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 2703 1.32 - 1.45: 7435 1.45 - 1.57: 8660 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19762 Sorted by residual: bond pdb=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.496 1.339 0.157 2.00e-02 2.50e+03 6.15e+01 bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.496 1.342 0.154 2.00e-02 2.50e+03 5.96e+01 bond pdb=" C2 5MC 1 967 " pdb=" N3 5MC 1 967 " ideal model delta sigma weight residual 1.493 1.341 0.152 2.00e-02 2.50e+03 5.80e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.475 1.340 0.135 2.00e-02 2.50e+03 4.55e+01 bond pdb=" C2 2MG 1 966 " pdb=" N2 2MG 1 966 " ideal model delta sigma weight residual 1.475 1.341 0.134 2.00e-02 2.50e+03 4.50e+01 ... (remaining 19757 not shown) Histogram of bond angle deviations from ideal: 98.99 - 106.55: 2805 106.55 - 114.12: 12384 114.12 - 121.69: 9322 121.69 - 129.25: 3914 129.25 - 136.82: 472 Bond angle restraints: 28897 Sorted by residual: angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C8 2MG 11207 " ideal model delta sigma weight residual 110.07 127.33 -17.26 3.00e+00 1.11e-01 3.31e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 138.70 122.93 15.77 3.00e+00 1.11e-01 2.76e+01 angle pdb=" C HIS M 14 " pdb=" CA HIS M 14 " pdb=" CB HIS M 14 " ideal model delta sigma weight residual 109.62 118.70 -9.08 1.79e+00 3.12e-01 2.57e+01 angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C8 2MG 1 966 " ideal model delta sigma weight residual 110.07 125.13 -15.06 3.00e+00 1.11e-01 2.52e+01 angle pdb=" CA GLY B 124 " pdb=" C GLY B 124 " pdb=" O GLY B 124 " ideal model delta sigma weight residual 121.30 116.92 4.38 9.80e-01 1.04e+00 1.99e+01 ... (remaining 28892 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.21: 11240 35.21 - 70.41: 1172 70.41 - 105.62: 156 105.62 - 140.82: 5 140.82 - 176.03: 4 Dihedral angle restraints: 12577 sinusoidal: 9422 harmonic: 3155 Sorted by residual: dihedral pdb=" C4' G 11279 " pdb=" C3' G 11279 " pdb=" C2' G 11279 " pdb=" C1' G 11279 " ideal model delta sinusoidal sigma weight residual -35.00 35.37 -70.37 1 8.00e+00 1.56e-02 9.96e+01 dihedral pdb=" C5' G 11279 " pdb=" C4' G 11279 " pdb=" C3' G 11279 " pdb=" O3' G 11279 " ideal model delta sinusoidal sigma weight residual 147.00 81.41 65.59 1 8.00e+00 1.56e-02 8.80e+01 dihedral pdb=" O4' U 11008 " pdb=" C1' U 11008 " pdb=" N1 U 11008 " pdb=" C2 U 11008 " ideal model delta sinusoidal sigma weight residual -160.00 16.03 -176.03 1 1.50e+01 4.44e-03 8.52e+01 ... (remaining 12574 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.066: 3080 0.066 - 0.131: 417 0.131 - 0.197: 75 0.197 - 0.263: 17 0.263 - 0.328: 3 Chirality restraints: 3592 Sorted by residual: chirality pdb=" C3' G 11279 " pdb=" C4' G 11279 " pdb=" O3' G 11279 " pdb=" C2' G 11279 " both_signs ideal model delta sigma weight residual False -2.74 -2.42 -0.33 2.00e-01 2.50e+01 2.69e+00 chirality pdb=" CA THR B 125 " pdb=" N THR B 125 " pdb=" C THR B 125 " pdb=" CB THR B 125 " both_signs ideal model delta sigma weight residual False 2.53 2.24 0.29 2.00e-01 2.50e+01 2.06e+00 chirality pdb=" CA HIS M 14 " pdb=" N HIS M 14 " pdb=" C HIS M 14 " pdb=" CB HIS M 14 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.27 2.00e-01 2.50e+01 1.76e+00 ... (remaining 3589 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " 0.024 2.00e-02 2.50e+03 5.84e-01 7.68e+03 pdb=" C4' 2MG 1 966 " 0.450 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " 0.716 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " -0.586 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " -0.553 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " -0.230 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " 0.876 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " 0.218 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " -0.915 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " 0.012 2.00e-02 2.50e+03 5.66e-01 7.21e+03 pdb=" C4' 5MC 1 967 " 0.442 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " 0.660 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " -0.584 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " -0.540 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " -0.228 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " 0.877 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " 0.226 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " -0.865 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " -0.043 2.00e-02 2.50e+03 5.63e-01 7.12e+03 pdb=" C4' 2MG 11207 " -0.431 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " -0.562 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " 0.587 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " 0.578 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " 0.195 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " -0.924 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " -0.245 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " 0.845 2.00e-02 2.50e+03 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 268 2.38 - 3.01: 11533 3.01 - 3.64: 38228 3.64 - 4.27: 54126 4.27 - 4.90: 74574 Nonbonded interactions: 178729 Sorted by model distance: nonbonded pdb=" O3' G 11365 " pdb="MG MG 11606 " model vdw 1.752 2.170 nonbonded pdb=" O3' G 11242 " pdb="MG MG 11610 " model vdw 1.796 2.170 nonbonded pdb=" OP1 U 11199 " pdb="MG MG 11609 " model vdw 1.842 2.170 nonbonded pdb=" OP1 C 11054 " pdb="MG MG 11608 " model vdw 1.849 2.170 nonbonded pdb=" OP1 A 1 964 " pdb="MG MG 11609 " model vdw 1.857 2.170 ... (remaining 178724 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 3.280 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: 13.000 Check model and map are aligned: 0.240 Set scattering table: 0.170 Process input model: 65.860 Find NCS groups from input model: 0.430 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:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 85.790 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8249 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 : 0.009 0.157 19762 Z= 0.570 Angle : 0.891 17.262 28897 Z= 0.538 Chirality : 0.050 0.328 3592 Planarity : 0.023 0.584 1991 Dihedral : 22.975 176.029 10535 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 32.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.54 % Favored : 92.46 % Rotamer: Outliers : 0.00 % Allowed : 7.73 % Favored : 92.27 % Cbeta Deviations : 0.20 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.59 (0.24), residues: 1087 helix: -1.42 (0.22), residues: 478 sheet: -1.84 (0.36), residues: 162 loop : -1.82 (0.29), residues: 447 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP C 201 HIS 0.006 0.001 HIS M 14 PHE 0.016 0.002 PHE C 37 TYR 0.016 0.002 TYR I 64 ARG 0.013 0.001 ARG I 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 244 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 244 time to evaluate : 1.722 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 96 TRP cc_start: 0.8038 (t-100) cc_final: 0.7647 (t-100) REVERT: B 101 LEU cc_start: 0.8609 (mt) cc_final: 0.8377 (mt) REVERT: C 183 ASP cc_start: 0.8739 (t0) cc_final: 0.8406 (t0) REVERT: J 91 ASP cc_start: 0.8062 (p0) cc_final: 0.7779 (p0) REVERT: J 97 ASP cc_start: 0.8734 (t70) cc_final: 0.8515 (t0) REVERT: M 34 LEU cc_start: 0.9321 (tp) cc_final: 0.9050 (tp) REVERT: M 81 MET cc_start: 0.9185 (mtp) cc_final: 0.8705 (ttm) REVERT: N 67 THR cc_start: 0.8772 (p) cc_final: 0.8094 (t) REVERT: S 66 MET cc_start: 0.8908 (mtp) cc_final: 0.8613 (mtp) outliers start: 0 outliers final: 0 residues processed: 244 average time/residue: 0.3613 time to fit residues: 126.3386 Evaluate side-chains 138 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 1.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 0.0170 chunk 115 optimal weight: 6.9990 chunk 63 optimal weight: 7.9990 chunk 39 optimal weight: 4.9990 chunk 77 optimal weight: 4.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 1.9990 chunk 46 optimal weight: 6.9990 chunk 72 optimal weight: 7.9990 chunk 88 optimal weight: 5.9990 chunk 138 optimal weight: 3.9990 overall best weight: 3.2026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 122 GLN ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 227 GLN ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 9 GLN ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** I 81 HIS ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 64 GLN ** J 70 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** N 4 GLN N 49 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8227 moved from start: 0.2274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 19762 Z= 0.274 Angle : 0.751 14.805 28897 Z= 0.407 Chirality : 0.039 0.229 3592 Planarity : 0.007 0.124 1991 Dihedral : 23.889 178.326 8318 Min Nonbonded Distance : 1.805 Molprobity Statistics. All-atom Clashscore : 28.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.38 % Allowed : 17.86 % Favored : 78.76 % 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: -1.64 (0.24), residues: 1087 helix: -0.56 (0.22), residues: 484 sheet: -1.29 (0.37), residues: 160 loop : -1.46 (0.28), residues: 443 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.005 0.001 HIS S 14 PHE 0.026 0.002 PHE B 198 TYR 0.016 0.002 TYR I 90 ARG 0.007 0.001 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 170 time to evaluate : 1.478 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: B 96 TRP cc_start: 0.7983 (t-100) cc_final: 0.7704 (t-100) REVERT: B 109 GLN cc_start: 0.8510 (tt0) cc_final: 0.8191 (tt0) REVERT: B 113 ARG cc_start: 0.7955 (OUTLIER) cc_final: 0.7693 (mtm180) REVERT: B 120 GLN cc_start: 0.8951 (tp-100) cc_final: 0.8463 (tp-100) REVERT: B 184 PHE cc_start: 0.6989 (OUTLIER) cc_final: 0.6496 (m-10) REVERT: B 192 ASP cc_start: 0.7340 (OUTLIER) cc_final: 0.7116 (t70) REVERT: C 36 ASP cc_start: 0.8561 (m-30) cc_final: 0.7855 (m-30) REVERT: C 152 GLU cc_start: 0.7945 (tm-30) cc_final: 0.7743 (tm-30) REVERT: C 183 ASP cc_start: 0.8491 (t0) cc_final: 0.8144 (t0) REVERT: G 21 GLU cc_start: 0.8839 (pp20) cc_final: 0.8327 (tp30) REVERT: I 88 MET cc_start: 0.9083 (ttm) cc_final: 0.8822 (ttm) REVERT: I 115 LYS cc_start: 0.9286 (mttt) cc_final: 0.8849 (mmtt) REVERT: J 46 LYS cc_start: 0.8702 (mmmm) cc_final: 0.8334 (mmtp) REVERT: J 52 LEU cc_start: 0.8840 (mt) cc_final: 0.8601 (mt) REVERT: J 91 ASP cc_start: 0.8197 (p0) cc_final: 0.7833 (p0) REVERT: J 92 LEU cc_start: 0.8539 (mp) cc_final: 0.8258 (mt) REVERT: M 81 MET cc_start: 0.9085 (mtp) cc_final: 0.8697 (ttm) REVERT: M 95 LEU cc_start: 0.9399 (mt) cc_final: 0.9076 (mp) REVERT: N 62 ASN cc_start: 0.8829 (m-40) cc_final: 0.8329 (t0) REVERT: N 67 THR cc_start: 0.9124 (p) cc_final: 0.8598 (t) REVERT: N 86 GLU cc_start: 0.9129 (mp0) cc_final: 0.8919 (mp0) REVERT: N 89 MET cc_start: 0.8910 (mmm) cc_final: 0.8706 (mmm) REVERT: S 66 MET cc_start: 0.8748 (mtp) cc_final: 0.8499 (mtt) outliers start: 31 outliers final: 18 residues processed: 185 average time/residue: 0.3242 time to fit residues: 90.4284 Evaluate side-chains 157 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 136 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 113 ARG Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 184 PHE Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain G residue 9 GLN Chi-restraints excluded: chain G residue 129 GLU Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain J residue 67 ILE Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 76 optimal weight: 5.9990 chunk 42 optimal weight: 10.0000 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 38 optimal weight: 8.9990 chunk 138 optimal weight: 1.9990 chunk 149 optimal weight: 6.9990 chunk 123 optimal weight: 3.9990 chunk 137 optimal weight: 0.0670 chunk 47 optimal weight: 5.9990 chunk 110 optimal weight: 2.9990 overall best weight: 3.0126 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS ** B 146 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 203 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 68 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** J 70 HIS N 66 GLN N 71 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8229 moved from start: 0.2751 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19762 Z= 0.260 Angle : 0.700 14.107 28897 Z= 0.383 Chirality : 0.037 0.211 3592 Planarity : 0.006 0.127 1991 Dihedral : 23.724 179.851 8318 Min Nonbonded Distance : 1.804 Molprobity Statistics. All-atom Clashscore : 25.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 3.92 % Allowed : 21.02 % Favored : 75.05 % 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: -1.37 (0.24), residues: 1087 helix: -0.29 (0.23), residues: 495 sheet: -1.06 (0.38), residues: 160 loop : -1.43 (0.28), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP G 103 HIS 0.014 0.001 HIS B 18 PHE 0.014 0.002 PHE B 198 TYR 0.017 0.002 TYR I 6 ARG 0.006 0.000 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 158 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 109 GLN cc_start: 0.8540 (tt0) cc_final: 0.8072 (tt0) REVERT: B 184 PHE cc_start: 0.7206 (m-80) cc_final: 0.6530 (m-10) REVERT: B 192 ASP cc_start: 0.7367 (m-30) cc_final: 0.6452 (t0) REVERT: C 36 ASP cc_start: 0.8596 (m-30) cc_final: 0.7878 (m-30) REVERT: C 183 ASP cc_start: 0.8481 (t0) cc_final: 0.8209 (t0) REVERT: G 21 GLU cc_start: 0.8825 (pp20) cc_final: 0.8323 (tp30) REVERT: I 88 MET cc_start: 0.9054 (ttm) cc_final: 0.8808 (tpp) REVERT: I 115 LYS cc_start: 0.9263 (mttt) cc_final: 0.9056 (mmtp) REVERT: J 66 GLU cc_start: 0.7994 (tp30) cc_final: 0.7645 (tp30) REVERT: J 82 LYS cc_start: 0.9027 (mppt) cc_final: 0.8807 (mmmm) REVERT: J 91 ASP cc_start: 0.8192 (p0) cc_final: 0.7856 (p0) REVERT: J 92 LEU cc_start: 0.8477 (mp) cc_final: 0.8200 (mt) REVERT: M 27 LYS cc_start: 0.9593 (tptm) cc_final: 0.9337 (tptt) REVERT: M 81 MET cc_start: 0.9094 (mtp) cc_final: 0.8734 (ttm) REVERT: N 62 ASN cc_start: 0.8796 (m-40) cc_final: 0.8491 (t0) REVERT: N 67 THR cc_start: 0.9148 (p) cc_final: 0.8552 (t) REVERT: S 66 MET cc_start: 0.8770 (mtp) cc_final: 0.8511 (mtt) outliers start: 36 outliers final: 24 residues processed: 179 average time/residue: 0.3281 time to fit residues: 89.0637 Evaluate side-chains 159 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 135 time to evaluate : 1.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain G residue 59 LEU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 62 ASP Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 58 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 136 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 71 optimal weight: 5.9990 chunk 15 optimal weight: 10.0000 chunk 65 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 138 optimal weight: 0.9980 chunk 146 optimal weight: 3.9990 chunk 72 optimal weight: 2.9990 chunk 131 optimal weight: 9.9990 chunk 39 optimal weight: 10.0000 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 120 GLN ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8222 moved from start: 0.3221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 19762 Z= 0.225 Angle : 0.674 12.812 28897 Z= 0.372 Chirality : 0.036 0.218 3592 Planarity : 0.006 0.123 1991 Dihedral : 23.621 179.282 8318 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 24.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 4.03 % Allowed : 22.66 % Favored : 73.31 % 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: -1.08 (0.24), residues: 1087 helix: -0.14 (0.23), residues: 493 sheet: -0.86 (0.39), residues: 160 loop : -1.20 (0.29), residues: 434 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP G 103 HIS 0.005 0.001 HIS S 14 PHE 0.009 0.001 PHE B 90 TYR 0.012 0.001 TYR I 6 ARG 0.005 0.000 ARG B 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 159 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 GLN cc_start: 0.8603 (tp40) cc_final: 0.8373 (tp-100) REVERT: B 161 LEU cc_start: 0.8348 (tp) cc_final: 0.8036 (tt) REVERT: B 184 PHE cc_start: 0.7351 (m-80) cc_final: 0.6592 (m-80) REVERT: B 192 ASP cc_start: 0.7251 (m-30) cc_final: 0.5716 (t0) REVERT: C 36 ASP cc_start: 0.8542 (m-30) cc_final: 0.7828 (m-30) REVERT: C 183 ASP cc_start: 0.8482 (t0) cc_final: 0.8159 (t0) REVERT: G 21 GLU cc_start: 0.8821 (pp20) cc_final: 0.8326 (tp30) REVERT: I 50 GLN cc_start: 0.9187 (mm-40) cc_final: 0.8837 (mm-40) REVERT: I 88 MET cc_start: 0.9037 (ttm) cc_final: 0.8753 (ttm) REVERT: I 115 LYS cc_start: 0.9239 (mttt) cc_final: 0.9038 (mmtp) REVERT: J 63 ASP cc_start: 0.8072 (t0) cc_final: 0.7490 (t70) REVERT: J 91 ASP cc_start: 0.8349 (p0) cc_final: 0.8125 (p0) REVERT: J 92 LEU cc_start: 0.8400 (mp) cc_final: 0.8141 (mt) REVERT: M 27 LYS cc_start: 0.9592 (tptm) cc_final: 0.9183 (tptt) REVERT: M 81 MET cc_start: 0.9075 (mtp) cc_final: 0.8668 (ttm) REVERT: N 62 ASN cc_start: 0.8774 (m-40) cc_final: 0.8476 (t0) REVERT: N 67 THR cc_start: 0.9159 (p) cc_final: 0.8548 (t) outliers start: 37 outliers final: 27 residues processed: 182 average time/residue: 0.3115 time to fit residues: 86.0362 Evaluate side-chains 161 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 134 time to evaluate : 1.226 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 9 THR Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain J residue 57 VAL Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 122 optimal weight: 0.0870 chunk 83 optimal weight: 8.9990 chunk 2 optimal weight: 8.9990 chunk 109 optimal weight: 9.9990 chunk 60 optimal weight: 6.9990 chunk 125 optimal weight: 5.9990 chunk 101 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 75 optimal weight: 0.8980 chunk 131 optimal weight: 0.9990 chunk 37 optimal weight: 10.0000 overall best weight: 2.9964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 15 HIS ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 60 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8228 moved from start: 0.3416 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 19762 Z= 0.249 Angle : 0.681 13.347 28897 Z= 0.375 Chirality : 0.036 0.215 3592 Planarity : 0.006 0.124 1991 Dihedral : 23.601 179.330 8318 Min Nonbonded Distance : 1.799 Molprobity Statistics. All-atom Clashscore : 26.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.32 % Favored : 95.68 % Rotamer: Outliers : 4.58 % Allowed : 24.84 % Favored : 70.59 % 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: -0.94 (0.25), residues: 1087 helix: -0.02 (0.23), residues: 495 sheet: -0.90 (0.38), residues: 165 loop : -1.07 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 103 HIS 0.007 0.001 HIS B 18 PHE 0.014 0.001 PHE B 184 TYR 0.021 0.001 TYR I 90 ARG 0.007 0.000 ARG M 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 151 time to evaluate : 1.383 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: B 120 GLN cc_start: 0.8303 (tp40) cc_final: 0.8052 (tp-100) REVERT: B 161 LEU cc_start: 0.8259 (tp) cc_final: 0.7905 (tt) REVERT: B 184 PHE cc_start: 0.7298 (m-80) cc_final: 0.6637 (m-80) REVERT: B 192 ASP cc_start: 0.6787 (OUTLIER) cc_final: 0.6044 (t0) REVERT: C 36 ASP cc_start: 0.8587 (m-30) cc_final: 0.7857 (m-30) REVERT: C 112 ASP cc_start: 0.8535 (OUTLIER) cc_final: 0.8075 (p0) REVERT: C 183 ASP cc_start: 0.8484 (t0) cc_final: 0.8150 (t0) REVERT: I 50 GLN cc_start: 0.9190 (mm-40) cc_final: 0.8844 (mm-40) REVERT: I 88 MET cc_start: 0.9073 (ttm) cc_final: 0.8805 (ttm) REVERT: I 115 LYS cc_start: 0.9235 (mttt) cc_final: 0.8801 (mmtt) REVERT: J 63 ASP cc_start: 0.8152 (t0) cc_final: 0.7531 (t70) REVERT: J 91 ASP cc_start: 0.8300 (p0) cc_final: 0.8074 (p0) REVERT: M 27 LYS cc_start: 0.9590 (tptm) cc_final: 0.9138 (tptt) REVERT: M 81 MET cc_start: 0.9082 (mtp) cc_final: 0.8652 (ttm) REVERT: M 103 LYS cc_start: 0.9175 (tptt) cc_final: 0.8783 (tptm) REVERT: N 62 ASN cc_start: 0.8772 (m-40) cc_final: 0.8403 (t0) REVERT: N 67 THR cc_start: 0.9200 (p) cc_final: 0.8610 (t) REVERT: S 49 ILE cc_start: 0.9254 (mp) cc_final: 0.9015 (tp) outliers start: 42 outliers final: 30 residues processed: 178 average time/residue: 0.3411 time to fit residues: 90.9291 Evaluate side-chains 166 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 134 time to evaluate : 1.412 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 192 ASP Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain M residue 31 LYS Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 49 optimal weight: 0.0870 chunk 132 optimal weight: 3.9990 chunk 29 optimal weight: 10.0000 chunk 86 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 chunk 147 optimal weight: 9.9990 chunk 122 optimal weight: 5.9990 chunk 68 optimal weight: 3.9990 chunk 12 optimal weight: 10.0000 chunk 48 optimal weight: 9.9990 chunk 77 optimal weight: 10.0000 overall best weight: 4.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 18 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 69 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 185 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 122 ASN ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.3457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.043 19762 Z= 0.342 Angle : 0.733 13.891 28897 Z= 0.399 Chirality : 0.038 0.213 3592 Planarity : 0.007 0.125 1991 Dihedral : 23.700 179.869 8318 Min Nonbonded Distance : 1.733 Molprobity Statistics. All-atom Clashscore : 30.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.06 % Favored : 94.94 % Rotamer: Outliers : 4.79 % Allowed : 25.71 % Favored : 69.50 % 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: -1.07 (0.25), residues: 1087 helix: -0.13 (0.23), residues: 490 sheet: -0.88 (0.39), residues: 165 loop : -1.16 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.002 TRP G 103 HIS 0.006 0.001 HIS S 14 PHE 0.012 0.002 PHE B 198 TYR 0.014 0.002 TYR I 90 ARG 0.007 0.001 ARG B 95 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 185 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 141 time to evaluate : 1.325 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: B 120 GLN cc_start: 0.8402 (tp40) cc_final: 0.8116 (tp-100) REVERT: B 184 PHE cc_start: 0.7412 (m-80) cc_final: 0.6858 (m-80) REVERT: C 36 ASP cc_start: 0.8556 (m-30) cc_final: 0.7772 (m-30) REVERT: C 112 ASP cc_start: 0.8664 (OUTLIER) cc_final: 0.8215 (p0) REVERT: C 183 ASP cc_start: 0.8474 (t0) cc_final: 0.8176 (t0) REVERT: I 115 LYS cc_start: 0.9248 (mttt) cc_final: 0.9036 (mmtp) REVERT: J 63 ASP cc_start: 0.8250 (t0) cc_final: 0.7689 (t70) REVERT: J 91 ASP cc_start: 0.8304 (p0) cc_final: 0.8040 (p0) REVERT: M 27 LYS cc_start: 0.9600 (tptm) cc_final: 0.9190 (tptt) REVERT: M 81 MET cc_start: 0.9123 (mtp) cc_final: 0.8789 (ttm) REVERT: M 103 LYS cc_start: 0.9072 (tptt) cc_final: 0.8750 (tptm) REVERT: N 62 ASN cc_start: 0.8755 (m-40) cc_final: 0.8412 (t0) REVERT: N 67 THR cc_start: 0.9299 (p) cc_final: 0.8716 (t) outliers start: 44 outliers final: 36 residues processed: 168 average time/residue: 0.3224 time to fit residues: 81.4594 Evaluate side-chains 169 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 37 poor density : 132 time to evaluate : 1.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 46 THR Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 35 LEU Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 54 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 105 THR Chi-restraints excluded: chain J residue 25 ILE Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 58 ASP Chi-restraints excluded: chain M residue 78 LYS Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain M residue 104 THR Chi-restraints excluded: chain N residue 14 VAL Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 141 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 83 optimal weight: 3.9990 chunk 107 optimal weight: 0.6980 chunk 123 optimal weight: 4.9990 chunk 82 optimal weight: 0.7980 chunk 146 optimal weight: 5.9990 chunk 91 optimal weight: 20.0000 chunk 89 optimal weight: 9.9990 chunk 67 optimal weight: 0.0670 chunk 90 optimal weight: 0.0670 overall best weight: 1.1258 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 94 HIS ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 19762 Z= 0.159 Angle : 0.672 13.617 28897 Z= 0.369 Chirality : 0.035 0.219 3592 Planarity : 0.006 0.120 1991 Dihedral : 23.517 177.068 8318 Min Nonbonded Distance : 1.919 Molprobity Statistics. All-atom Clashscore : 21.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.05 % Favored : 95.95 % Rotamer: Outliers : 3.16 % Allowed : 28.21 % Favored : 68.63 % 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: -0.73 (0.25), residues: 1087 helix: 0.02 (0.23), residues: 485 sheet: -0.69 (0.40), residues: 165 loop : -0.81 (0.30), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP G 103 HIS 0.003 0.001 HIS S 14 PHE 0.019 0.001 PHE B 90 TYR 0.015 0.001 TYR I 6 ARG 0.010 0.000 ARG I 95 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 154 time to evaluate : 1.550 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 120 GLN cc_start: 0.8427 (tp40) cc_final: 0.8003 (tp-100) REVERT: B 184 PHE cc_start: 0.7237 (m-80) cc_final: 0.6811 (m-80) REVERT: C 36 ASP cc_start: 0.8498 (m-30) cc_final: 0.7769 (m-30) REVERT: C 112 ASP cc_start: 0.8389 (OUTLIER) cc_final: 0.7921 (p0) REVERT: C 183 ASP cc_start: 0.8405 (t0) cc_final: 0.8110 (t0) REVERT: I 6 TYR cc_start: 0.7886 (m-10) cc_final: 0.7490 (m-10) REVERT: I 50 GLN cc_start: 0.9158 (mm-40) cc_final: 0.8777 (mm-40) REVERT: I 115 LYS cc_start: 0.9220 (mttt) cc_final: 0.8848 (mmtt) REVERT: J 63 ASP cc_start: 0.8259 (t0) cc_final: 0.7685 (t70) REVERT: M 27 LYS cc_start: 0.9571 (tptm) cc_final: 0.9125 (tptt) REVERT: M 81 MET cc_start: 0.9086 (mtp) cc_final: 0.8760 (ttm) REVERT: M 103 LYS cc_start: 0.9011 (tptt) cc_final: 0.8729 (tptm) REVERT: N 62 ASN cc_start: 0.8662 (m-40) cc_final: 0.8322 (t0) REVERT: N 67 THR cc_start: 0.9177 (p) cc_final: 0.8589 (t) REVERT: S 17 LYS cc_start: 0.9690 (mmmm) cc_final: 0.9270 (mmtm) REVERT: S 49 ILE cc_start: 0.9162 (mp) cc_final: 0.8927 (tp) outliers start: 29 outliers final: 23 residues processed: 175 average time/residue: 0.3247 time to fit residues: 86.5544 Evaluate side-chains 151 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 127 time to evaluate : 1.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 70 VAL Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 58 optimal weight: 7.9990 chunk 87 optimal weight: 10.0000 chunk 44 optimal weight: 10.0000 chunk 28 optimal weight: 10.0000 chunk 93 optimal weight: 9.9990 chunk 99 optimal weight: 1.9990 chunk 72 optimal weight: 0.4980 chunk 13 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 133 optimal weight: 6.9990 chunk 140 optimal weight: 0.9990 overall best weight: 2.4988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 69 HIS ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.4026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 19762 Z= 0.225 Angle : 0.700 13.836 28897 Z= 0.381 Chirality : 0.036 0.223 3592 Planarity : 0.006 0.122 1991 Dihedral : 23.515 178.064 8318 Min Nonbonded Distance : 1.824 Molprobity Statistics. All-atom Clashscore : 24.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.60 % Favored : 95.40 % Rotamer: Outliers : 3.49 % Allowed : 28.87 % Favored : 67.65 % 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: -0.83 (0.25), residues: 1087 helix: -0.15 (0.23), residues: 486 sheet: -0.64 (0.40), residues: 165 loop : -0.80 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP G 103 HIS 0.008 0.001 HIS S 14 PHE 0.019 0.001 PHE B 198 TYR 0.016 0.001 TYR I 6 ARG 0.004 0.000 ARG S 3 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 135 time to evaluate : 1.855 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.6100 (OUTLIER) cc_final: 0.5893 (t70) REVERT: B 120 GLN cc_start: 0.8381 (tp40) cc_final: 0.8005 (tp-100) REVERT: B 184 PHE cc_start: 0.7267 (m-80) cc_final: 0.6841 (m-10) REVERT: C 36 ASP cc_start: 0.8563 (m-30) cc_final: 0.7844 (m-30) REVERT: C 112 ASP cc_start: 0.8454 (OUTLIER) cc_final: 0.7961 (p0) REVERT: C 183 ASP cc_start: 0.8422 (t0) cc_final: 0.8096 (t0) REVERT: I 6 TYR cc_start: 0.7938 (m-10) cc_final: 0.7442 (m-10) REVERT: I 50 GLN cc_start: 0.9151 (mm-40) cc_final: 0.8447 (mm-40) REVERT: I 53 GLU cc_start: 0.8994 (tm-30) cc_final: 0.8689 (pp20) REVERT: I 115 LYS cc_start: 0.9220 (mttt) cc_final: 0.8820 (mmtt) REVERT: I 129 LYS cc_start: 0.8635 (mptt) cc_final: 0.7569 (mppt) REVERT: J 11 LYS cc_start: 0.9213 (OUTLIER) cc_final: 0.8904 (mppt) REVERT: J 63 ASP cc_start: 0.8303 (t0) cc_final: 0.7729 (t70) REVERT: J 88 MET cc_start: 0.8758 (mmm) cc_final: 0.8350 (ptp) REVERT: M 27 LYS cc_start: 0.9573 (tptm) cc_final: 0.9171 (tptt) REVERT: M 81 MET cc_start: 0.9117 (mtp) cc_final: 0.8774 (ttm) REVERT: M 103 LYS cc_start: 0.8923 (tttt) cc_final: 0.8625 (tptm) REVERT: N 62 ASN cc_start: 0.8717 (m-40) cc_final: 0.8357 (t0) REVERT: N 67 THR cc_start: 0.9169 (p) cc_final: 0.8610 (t) REVERT: S 5 LEU cc_start: 0.9388 (OUTLIER) cc_final: 0.9143 (mm) outliers start: 32 outliers final: 23 residues processed: 157 average time/residue: 0.3148 time to fit residues: 74.8061 Evaluate side-chains 155 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 128 time to evaluate : 1.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 1.9990 chunk 136 optimal weight: 8.9990 chunk 140 optimal weight: 0.9990 chunk 82 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 0.9990 chunk 41 optimal weight: 10.0000 chunk 123 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 89 optimal weight: 10.0000 chunk 144 optimal weight: 6.9990 overall best weight: 1.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8196 moved from start: 0.4256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 19762 Z= 0.182 Angle : 0.700 13.798 28897 Z= 0.380 Chirality : 0.035 0.237 3592 Planarity : 0.006 0.121 1991 Dihedral : 23.472 177.496 8318 Min Nonbonded Distance : 1.893 Molprobity Statistics. All-atom Clashscore : 23.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 3.92 % Allowed : 28.76 % Favored : 67.32 % 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: -0.80 (0.25), residues: 1087 helix: -0.20 (0.23), residues: 486 sheet: -0.52 (0.40), residues: 165 loop : -0.72 (0.30), residues: 436 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP G 103 HIS 0.007 0.001 HIS S 14 PHE 0.020 0.001 PHE B 198 TYR 0.014 0.001 TYR I 6 ARG 0.004 0.000 ARG N 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 174 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 138 time to evaluate : 1.455 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 94 HIS cc_start: 0.6037 (OUTLIER) cc_final: 0.5819 (t70) REVERT: B 120 GLN cc_start: 0.8442 (tp40) cc_final: 0.8117 (tp-100) REVERT: B 184 PHE cc_start: 0.7216 (m-80) cc_final: 0.6853 (m-80) REVERT: C 4 LYS cc_start: 0.9330 (OUTLIER) cc_final: 0.9076 (mmtt) REVERT: C 36 ASP cc_start: 0.8541 (OUTLIER) cc_final: 0.7783 (m-30) REVERT: C 112 ASP cc_start: 0.8380 (OUTLIER) cc_final: 0.7885 (p0) REVERT: C 183 ASP cc_start: 0.8410 (t0) cc_final: 0.8075 (t0) REVERT: I 6 TYR cc_start: 0.7871 (m-10) cc_final: 0.7495 (m-10) REVERT: I 50 GLN cc_start: 0.9166 (mm-40) cc_final: 0.8391 (mm-40) REVERT: I 53 GLU cc_start: 0.8967 (tm-30) cc_final: 0.8676 (pp20) REVERT: I 115 LYS cc_start: 0.9199 (mttt) cc_final: 0.8820 (mmtt) REVERT: I 129 LYS cc_start: 0.8713 (mptt) cc_final: 0.7755 (mppt) REVERT: J 63 ASP cc_start: 0.8366 (t0) cc_final: 0.7461 (t70) REVERT: J 64 GLN cc_start: 0.8976 (mt0) cc_final: 0.8754 (mm110) REVERT: M 27 LYS cc_start: 0.9551 (tptm) cc_final: 0.9104 (tptt) REVERT: M 81 MET cc_start: 0.9102 (mtp) cc_final: 0.8754 (ttm) REVERT: M 103 LYS cc_start: 0.8923 (tttt) cc_final: 0.8563 (tptm) REVERT: N 62 ASN cc_start: 0.8667 (m-40) cc_final: 0.8309 (t0) REVERT: N 67 THR cc_start: 0.9188 (p) cc_final: 0.8617 (t) REVERT: S 5 LEU cc_start: 0.9381 (OUTLIER) cc_final: 0.9142 (mm) REVERT: S 49 ILE cc_start: 0.9165 (mp) cc_final: 0.8934 (tp) REVERT: S 66 MET cc_start: 0.8553 (mtt) cc_final: 0.8248 (ptp) outliers start: 36 outliers final: 25 residues processed: 162 average time/residue: 0.3418 time to fit residues: 83.2044 Evaluate side-chains 163 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 133 time to evaluate : 1.331 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 4 LYS Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 36 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain S residue 5 LEU Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 88 optimal weight: 5.9990 chunk 68 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 151 optimal weight: 8.9990 chunk 139 optimal weight: 0.0470 chunk 120 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 73 optimal weight: 5.9990 chunk 95 optimal weight: 20.0000 chunk 128 optimal weight: 3.9990 overall best weight: 3.6086 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8235 moved from start: 0.4106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 19762 Z= 0.294 Angle : 0.742 14.272 28897 Z= 0.401 Chirality : 0.038 0.245 3592 Planarity : 0.006 0.124 1991 Dihedral : 23.572 179.116 8318 Min Nonbonded Distance : 1.768 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 3.38 % Allowed : 29.52 % Favored : 67.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.89 (0.25), residues: 1087 helix: -0.26 (0.22), residues: 485 sheet: -0.61 (0.40), residues: 165 loop : -0.76 (0.31), residues: 437 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP B 96 HIS 0.004 0.001 HIS B 18 PHE 0.022 0.002 PHE B 198 TYR 0.019 0.002 TYR C 42 ARG 0.005 0.001 ARG B 137 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2174 Ramachandran restraints generated. 1087 Oldfield, 0 Emsley, 1087 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 133 time to evaluate : 1.345 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: B 94 HIS cc_start: 0.5918 (OUTLIER) cc_final: 0.5665 (t70) REVERT: B 120 GLN cc_start: 0.8440 (tp40) cc_final: 0.8090 (tp-100) REVERT: B 184 PHE cc_start: 0.7289 (m-80) cc_final: 0.6885 (m-80) REVERT: C 36 ASP cc_start: 0.8573 (m-30) cc_final: 0.7829 (m-30) REVERT: C 112 ASP cc_start: 0.8529 (OUTLIER) cc_final: 0.8221 (p0) REVERT: C 183 ASP cc_start: 0.8444 (t0) cc_final: 0.8177 (t0) REVERT: G 116 MET cc_start: 0.7969 (pmm) cc_final: 0.7747 (pmm) REVERT: I 6 TYR cc_start: 0.7909 (m-10) cc_final: 0.7434 (m-10) REVERT: I 50 GLN cc_start: 0.9196 (mm-40) cc_final: 0.8751 (mm-40) REVERT: I 115 LYS cc_start: 0.9223 (mttt) cc_final: 0.8803 (mmtt) REVERT: J 11 LYS cc_start: 0.9235 (OUTLIER) cc_final: 0.8915 (mppt) REVERT: J 63 ASP cc_start: 0.8328 (t0) cc_final: 0.7783 (t70) REVERT: M 27 LYS cc_start: 0.9599 (tptm) cc_final: 0.9158 (tptt) REVERT: M 81 MET cc_start: 0.9136 (mtp) cc_final: 0.8803 (ttm) REVERT: M 103 LYS cc_start: 0.8984 (tttt) cc_final: 0.8609 (tptm) REVERT: N 62 ASN cc_start: 0.8617 (m-40) cc_final: 0.8281 (t0) REVERT: N 67 THR cc_start: 0.9273 (p) cc_final: 0.8721 (t) outliers start: 31 outliers final: 27 residues processed: 153 average time/residue: 0.3241 time to fit residues: 74.1699 Evaluate side-chains 162 residues out of total 918 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 132 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 38 VAL Chi-restraints excluded: chain B residue 58 ASN Chi-restraints excluded: chain B residue 94 HIS Chi-restraints excluded: chain B residue 130 THR Chi-restraints excluded: chain B residue 141 LEU Chi-restraints excluded: chain B residue 190 ASN Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain C residue 31 ASP Chi-restraints excluded: chain C residue 52 VAL Chi-restraints excluded: chain C residue 62 LYS Chi-restraints excluded: chain C residue 84 VAL Chi-restraints excluded: chain C residue 106 VAL Chi-restraints excluded: chain C residue 112 ASP Chi-restraints excluded: chain G residue 63 GLU Chi-restraints excluded: chain G residue 80 VAL Chi-restraints excluded: chain I residue 30 ILE Chi-restraints excluded: chain I residue 52 LEU Chi-restraints excluded: chain I residue 79 ILE Chi-restraints excluded: chain I residue 100 LYS Chi-restraints excluded: chain J residue 11 LYS Chi-restraints excluded: chain J residue 47 GLU Chi-restraints excluded: chain M residue 43 VAL Chi-restraints excluded: chain M residue 56 LEU Chi-restraints excluded: chain M residue 89 LEU Chi-restraints excluded: chain N residue 49 GLN Chi-restraints excluded: chain S residue 15 LEU Chi-restraints excluded: chain S residue 51 VAL Chi-restraints excluded: chain S residue 58 VAL Chi-restraints excluded: chain S residue 60 VAL Chi-restraints excluded: chain S residue 71 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 10.0000 chunk 111 optimal weight: 0.0570 chunk 17 optimal weight: 10.0000 chunk 33 optimal weight: 10.0000 chunk 120 optimal weight: 7.9990 chunk 50 optimal weight: 2.9990 chunk 124 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 22 optimal weight: 10.0000 chunk 106 optimal weight: 0.6980 chunk 6 optimal weight: 10.0000 overall best weight: 3.7504 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 120 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 190 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 140 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 52 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 37 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 75 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 58 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** N 49 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3052 r_free = 0.3052 target = 0.037865 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2786 r_free = 0.2786 target = 0.027744 restraints weight = 170364.126| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 57)----------------| | r_work = 0.2814 r_free = 0.2814 target = 0.028401 restraints weight = 82709.141| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.2829 r_free = 0.2829 target = 0.028718 restraints weight = 54875.072| |-----------------------------------------------------------------------------| r_work (final): 0.2800 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8635 moved from start: 0.4118 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 19762 Z= 0.299 Angle : 0.752 14.318 28897 Z= 0.406 Chirality : 0.038 0.262 3592 Planarity : 0.006 0.123 1991 Dihedral : 23.593 178.968 8318 Min Nonbonded Distance : 1.771 Molprobity Statistics. All-atom Clashscore : 28.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.80 % Favored : 94.20 % Rotamer: Outliers : 3.70 % Allowed : 29.41 % Favored : 66.88 % 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: -1.06 (0.25), residues: 1087 helix: -0.31 (0.22), residues: 479 sheet: -0.78 (0.38), residues: 175 loop : -0.92 (0.30), residues: 433 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP G 103 HIS 0.006 0.001 HIS S 14 PHE 0.020 0.001 PHE B 90 TYR 0.016 0.002 TYR C 42 ARG 0.007 0.001 ARG B 95 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3084.19 seconds wall clock time: 59 minutes 5.98 seconds (3545.98 seconds total)