Starting phenix.real_space_refine (version: 1.21rc1) on Mon Apr 24 21:44:40 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/04_2023/7af8_11756_neut_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/04_2023/7af8_11756.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/04_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_11756/04_2023/7af8_11756_neut_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/04_2023/7af8_11756_neut_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/04_2023/7af8_11756.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/04_2023/7af8_11756.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/04_2023/7af8_11756_neut_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7af8_11756/04_2023/7af8_11756_neut_updated.pdb" } resolution = 2.75 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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-1.21rc1-4938/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: 10.59, per 1000 atoms: 0.57 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: 9.58 Conformation dependent library (CDL) restraints added in 1.3 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: 8.81 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: 10.04 Time building geometry restraints manager: 10.16 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: 10663 35.62 - 71.24: 299 71.24 - 106.86: 20 106.86 - 142.48: 1 142.48 - 178.09: 2 Dihedral angle restraints: 10985 sinusoidal: 7812 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 10982 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: 2.900 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: 0.020 Extract box with map and model: 15.000 Check model and map are aligned: 0.290 Set scattering table: 0.170 Process input model: 63.180 Find NCS groups from input model: 0.460 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: 0.010 Load rotamer database and sin/cos tables:13.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 95.650 ------------------------------------------------------------------------------- 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 : 13.694 178.094 8931 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 % 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 *********************** 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 : 1.467 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: 1.2911 time to fit residues: 408.9361 Evaluate side-chains 221 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 220 time to evaluate : 1.358 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 1 average time/residue: 0.2078 time to fit residues: 1.8758 ------------------------------------------------------------------------------- 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: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 19806 Z= 0.254 Angle : 0.649 13.836 28956 Z= 0.366 Chirality : 0.038 0.261 3598 Planarity : 0.006 0.128 1999 Dihedral : 12.971 176.408 6706 Min Nonbonded Distance : 1.926 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.30 % Favored : 95.70 % Rotamer Outliers : 3.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.25), residues: 1093 helix: 0.92 (0.23), residues: 506 sheet: 0.13 (0.39), residues: 171 loop : -0.88 (0.29), residues: 416 *********************** 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 269 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 233 time to evaluate : 1.439 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 36 outliers final: 12 residues processed: 248 average time/residue: 1.2581 time to fit residues: 351.9670 Evaluate side-chains 222 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 210 time to evaluate : 1.421 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 6 residues processed: 6 average time/residue: 0.4444 time to fit residues: 5.1868 ------------------------------------------------------------------------------- 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: 0.8980 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: 3.9990 chunk 150 optimal weight: 2.9990 chunk 123 optimal weight: 0.8980 chunk 138 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 111 optimal weight: 1.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 I 110 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8628 moved from start: 0.1967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.043 19806 Z= 0.320 Angle : 0.663 12.952 28956 Z= 0.374 Chirality : 0.039 0.191 3598 Planarity : 0.007 0.130 1999 Dihedral : 13.097 176.741 6706 Min Nonbonded Distance : 1.896 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.21 % Favored : 95.79 % Rotamer Outliers : 5.10 % 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: 0.44 (0.25), residues: 1093 helix: 1.17 (0.23), residues: 504 sheet: 0.30 (0.40), residues: 172 loop : -0.72 (0.30), residues: 417 *********************** 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 269 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 222 time to evaluate : 1.582 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 47 outliers final: 24 residues processed: 247 average time/residue: 1.2452 time to fit residues: 347.6734 Evaluate side-chains 238 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 214 time to evaluate : 1.488 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 12 residues processed: 12 average time/residue: 0.3159 time to fit residues: 7.1886 ------------------------------------------------------------------------------- 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: 0.9990 chunk 72 optimal weight: 2.9990 chunk 15 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 139 optimal weight: 0.6980 chunk 147 optimal weight: 1.9990 chunk 132 optimal weight: 0.9990 chunk 39 optimal weight: 3.9990 chunk 123 optimal weight: 6.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- 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 ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN G 68 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: 0.8598 moved from start: 0.2183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 19806 Z= 0.220 Angle : 0.629 12.816 28956 Z= 0.357 Chirality : 0.036 0.186 3598 Planarity : 0.006 0.126 1999 Dihedral : 13.024 177.704 6706 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.12 % Favored : 95.88 % Rotamer Outliers : 4.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.25), residues: 1093 helix: 1.43 (0.23), residues: 504 sheet: 0.51 (0.39), residues: 171 loop : -0.62 (0.30), residues: 418 *********************** 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: 42 poor density : 220 time to evaluate : 1.500 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 42 outliers final: 24 residues processed: 245 average time/residue: 1.2864 time to fit residues: 355.8547 Evaluate side-chains 234 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 210 time to evaluate : 1.687 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 19 residues processed: 6 average time/residue: 0.3223 time to fit residues: 5.0715 ------------------------------------------------------------------------------- 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: 0.9980 chunk 2 optimal weight: 4.9990 chunk 110 optimal weight: 3.9990 chunk 61 optimal weight: 9.9990 chunk 126 optimal weight: 3.9990 chunk 102 optimal weight: 10.0000 chunk 0 optimal weight: 5.9990 chunk 75 optimal weight: 3.9990 chunk 132 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 49 optimal weight: 6.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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: 0.8658 moved from start: 0.2295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 19806 Z= 0.448 Angle : 0.726 13.364 28956 Z= 0.401 Chirality : 0.043 0.197 3598 Planarity : 0.007 0.133 1999 Dihedral : 13.173 177.524 6706 Min Nonbonded Distance : 1.854 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.94 % Favored : 94.97 % Rotamer Outliers : 5.32 % 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: 0.60 (0.25), residues: 1093 helix: 1.34 (0.23), residues: 501 sheet: 0.33 (0.39), residues: 176 loop : -0.68 (0.30), residues: 416 *********************** 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 260 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 211 time to evaluate : 1.418 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 49 outliers final: 34 residues processed: 240 average time/residue: 1.2471 time to fit residues: 337.7235 Evaluate side-chains 239 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 205 time to evaluate : 1.350 Switching outliers to nearest non-outliers outliers start: 34 outliers final: 24 residues processed: 12 average time/residue: 0.4002 time to fit residues: 8.1803 ------------------------------------------------------------------------------- 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: 0.8980 chunk 36 optimal weight: 4.9990 chunk 148 optimal weight: 0.8980 chunk 122 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 12 optimal weight: 2.9990 chunk 48 optimal weight: 10.0000 chunk 77 optimal weight: 4.9990 chunk 142 optimal weight: 0.9990 overall best weight: 1.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 51 ASN B 146 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 185 ASN I 4 ASN I 37 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8609 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.040 19806 Z= 0.227 Angle : 0.643 12.736 28956 Z= 0.364 Chirality : 0.037 0.187 3598 Planarity : 0.006 0.126 1999 Dihedral : 13.066 178.173 6706 Min Nonbonded Distance : 1.955 Molprobity Statistics. All-atom Clashscore : 9.81 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer Outliers : 4.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.26), residues: 1093 helix: 1.49 (0.24), residues: 502 sheet: 0.45 (0.39), residues: 176 loop : -0.59 (0.30), residues: 415 *********************** 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 257 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 213 time to evaluate : 1.548 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 44 outliers final: 31 residues processed: 242 average time/residue: 1.2848 time to fit residues: 351.6674 Evaluate side-chains 231 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 200 time to evaluate : 1.459 Switching outliers to nearest non-outliers outliers start: 31 outliers final: 22 residues processed: 10 average time/residue: 0.3729 time to fit residues: 7.0059 ------------------------------------------------------------------------------- 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: 0.9990 chunk 108 optimal weight: 4.9990 chunk 83 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 82 optimal weight: 0.8980 chunk 147 optimal weight: 2.9990 chunk 92 optimal weight: 4.9990 chunk 89 optimal weight: 8.9990 chunk 68 optimal weight: 0.8980 chunk 91 optimal weight: 3.9990 overall best weight: 1.7586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN I 37 GLN I 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.066 19806 Z= 0.276 Angle : 0.657 12.804 28956 Z= 0.369 Chirality : 0.037 0.187 3598 Planarity : 0.006 0.128 1999 Dihedral : 13.033 178.622 6706 Min Nonbonded Distance : 1.910 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.57 % Favored : 95.33 % Rotamer Outliers : 4.45 % 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: 1.50 (0.24), residues: 502 sheet: 0.54 (0.39), residues: 176 loop : -0.59 (0.30), residues: 415 *********************** 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 241 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 200 time to evaluate : 1.477 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 41 outliers final: 30 residues processed: 227 average time/residue: 1.2248 time to fit residues: 315.6601 Evaluate side-chains 223 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 1.654 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 21 residues processed: 9 average time/residue: 0.4729 time to fit residues: 7.4917 ------------------------------------------------------------------------------- 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: 3.9990 chunk 88 optimal weight: 3.9990 chunk 44 optimal weight: 4.9990 chunk 28 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 100 optimal weight: 3.9990 chunk 72 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 115 optimal weight: 5.9990 chunk 134 optimal weight: 0.9990 chunk 141 optimal weight: 1.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN ** C 6 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** I 4 ASN I 37 GLN I 110 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8654 moved from start: 0.2496 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.082 19806 Z= 0.426 Angle : 0.725 13.323 28956 Z= 0.400 Chirality : 0.042 0.189 3598 Planarity : 0.007 0.132 1999 Dihedral : 13.161 178.138 6706 Min Nonbonded Distance : 1.859 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.85 % Favored : 95.06 % Rotamer Outliers : 4.89 % 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: 0.67 (0.26), residues: 1093 helix: 1.41 (0.23), residues: 502 sheet: 0.44 (0.39), residues: 176 loop : -0.70 (0.30), residues: 415 *********************** 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 249 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 204 time to evaluate : 1.478 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 45 outliers final: 30 residues processed: 235 average time/residue: 1.3090 time to fit residues: 347.6399 Evaluate side-chains 223 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 193 time to evaluate : 1.509 Switching outliers to nearest non-outliers outliers start: 30 outliers final: 22 residues processed: 9 average time/residue: 0.3961 time to fit residues: 6.7060 ------------------------------------------------------------------------------- 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: 4.9990 chunk 137 optimal weight: 0.8980 chunk 141 optimal weight: 0.5980 chunk 82 optimal weight: 0.6980 chunk 59 optimal weight: 9.9990 chunk 107 optimal weight: 0.8980 chunk 42 optimal weight: 2.9990 chunk 124 optimal weight: 2.9990 chunk 129 optimal weight: 0.6980 chunk 136 optimal weight: 0.0170 chunk 90 optimal weight: 2.9990 overall best weight: 0.5818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 146 ASN C 6 HIS I 4 ASN I 37 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.2667 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.066 19806 Z= 0.170 Angle : 0.647 12.760 28956 Z= 0.364 Chirality : 0.035 0.181 3598 Planarity : 0.006 0.124 1999 Dihedral : 13.045 179.207 6706 Min Nonbonded Distance : 1.992 Molprobity Statistics. All-atom Clashscore : 10.64 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.12 % Favored : 95.79 % Rotamer Outliers : 3.37 % 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: 0.85 (0.26), residues: 1093 helix: 1.47 (0.24), residues: 503 sheet: 0.69 (0.40), residues: 175 loop : -0.57 (0.31), residues: 415 *********************** 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 237 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 206 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 31 outliers final: 25 residues processed: 232 average time/residue: 1.1627 time to fit residues: 308.5891 Evaluate side-chains 222 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 197 time to evaluate : 1.496 Switching outliers to nearest non-outliers outliers start: 25 outliers final: 21 residues processed: 5 average time/residue: 0.6269 time to fit residues: 5.6850 ------------------------------------------------------------------------------- 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: 0.7980 chunk 88 optimal weight: 9.9990 chunk 68 optimal weight: 2.9990 chunk 101 optimal weight: 8.9990 chunk 152 optimal weight: 1.9990 chunk 140 optimal weight: 0.1980 chunk 121 optimal weight: 5.9990 chunk 12 optimal weight: 4.9990 chunk 93 optimal weight: 0.9990 chunk 74 optimal weight: 0.0980 chunk 96 optimal weight: 1.9990 overall best weight: 0.8184 ------------------------------------------------------------------------------- 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 I 4 ASN I 32 GLN I 37 GLN J 20 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8569 moved from start: 0.2782 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.071 19806 Z= 0.191 Angle : 0.647 12.754 28956 Z= 0.362 Chirality : 0.035 0.219 3598 Planarity : 0.006 0.125 1999 Dihedral : 12.958 179.932 6706 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 9.97 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.21 % Favored : 95.70 % Rotamer Outliers : 2.82 % 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 (0.26), residues: 1093 helix: 1.53 (0.23), residues: 500 sheet: 0.77 (0.40), residues: 175 loop : -0.51 (0.30), residues: 418 ********************** 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 237 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 211 time to evaluate : 1.567 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 22 residues processed: 234 average time/residue: 1.1366 time to fit residues: 303.8960 Evaluate side-chains 224 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 202 time to evaluate : 1.446 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 20 residues processed: 3 average time/residue: 0.6062 time to fit residues: 3.9296 ------------------------------------------------------------------------------- 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: 0.5980 chunk 37 optimal weight: 4.9990 chunk 111 optimal weight: 0.8980 chunk 17 optimal weight: 5.9990 chunk 33 optimal weight: 5.9990 chunk 121 optimal weight: 0.9980 chunk 50 optimal weight: 10.0000 chunk 124 optimal weight: 0.3980 chunk 15 optimal weight: 5.9990 chunk 22 optimal weight: 5.9990 chunk 106 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- 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 I 4 ASN I 5 GLN I 37 GLN J 20 GLN N 43 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3476 r_free = 0.3476 target = 0.085307 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 80)----------------| | r_work = 0.3023 r_free = 0.3023 target = 0.062014 restraints weight = 45611.943| |-----------------------------------------------------------------------------| r_work (start): 0.2985 rms_B_bonded: 1.67 r_work: 0.2861 rms_B_bonded: 2.54 restraints_weight: 0.5000 r_work: 0.2769 rms_B_bonded: 3.76 restraints_weight: 0.2500 r_work (final): 0.2769 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8843 moved from start: 0.2947 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.064 19806 Z= 0.175 Angle : 0.640 12.829 28956 Z= 0.359 Chirality : 0.034 0.245 3598 Planarity : 0.006 0.124 1999 Dihedral : 12.899 179.634 6706 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 10.15 Ramachandran Plot: Outliers : 0.09 % Allowed : 4.30 % Favored : 95.61 % Rotamer Outliers : 2.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.97 (0.26), residues: 1093 helix: 1.54 (0.23), residues: 500 sheet: 0.96 (0.41), residues: 169 loop : -0.54 (0.30), residues: 424 =============================================================================== Job complete usr+sys time: 6072.90 seconds wall clock time: 108 minutes 59.09 seconds (6539.09 seconds total)