Starting phenix.real_space_refine on Mon Dec 11 17:05:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756_neut_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.75 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/12_2023/7af8_11756_neut_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs 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 51 5.21 5 S 28 5.16 5 C 9848 2.51 5 N 3450 2.21 5 O 4731 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 GLU 110": "OE1" <-> "OE2" Residue "C PHE 130": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 21": "OE1" <-> "OE2" Residue "G GLU 139": "OE1" <-> "OE2" Residue "G GLU 146": "OE1" <-> "OE2" Residue "I TYR 6": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 38": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I PHE 103": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "I GLU 112": "OE1" <-> "OE2" Residue "J PHE 13": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "J GLU 24": "OE1" <-> "OE2" Residue "M GLU 41": "OE1" <-> "OE2" Residue "M PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "M TYR 86": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "N GLU 86": "OE1" <-> "OE2" Residue "S PHE 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "S GLU 73": "OE1" <-> "OE2" Residue "S PHE 74": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 18565 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': 36, 'rna2p_pyr': 34, 'rna3p': 3, 'rna3p_pur': 212, 'rna3p_pyr': 171} Link IDs: {'rna2p': 70, 'rna3p': 385} 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: 1181 Number of conformers: 1 Conformer: "" Number of residues, atoms: 151, 1181 Classifications: {'peptide': 151} Link IDs: {'PTRANS': 5, 'TRANS': 145} 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: 663 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 663 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 5, 'TRANS': 77} Chain: "1" Number of atoms: 51 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 51 Unusual residues: {' MG': 51} Classifications: {'undetermined': 51} Link IDs: {None: 50} 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: 10.12, per 1000 atoms: 0.55 Number of scatterers: 18565 At special positions: 0 Unit cell: (114.45, 150.15, 126, 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 51 11.99 O 4731 8.00 N 3450 7.00 C 9848 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: 10.39 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN B 301 " pdb="ZN ZN B 301 " - pdb=" NE2 HIS B 18 " 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2054 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 47 helices and 9 sheets defined 43.4% alpha, 13.1% beta 138 base pairs and 257 stacking pairs defined. Time for finding SS restraints: 9.03 Creating SS restraints... Processing helix chain 'B' and resid 6 through 12 removed outlier: 3.706A 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: 3.673A 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 9 through 11 No H-bonds generated for 'chain 'C' and resid 9 through 11' Processing helix chain 'C' and resid 29 through 46 Processing helix chain 'C' and resid 73 through 77 Processing helix chain 'C' and resid 79 through 81 No H-bonds generated for 'chain 'C' and resid 79 through 81' Processing helix chain 'C' and resid 83 through 95 removed outlier: 3.661A pdb=" N VAL C 90 " --> pdb=" O LYS C 86 " (cutoff:3.500A) 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 113 through 125 Processing helix chain 'C' and resid 130 through 143 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 54 removed outlier: 3.689A pdb=" N ARG G 53 " --> pdb=" O THR G 49 " (cutoff:3.500A) Processing helix chain 'G' and resid 58 through 67 Processing helix chain 'G' and resid 93 through 111 Processing helix chain 'G' and resid 117 through 128 Processing helix chain 'G' and resid 133 through 146 Processing helix chain 'G' and resid 149 through 151 No H-bonds generated for 'chain 'G' and resid 149 through 151' 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 47 Processing helix chain 'I' and resid 50 through 55 Processing helix chain 'I' and resid 72 through 90 Processing helix chain 'I' and resid 95 through 101 Processing helix chain 'J' and resid 15 through 31 Processing helix chain 'J' and resid 81 through 89 removed outlier: 3.816A pdb=" N ASP J 85 " --> pdb=" O GLU J 81 " (cutoff:3.500A) removed outlier: 4.397A pdb=" N ALA J 86 " --> pdb=" O LYS J 82 " (cutoff:3.500A) Processing helix chain 'M' and resid 15 through 21 removed outlier: 4.389A pdb=" N THR M 20 " --> pdb=" O VAL M 16 " (cutoff:3.500A) removed outlier: 4.057A pdb=" N SER M 21 " --> pdb=" O ILE M 17 " (cutoff:3.500A) Processing helix chain 'M' and resid 27 through 37 Processing helix chain 'M' and resid 50 through 62 removed outlier: 4.136A pdb=" N GLU M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N LYS M 62 " --> pdb=" O ASP M 58 " (cutoff:3.500A) Processing helix chain 'M' and resid 66 through 83 removed outlier: 3.652A pdb=" N LEU M 80 " --> pdb=" O SER M 76 " (cutoff:3.500A) Processing helix chain 'M' and resid 86 through 93 Processing helix chain 'M' and resid 107 through 109 No H-bonds generated for 'chain 'M' and resid 107 through 109' Processing helix chain 'N' and resid 4 through 19 Processing helix chain 'N' and resid 21 through 31 Processing helix chain 'N' and resid 38 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 57 through 59 No H-bonds generated for 'chain 'N' and resid 57 through 59' Processing helix chain 'N' and resid 81 through 89 Processing helix chain 'S' and resid 13 through 25 Processing helix chain 'S' and resid 42 through 44 No H-bonds generated for 'chain 'S' and resid 42 through 44' 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: 6.244A 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: 4.431A pdb=" N ALA B 34 " --> pdb=" O VAL B 38 " (cutoff:3.500A) removed outlier: 6.123A pdb=" N VAL B 38 " --> pdb=" O ALA B 34 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'C' and resid 98 through 105 Processing sheet with id= D, first strand: chain 'C' and resid 165 through 171 removed outlier: 3.640A pdb=" N GLY C 148 " --> pdb=" O PHE C 203 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'G' and resid 73 through 78 Processing sheet with id= F, first strand: chain 'I' and resid 6 through 11 Processing sheet with id= G, first strand: chain 'J' and resid 70 through 76 Processing sheet with id= H, first strand: chain 'J' and resid 45 through 52 Processing sheet with id= I, first strand: chain 'S' and resid 31 through 33 384 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 348 hydrogen bonds 570 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 257 stacking parallelities Total time for adding SS restraints: 8.61 Time building geometry restraints manager: 10.86 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: 2716 1.33 - 1.45: 7337 1.45 - 1.57: 8789 1.57 - 1.69: 911 1.69 - 1.81: 53 Bond restraints: 19806 Sorted by residual: bond pdb=" N3 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 1.496 1.351 0.145 2.00e-02 2.50e+03 5.26e+01 bond pdb=" N3 2MG 11207 " pdb=" C4 2MG 11207 " ideal model delta sigma weight residual 1.496 1.352 0.144 2.00e-02 2.50e+03 5.20e+01 bond pdb=" C2 5MC 1 967 " pdb=" N3 5MC 1 967 " ideal model delta sigma weight residual 1.493 1.351 0.142 2.00e-02 2.50e+03 5.06e+01 bond pdb=" C2 2MG 11207 " pdb=" N2 2MG 11207 " ideal model delta sigma weight residual 1.475 1.347 0.128 2.00e-02 2.50e+03 4.07e+01 bond pdb=" C2 2MG 1 966 " pdb=" N2 2MG 1 966 " ideal model delta sigma weight residual 1.475 1.348 0.127 2.00e-02 2.50e+03 4.01e+01 ... (remaining 19801 not shown) Histogram of bond angle deviations from ideal: 100.19 - 107.42: 3033 107.42 - 114.64: 12416 114.64 - 121.87: 9193 121.87 - 129.10: 3900 129.10 - 136.32: 414 Bond angle restraints: 28956 Sorted by residual: angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C8 2MG 1 966 " ideal model delta sigma weight residual 110.07 126.17 -16.10 3.00e+00 1.11e-01 2.88e+01 angle pdb=" C1' 2MG 11207 " pdb=" N9 2MG 11207 " pdb=" C8 2MG 11207 " ideal model delta sigma weight residual 110.07 125.76 -15.69 3.00e+00 1.11e-01 2.74e+01 angle pdb=" N ARG J 37 " pdb=" CA ARG J 37 " pdb=" C ARG J 37 " ideal model delta sigma weight residual 110.14 102.36 7.78 1.55e+00 4.16e-01 2.52e+01 angle pdb=" N VAL I 104 " pdb=" CA VAL I 104 " pdb=" C VAL I 104 " ideal model delta sigma weight residual 112.29 107.61 4.68 9.40e-01 1.13e+00 2.48e+01 angle pdb=" C1' 2MG 1 966 " pdb=" N9 2MG 1 966 " pdb=" C4 2MG 1 966 " ideal model delta sigma weight residual 138.70 125.30 13.40 3.00e+00 1.11e-01 1.99e+01 ... (remaining 28951 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 11185 35.62 - 71.24: 902 71.24 - 106.86: 129 106.86 - 142.48: 1 142.48 - 178.09: 2 Dihedral angle restraints: 12219 sinusoidal: 9046 harmonic: 3173 Sorted by residual: dihedral pdb=" O4' C 11158 " pdb=" C1' C 11158 " pdb=" N1 C 11158 " pdb=" C2 C 11158 " ideal model delta sinusoidal sigma weight residual 200.00 66.75 133.25 1 1.50e+01 4.44e-03 7.19e+01 dihedral pdb=" O4' U 11168 " pdb=" C1' U 11168 " pdb=" N1 U 11168 " pdb=" C2 U 11168 " ideal model delta sinusoidal sigma weight residual 232.00 53.91 178.09 1 1.70e+01 3.46e-03 6.64e+01 dihedral pdb=" O4' U 1 960 " pdb=" C1' U 1 960 " pdb=" N1 U 1 960 " pdb=" C2 U 1 960 " ideal model delta sinusoidal sigma weight residual 232.00 65.72 166.28 1 1.70e+01 3.46e-03 6.55e+01 ... (remaining 12216 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.080: 3364 0.080 - 0.160: 197 0.160 - 0.240: 29 0.240 - 0.320: 6 0.320 - 0.400: 2 Chirality restraints: 3598 Sorted by residual: chirality pdb=" CA VAL J 57 " pdb=" N VAL J 57 " pdb=" C VAL J 57 " pdb=" CB VAL J 57 " both_signs ideal model delta sigma weight residual False 2.44 2.04 0.40 2.00e-01 2.50e+01 3.99e+00 chirality pdb=" CA ASN N 35 " pdb=" N ASN N 35 " pdb=" C ASN N 35 " pdb=" CB ASN N 35 " both_signs ideal model delta sigma weight residual False 2.51 2.15 0.36 2.00e-01 2.50e+01 3.32e+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 2.22 0.30 2.00e-01 2.50e+01 2.31e+00 ... (remaining 3595 not shown) Planarity restraints: 1999 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 11207 " -0.043 2.00e-02 2.50e+03 5.74e-01 7.41e+03 pdb=" C4' 2MG 11207 " -0.433 2.00e-02 2.50e+03 pdb=" O4' 2MG 11207 " -0.604 2.00e-02 2.50e+03 pdb=" C3' 2MG 11207 " 0.589 2.00e-02 2.50e+03 pdb=" O3' 2MG 11207 " 0.587 2.00e-02 2.50e+03 pdb=" C2' 2MG 11207 " 0.198 2.00e-02 2.50e+03 pdb=" O2' 2MG 11207 " -0.932 2.00e-02 2.50e+03 pdb=" C1' 2MG 11207 " -0.232 2.00e-02 2.50e+03 pdb=" N9 2MG 11207 " 0.869 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 2MG 1 966 " 0.018 2.00e-02 2.50e+03 5.38e-01 6.50e+03 pdb=" C4' 2MG 1 966 " 0.426 2.00e-02 2.50e+03 pdb=" O4' 2MG 1 966 " 0.567 2.00e-02 2.50e+03 pdb=" C3' 2MG 1 966 " -0.580 2.00e-02 2.50e+03 pdb=" O3' 2MG 1 966 " -0.512 2.00e-02 2.50e+03 pdb=" C2' 2MG 1 966 " -0.228 2.00e-02 2.50e+03 pdb=" O2' 2MG 1 966 " 0.866 2.00e-02 2.50e+03 pdb=" C1' 2MG 1 966 " 0.243 2.00e-02 2.50e+03 pdb=" N9 2MG 1 966 " -0.799 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C5' 5MC 1 967 " 0.013 2.00e-02 2.50e+03 5.26e-01 6.22e+03 pdb=" C4' 5MC 1 967 " 0.419 2.00e-02 2.50e+03 pdb=" O4' 5MC 1 967 " 0.550 2.00e-02 2.50e+03 pdb=" C3' 5MC 1 967 " -0.579 2.00e-02 2.50e+03 pdb=" O3' 5MC 1 967 " -0.489 2.00e-02 2.50e+03 pdb=" C2' 5MC 1 967 " -0.236 2.00e-02 2.50e+03 pdb=" O2' 5MC 1 967 " 0.848 2.00e-02 2.50e+03 pdb=" C1' 5MC 1 967 " 0.248 2.00e-02 2.50e+03 pdb=" N1 5MC 1 967 " -0.774 2.00e-02 2.50e+03 ... (remaining 1996 not shown) Histogram of nonbonded interaction distances: 2.00 - 2.58: 161 2.58 - 3.16: 14389 3.16 - 3.74: 35120 3.74 - 4.32: 50115 4.32 - 4.90: 68461 Nonbonded interactions: 168246 Sorted by model distance: nonbonded pdb=" OP1 G 1 993 " pdb="MG MG 11604 " model vdw 2.002 2.170 nonbonded pdb=" OP1 G 1 945 " pdb="MG MG 11642 " model vdw 2.004 2.170 nonbonded pdb=" OP2 C 11158 " pdb="MG MG 11637 " model vdw 2.030 2.170 nonbonded pdb=" O6 G 11108 " pdb="MG MG 11626 " model vdw 2.035 2.170 nonbonded pdb=" OP2 U 11085 " pdb="MG MG 11651 " model vdw 2.061 2.170 ... (remaining 168241 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 individual isotropic 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: 3.480 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: 14.260 Check model and map are aligned: 0.280 Set scattering table: 0.170 Process input model: 62.390 Find NCS groups from input model: 0.360 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:12.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 93.070 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8595 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 : 0.006 0.145 19806 Z= 0.359 Angle : 0.627 16.095 28956 Z= 0.409 Chirality : 0.042 0.400 3598 Planarity : 0.021 0.574 1999 Dihedral : 20.365 178.094 10165 Min Nonbonded Distance : 2.002 Molprobity Statistics. All-atom Clashscore : 6.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.57 % Favored : 96.43 % Rotamer: Outliers : 0.00 % Allowed : 3.26 % Favored : 96.74 % Cbeta Deviations : 0.39 % 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: -0.93 (0.24), residues: 1093 helix: 0.04 (0.22), residues: 508 sheet: -0.48 (0.38), residues: 173 loop : -1.38 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.006 0.001 HIS S 52 PHE 0.009 0.001 PHE B 90 TYR 0.007 0.001 TYR J 65 ARG 0.006 0.000 ARG I 106 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 282 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 282 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 1 residues processed: 282 average time/residue: 1.2450 time to fit residues: 394.5608 Evaluate side-chains 221 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.199 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2045 time to fit residues: 1.8294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 64 optimal weight: 10.0000 chunk 39 optimal weight: 4.9990 chunk 78 optimal weight: 1.9990 chunk 61 optimal weight: 0.0570 chunk 119 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 72 optimal weight: 1.9990 chunk 89 optimal weight: 20.0000 chunk 138 optimal weight: 5.9990 overall best weight: 1.5704 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 122 GLN B 227 GLN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 32 ASN C 102 ASN C 140 ASN I 4 ASN I 37 GLN J 64 GLN J 99 GLN M 52 GLN N 43 ASN N 62 ASN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8603 moved from start: 0.1652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 19806 Z= 0.253 Angle : 0.655 13.672 28956 Z= 0.370 Chirality : 0.038 0.249 3598 Planarity : 0.006 0.126 1999 Dihedral : 21.130 176.383 7940 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 3.80 % Allowed : 16.83 % Favored : 79.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.25), residues: 1093 helix: 0.93 (0.23), residues: 506 sheet: 0.13 (0.39), residues: 171 loop : -0.87 (0.29), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 PHE 0.011 0.001 PHE B 90 TYR 0.011 0.001 TYR M 86 ARG 0.009 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 270 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 235 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 12 residues processed: 249 average time/residue: 1.2595 time to fit residues: 353.1781 Evaluate side-chains 222 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 210 time to evaluate : 1.324 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.4403 time to fit residues: 5.0863 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 77 optimal weight: 0.9980 chunk 43 optimal weight: 3.9990 chunk 115 optimal weight: 4.9990 chunk 94 optimal weight: 10.0000 chunk 38 optimal weight: 3.9990 chunk 139 optimal weight: 0.9990 chunk 150 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 138 optimal weight: 2.9990 chunk 47 optimal weight: 6.9990 chunk 111 optimal weight: 1.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 39 HIS B 146 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN I 4 ASN I 32 GLN I 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8616 moved from start: 0.1948 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 19806 Z= 0.275 Angle : 0.646 12.919 28956 Z= 0.366 Chirality : 0.038 0.185 3598 Planarity : 0.006 0.129 1999 Dihedral : 21.104 176.831 7940 Min Nonbonded Distance : 1.918 Molprobity Statistics. All-atom Clashscore : 9.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 4.78 % Allowed : 18.78 % Favored : 76.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.50 (0.25), residues: 1093 helix: 1.22 (0.23), residues: 504 sheet: 0.32 (0.40), residues: 172 loop : -0.69 (0.29), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 PHE 0.019 0.001 PHE B 198 TYR 0.014 0.002 TYR I 6 ARG 0.005 0.000 ARG C 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 268 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 224 time to evaluate : 1.325 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 22 residues processed: 247 average time/residue: 1.2186 time to fit residues: 340.4571 Evaluate side-chains 233 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 211 time to evaluate : 1.389 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 11 residues processed: 11 average time/residue: 0.4353 time to fit residues: 7.9522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 137 optimal weight: 1.9990 chunk 104 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 9.9990 chunk 93 optimal weight: 9.9990 chunk 139 optimal weight: 0.9990 chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 1.9990 chunk 39 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 185 ASN G 68 ASN I 4 ASN I 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8608 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 19806 Z= 0.249 Angle : 0.637 12.859 28956 Z= 0.361 Chirality : 0.037 0.183 3598 Planarity : 0.006 0.127 1999 Dihedral : 21.076 177.738 7940 Min Nonbonded Distance : 1.934 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer: Outliers : 4.78 % Allowed : 20.63 % Favored : 74.59 % 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: 0.78 (0.26), residues: 1093 helix: 1.45 (0.24), residues: 504 sheet: 0.47 (0.39), residues: 172 loop : -0.56 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 PHE 0.024 0.001 PHE I 127 TYR 0.013 0.002 TYR C 42 ARG 0.004 0.000 ARG I 119 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 218 time to evaluate : 1.410 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 26 residues processed: 243 average time/residue: 1.2383 time to fit residues: 339.8662 Evaluate side-chains 233 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 207 time to evaluate : 1.293 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 19 residues processed: 7 average time/residue: 0.5606 time to fit residues: 6.4178 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 83 optimal weight: 4.9990 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 4.9990 chunk 61 optimal weight: 10.0000 chunk 126 optimal weight: 0.7980 chunk 102 optimal weight: 7.9990 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 2.9990 chunk 132 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 146 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 140 ASN C 185 ASN I 4 ASN I 32 GLN I 37 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.057 19806 Z= 0.445 Angle : 0.721 13.328 28956 Z= 0.399 Chirality : 0.043 0.197 3598 Planarity : 0.007 0.132 1999 Dihedral : 21.139 177.493 7940 Min Nonbonded Distance : 1.855 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 5.43 % Allowed : 21.93 % Favored : 72.64 % 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: 0.61 (0.25), residues: 1093 helix: 1.35 (0.23), residues: 501 sheet: 0.34 (0.39), residues: 176 loop : -0.66 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP C 201 HIS 0.005 0.001 HIS J 15 PHE 0.020 0.002 PHE B 198 TYR 0.015 0.002 TYR I 6 ARG 0.004 0.001 ARG I 106 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 262 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 212 time to evaluate : 1.306 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 50 outliers final: 32 residues processed: 241 average time/residue: 1.2545 time to fit residues: 340.9564 Evaluate side-chains 239 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 207 time to evaluate : 1.426 Switching outliers to nearest non-outliers outliers start: 32 outliers final: 22 residues processed: 11 average time/residue: 0.3553 time to fit residues: 7.2776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 133 optimal weight: 1.9990 chunk 29 optimal weight: 2.9990 chunk 86 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 148 optimal weight: 3.9990 chunk 122 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 0.9980 chunk 77 optimal weight: 3.9990 chunk 142 optimal weight: 0.7980 overall best weight: 0.9580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 42 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 51 ASN B 146 ASN C 6 HIS C 185 ASN I 4 ASN I 37 GLN I 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8590 moved from start: 0.2444 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 19806 Z= 0.190 Angle : 0.632 12.621 28956 Z= 0.359 Chirality : 0.036 0.185 3598 Planarity : 0.006 0.125 1999 Dihedral : 21.106 178.431 7940 Min Nonbonded Distance : 1.984 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.39 % Favored : 95.52 % Rotamer: Outliers : 4.67 % Allowed : 23.34 % Favored : 71.99 % 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: 0.83 (0.26), residues: 1093 helix: 1.51 (0.24), residues: 502 sheet: 0.57 (0.39), residues: 175 loop : -0.59 (0.30), residues: 416 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 201 HIS 0.003 0.001 HIS J 15 PHE 0.013 0.001 PHE B 198 TYR 0.015 0.002 TYR C 42 ARG 0.007 0.000 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 254 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 43 poor density : 211 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 43 outliers final: 28 residues processed: 240 average time/residue: 1.2206 time to fit residues: 331.9358 Evaluate side-chains 229 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 201 time to evaluate : 1.328 Switching outliers to nearest non-outliers outliers start: 28 outliers final: 22 residues processed: 7 average time/residue: 0.4534 time to fit residues: 5.8099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 16 optimal weight: 5.9990 chunk 84 optimal weight: 0.8980 chunk 108 optimal weight: 3.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 0.0000 chunk 82 optimal weight: 0.3980 chunk 147 optimal weight: 0.9990 chunk 92 optimal weight: 5.9990 chunk 89 optimal weight: 4.9990 chunk 68 optimal weight: 1.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.6588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 42 ASN B 146 ASN I 4 ASN I 32 GLN I 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.2676 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 19806 Z= 0.165 Angle : 0.617 12.754 28956 Z= 0.350 Chirality : 0.034 0.178 3598 Planarity : 0.006 0.124 1999 Dihedral : 21.047 179.825 7940 Min Nonbonded Distance : 2.000 Molprobity Statistics. All-atom Clashscore : 9.41 Ramachandran Plot: Outliers : 0.09 % Allowed : 3.57 % Favored : 96.34 % Rotamer: Outliers : 4.45 % Allowed : 24.65 % Favored : 70.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.92 (0.26), residues: 1093 helix: 1.53 (0.24), residues: 503 sheet: 0.73 (0.39), residues: 173 loop : -0.52 (0.30), residues: 417 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 PHE 0.029 0.001 PHE I 127 TYR 0.013 0.001 TYR C 42 ARG 0.004 0.000 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 258 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 217 time to evaluate : 1.491 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 26 residues processed: 247 average time/residue: 1.2749 time to fit residues: 359.3708 Evaluate side-chains 220 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 194 time to evaluate : 1.320 Switching outliers to nearest non-outliers outliers start: 26 outliers final: 21 residues processed: 5 average time/residue: 0.5812 time to fit residues: 5.5122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 58 optimal weight: 2.9990 chunk 88 optimal weight: 0.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 100 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 134 optimal weight: 0.9980 chunk 141 optimal weight: 0.1980 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 140 ASN G 68 ASN I 4 ASN I 37 GLN J 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8621 moved from start: 0.2612 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 19806 Z= 0.310 Angle : 0.672 12.869 28956 Z= 0.374 Chirality : 0.037 0.180 3598 Planarity : 0.006 0.128 1999 Dihedral : 21.033 179.234 7940 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.67 % Favored : 95.24 % Rotamer: Outliers : 3.80 % Allowed : 26.71 % Favored : 69.49 % 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 (0.26), residues: 1093 helix: 1.56 (0.24), residues: 503 sheet: 0.66 (0.39), residues: 175 loop : -0.57 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 PHE 0.013 0.001 PHE G 18 TYR 0.018 0.002 TYR C 42 ARG 0.007 0.000 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 195 time to evaluate : 1.485 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 29 residues processed: 221 average time/residue: 1.3935 time to fit residues: 350.2909 Evaluate side-chains 221 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 192 time to evaluate : 1.382 Switching outliers to nearest non-outliers outliers start: 29 outliers final: 22 residues processed: 8 average time/residue: 0.4381 time to fit residues: 6.2974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 128 optimal weight: 5.9990 chunk 137 optimal weight: 0.9980 chunk 141 optimal weight: 0.4980 chunk 82 optimal weight: 0.2980 chunk 59 optimal weight: 10.0000 chunk 107 optimal weight: 0.8980 chunk 42 optimal weight: 3.9990 chunk 124 optimal weight: 0.3980 chunk 129 optimal weight: 6.9990 chunk 136 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 overall best weight: 0.5180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN I 4 ASN I 37 GLN J 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8582 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 19806 Z= 0.173 Angle : 0.655 12.940 28956 Z= 0.368 Chirality : 0.035 0.182 3598 Planarity : 0.006 0.124 1999 Dihedral : 21.097 179.413 7940 Min Nonbonded Distance : 1.977 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer: Outliers : 3.15 % Allowed : 27.36 % Favored : 69.49 % 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: 0.92 (0.26), residues: 1093 helix: 1.54 (0.24), residues: 503 sheet: 0.66 (0.40), residues: 175 loop : -0.52 (0.31), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 201 HIS 0.003 0.001 HIS J 15 PHE 0.041 0.002 PHE I 127 TYR 0.035 0.002 TYR I 6 ARG 0.009 0.000 ARG J 89 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 199 time to evaluate : 1.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 25 residues processed: 221 average time/residue: 1.1871 time to fit residues: 299.2253 Evaluate side-chains 222 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 5 average time/residue: 0.7930 time to fit residues: 6.4916 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 145 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 68 optimal weight: 1.9990 chunk 101 optimal weight: 6.9990 chunk 152 optimal weight: 3.9990 chunk 140 optimal weight: 0.0270 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 6.9990 chunk 74 optimal weight: 0.0270 chunk 96 optimal weight: 8.9990 overall best weight: 1.8102 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN I 4 ASN I 37 GLN J 20 GLN N 43 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8615 moved from start: 0.2693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.081 19806 Z= 0.288 Angle : 0.672 12.728 28956 Z= 0.374 Chirality : 0.037 0.182 3598 Planarity : 0.006 0.128 1999 Dihedral : 21.036 179.362 7940 Min Nonbonded Distance : 1.891 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer: Outliers : 3.15 % Allowed : 27.47 % Favored : 69.38 % 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: 0.92 (0.26), residues: 1093 helix: 1.55 (0.24), residues: 504 sheet: 0.71 (0.40), residues: 175 loop : -0.56 (0.30), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 PHE 0.011 0.001 PHE B 198 TYR 0.017 0.002 TYR C 42 ARG 0.005 0.000 ARG C 107 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2186 Ramachandran restraints generated. 1093 Oldfield, 0 Emsley, 1093 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 200 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 29 outliers final: 24 residues processed: 222 average time/residue: 1.2248 time to fit residues: 309.2835 Evaluate side-chains 217 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 193 time to evaluate : 1.303 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 22 residues processed: 4 average time/residue: 0.2917 time to fit residues: 3.4669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 153 random chunks: chunk 129 optimal weight: 3.9990 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 0.7980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 4.9990 chunk 50 optimal weight: 8.9990 chunk 124 optimal weight: 0.0470 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 106 optimal weight: 0.8980 overall best weight: 2.1482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN I 4 ASN I 37 GLN J 20 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3405 r_free = 0.3405 target = 0.081743 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.2914 r_free = 0.2914 target = 0.057736 restraints weight = 45532.859| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 1.74 r_work: 0.2752 rms_B_bonded: 2.62 restraints_weight: 0.5000 r_work: 0.2654 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.2654 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8932 moved from start: 0.2688 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.077 19806 Z= 0.326 Angle : 0.690 12.970 28956 Z= 0.384 Chirality : 0.039 0.189 3598 Planarity : 0.006 0.128 1999 Dihedral : 21.065 179.094 7940 Min Nonbonded Distance : 1.897 Molprobity Statistics. All-atom Clashscore : 10.61 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer: Outliers : 3.69 % Allowed : 27.04 % Favored : 69.27 % 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: 0.82 (0.26), residues: 1093 helix: 1.47 (0.24), residues: 503 sheet: 0.64 (0.39), residues: 175 loop : -0.59 (0.30), residues: 415 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 201 HIS 0.004 0.001 HIS J 15 PHE 0.035 0.002 PHE I 127 TYR 0.018 0.002 TYR C 42 ARG 0.008 0.000 ARG J 89 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6087.28 seconds wall clock time: 109 minutes 34.20 seconds (6574.20 seconds total)