Starting phenix.real_space_refine (version: 1.21rc1) on Wed Apr 26 18:06:06 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/04_2023/7e9c_31029_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/04_2023/7e9c_31029.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/04_2023/7e9c_31029.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/04_2023/7e9c_31029.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/04_2023/7e9c_31029_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7e9c_31029/04_2023/7e9c_31029_updated.pdb" } resolution = 3.5 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= 0.008 sd= 0.079 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 11439 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 260 5.49 5 S 3 5.16 5 C 6945 2.51 5 N 2302 2.21 5 O 2828 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 40": "NH1" <-> "NH2" Residue "A GLU 73": "OE1" <-> "OE2" Residue "B ARG 19": "NH1" <-> "NH2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 40": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ARG 43": "NH1" <-> "NH2" Residue "C GLU 65": "OE1" <-> "OE2" Residue "C ARG 78": "NH1" <-> "NH2" Residue "D ARG 36": "NH1" <-> "NH2" Residue "D ASP 54": "OD1" <-> "OD2" Residue "D GLU 116": "OE1" <-> "OE2" Residue "E ARG 49": "NH1" <-> "NH2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G ARG 36": "NH1" <-> "NH2" Residue "G GLU 62": "OE1" <-> "OE2" Residue "G ARG 72": "NH1" <-> "NH2" Residue "G GLU 93": "OE1" <-> "OE2" Residue "H GLU 108": "OE1" <-> "OE2" Residue "H GLU 116": "OE1" <-> "OE2" Residue "K ARG 29": "NH1" <-> "NH2" Residue "K GLU 61": "OE1" <-> "OE2" Residue "K TYR 69": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K ARG 148": "NH1" <-> "NH2" Residue "K GLU 178": "OE1" <-> "OE2" Residue "K GLU 182": "OE1" <-> "OE2" 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: 12338 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 770 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 770 Classifications: {'peptide': 94} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 91} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "B" Number of atoms: 690 Number of conformers: 1 Conformer: "" Number of residues, atoms: 85, 690 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 776 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 776 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLN:plan1': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "E" Number of atoms: 710 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 710 Classifications: {'peptide': 87} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "F" Number of atoms: 649 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 649 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 102, 781 Classifications: {'peptide': 102} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 97} Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Chain: "H" Number of atoms: 714 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 714 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 8 Chain: "I" Number of atoms: 2652 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2652 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "J" Number of atoms: 2678 Number of conformers: 1 Conformer: "" Number of residues, atoms: 130, 2678 Classifications: {'DNA': 130} Link IDs: {'rna3p': 129} Chain: "K" Number of atoms: 1204 Number of conformers: 1 Conformer: "" Number of residues, atoms: 162, 1204 Classifications: {'peptide': 162} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'PTRANS': 2, 'TRANS': 159} Chain breaks: 2 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 156 Unresolved non-hydrogen dihedrals: 106 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 2, 'AYA:plan-2': 1, 'TYR:plan': 2, 'ASN:plan1': 1, 'ASP:plan': 2, 'PHE:plan': 2, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 75 Time building chain proxies: 6.84, per 1000 atoms: 0.55 Number of scatterers: 12338 At special positions: 0 Unit cell: (116, 117, 111, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 3 16.00 P 260 15.00 O 2828 8.00 N 2302 7.00 C 6945 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.89 Conformation dependent library (CDL) restraints added in 1.1 seconds 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1688 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 36 helices and 3 sheets defined 54.6% alpha, 4.1% beta 116 base pairs and 176 stacking pairs defined. Time for finding SS restraints: 5.26 Creating SS restraints... Processing helix chain 'A' and resid 46 through 56 Processing helix chain 'A' and resid 64 through 77 Processing helix chain 'A' and resid 86 through 114 Processing helix chain 'A' and resid 121 through 129 Processing helix chain 'B' and resid 25 through 28 Processing helix chain 'B' and resid 31 through 41 Processing helix chain 'B' and resid 54 through 75 removed outlier: 3.656A pdb=" N ARG B 67 " --> pdb=" O GLU B 63 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 92 Processing helix chain 'C' and resid 18 through 22 removed outlier: 3.661A pdb=" N ALA C 22 " --> pdb=" O ARG C 18 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 18 through 22' Processing helix chain 'C' and resid 29 through 36 Processing helix chain 'C' and resid 47 through 74 removed outlier: 3.533A pdb=" N ASP C 73 " --> pdb=" O ASN C 69 " (cutoff:3.500A) removed outlier: 3.547A pdb=" N ASN C 74 " --> pdb=" O ALA C 70 " (cutoff:3.500A) Processing helix chain 'C' and resid 81 through 90 Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.522A pdb=" N LYS C 96 " --> pdb=" O ASP C 92 " (cutoff:3.500A) removed outlier: 3.879A pdb=" N LEU C 97 " --> pdb=" O GLU C 93 " (cutoff:3.500A) No H-bonds generated for 'chain 'C' and resid 92 through 97' Processing helix chain 'D' and resid 41 through 51 removed outlier: 4.037A pdb=" N THR D 51 " --> pdb=" O VAL D 47 " (cutoff:3.500A) Processing helix chain 'D' and resid 59 through 87 removed outlier: 3.673A pdb=" N ASN D 87 " --> pdb=" O LEU D 83 " (cutoff:3.500A) Processing helix chain 'D' and resid 94 through 104 Processing helix chain 'D' and resid 108 through 125 removed outlier: 3.853A pdb=" N ARG D 119 " --> pdb=" O SER D 115 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N ALA D 120 " --> pdb=" O GLU D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 47 through 54 removed outlier: 4.130A pdb=" N ARG E 52 " --> pdb=" O LEU E 48 " (cutoff:3.500A) Processing helix chain 'E' and resid 64 through 76 Processing helix chain 'E' and resid 86 through 113 removed outlier: 3.506A pdb=" N GLY E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 121 through 131 removed outlier: 3.662A pdb=" N ARG E 131 " --> pdb=" O ALA E 127 " (cutoff:3.500A) Processing helix chain 'F' and resid 26 through 28 No H-bonds generated for 'chain 'F' and resid 26 through 28' Processing helix chain 'F' and resid 31 through 41 Processing helix chain 'F' and resid 48 through 75 removed outlier: 3.918A pdb=" N TYR F 51 " --> pdb=" O GLY F 48 " (cutoff:3.500A) removed outlier: 4.370A pdb=" N GLU F 52 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N LEU F 62 " --> pdb=" O LYS F 59 " (cutoff:3.500A) Processing helix chain 'F' and resid 83 through 92 Processing helix chain 'G' and resid 18 through 21 No H-bonds generated for 'chain 'G' and resid 18 through 21' Processing helix chain 'G' and resid 28 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 4.383A pdb=" N VAL G 50 " --> pdb=" O SER G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 81 through 90 Processing helix chain 'G' and resid 94 through 97 No H-bonds generated for 'chain 'G' and resid 94 through 97' Processing helix chain 'H' and resid 41 through 51 removed outlier: 3.881A pdb=" N THR H 51 " --> pdb=" O VAL H 47 " (cutoff:3.500A) Processing helix chain 'H' and resid 59 through 86 Processing helix chain 'H' and resid 94 through 104 Processing helix chain 'H' and resid 108 through 124 removed outlier: 4.152A pdb=" N ARG H 119 " --> pdb=" O SER H 115 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N ALA H 120 " --> pdb=" O GLU H 116 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N VAL H 121 " --> pdb=" O GLY H 117 " (cutoff:3.500A) Processing helix chain 'K' and resid 190 through 198 removed outlier: 4.219A pdb=" N ALA K 194 " --> pdb=" O GLU K 190 " (cutoff:3.500A) removed outlier: 4.623A pdb=" N TYR K 195 " --> pdb=" O ASP K 191 " (cutoff:3.500A) Processing helix chain 'K' and resid 201 through 211 Processing sheet with id= A, first strand: chain 'K' and resid 14 through 16 Processing sheet with id= B, first strand: chain 'K' and resid 146 through 149 removed outlier: 4.059A pdb=" N ILE K 147 " --> pdb=" O VAL K 57 " (cutoff:3.500A) removed outlier: 7.892A pdb=" N VAL K 57 " --> pdb=" O ILE K 147 " (cutoff:3.500A) removed outlier: 5.469A pdb=" N VAL K 149 " --> pdb=" O SER K 55 " (cutoff:3.500A) removed outlier: 7.629A pdb=" N SER K 55 " --> pdb=" O VAL K 149 " (cutoff:3.500A) removed outlier: 6.818A pdb=" N TRP K 86 " --> pdb=" O GLN K 72 " (cutoff:3.500A) removed outlier: 4.383A pdb=" N LEU K 74 " --> pdb=" O GLU K 84 " (cutoff:3.500A) removed outlier: 6.552A pdb=" N GLU K 84 " --> pdb=" O LEU K 74 " (cutoff:3.500A) removed outlier: 4.187A pdb=" N LEU K 85 " --> pdb=" O LEU K 141 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'K' and resid 131 through 134 removed outlier: 6.938A pdb=" N THR K 172 " --> pdb=" O LEU K 132 " (cutoff:3.500A) removed outlier: 8.577A pdb=" N LEU K 134 " --> pdb=" O THR K 172 " (cutoff:3.500A) removed outlier: 8.923A pdb=" N ARG K 174 " --> pdb=" O LEU K 134 " (cutoff:3.500A) No H-bonds generated for sheet with id= C 340 hydrogen bonds defined for protein. 945 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 301 hydrogen bonds 598 hydrogen bond angles 0 basepair planarities 116 basepair parallelities 176 stacking parallelities Total time for adding SS restraints: 4.06 Time building geometry restraints manager: 7.14 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 2508 1.33 - 1.45: 4019 1.45 - 1.57: 6024 1.57 - 1.69: 518 1.69 - 1.81: 5 Bond restraints: 13074 Sorted by residual: bond pdb=" N AYA K 2 " pdb=" CT AYA K 2 " ideal model delta sigma weight residual 1.340 1.387 -0.047 2.00e-02 2.50e+03 5.43e+00 bond pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.31e+00 bond pdb=" N AYA K 2 " pdb=" CA AYA K 2 " ideal model delta sigma weight residual 1.458 1.437 0.021 1.90e-02 2.77e+03 1.23e+00 bond pdb=" CA ILE C 80 " pdb=" CB ILE C 80 " ideal model delta sigma weight residual 1.546 1.537 0.009 8.80e-03 1.29e+04 9.91e-01 bond pdb=" CT AYA K 2 " pdb=" OT AYA K 2 " ideal model delta sigma weight residual 1.226 1.246 -0.020 2.00e-02 2.50e+03 9.76e-01 ... (remaining 13069 not shown) Histogram of bond angle deviations from ideal: 98.07 - 105.25: 1104 105.25 - 112.43: 7290 112.43 - 119.61: 3902 119.61 - 126.79: 5732 126.79 - 133.97: 756 Bond angle restraints: 18784 Sorted by residual: angle pdb=" C ALA K 204 " pdb=" N GLN K 205 " pdb=" CA GLN K 205 " ideal model delta sigma weight residual 120.31 114.85 5.46 1.52e+00 4.33e-01 1.29e+01 angle pdb=" CB ARG A 52 " pdb=" CG ARG A 52 " pdb=" CD ARG A 52 " ideal model delta sigma weight residual 111.30 119.52 -8.22 2.30e+00 1.89e-01 1.28e+01 angle pdb=" N GLN K 205 " pdb=" CA GLN K 205 " pdb=" CB GLN K 205 " ideal model delta sigma weight residual 110.28 115.34 -5.06 1.55e+00 4.16e-01 1.06e+01 angle pdb=" CB ARG A 53 " pdb=" CG ARG A 53 " pdb=" CD ARG A 53 " ideal model delta sigma weight residual 111.30 118.79 -7.49 2.30e+00 1.89e-01 1.06e+01 angle pdb=" N GLU K 206 " pdb=" CA GLU K 206 " pdb=" CB GLU K 206 " ideal model delta sigma weight residual 110.12 114.67 -4.55 1.47e+00 4.63e-01 9.56e+00 ... (remaining 18779 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.14: 5509 29.14 - 58.29: 1289 58.29 - 87.43: 144 87.43 - 116.57: 3 116.57 - 145.72: 2 Dihedral angle restraints: 6947 sinusoidal: 4339 harmonic: 2608 Sorted by residual: dihedral pdb=" C4' DC I 24 " pdb=" C3' DC I 24 " pdb=" O3' DC I 24 " pdb=" P DG I 25 " ideal model delta sinusoidal sigma weight residual 220.00 74.28 145.72 1 3.50e+01 8.16e-04 1.43e+01 dihedral pdb=" C4' DG I 63 " pdb=" C3' DG I 63 " pdb=" O3' DG I 63 " pdb=" P DC I 64 " ideal model delta sinusoidal sigma weight residual 220.00 75.24 144.76 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA ILE B 29 " pdb=" C ILE B 29 " pdb=" N THR B 30 " pdb=" CA THR B 30 " ideal model delta harmonic sigma weight residual -180.00 -163.20 -16.80 0 5.00e+00 4.00e-02 1.13e+01 ... (remaining 6944 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1878 0.047 - 0.094: 223 0.094 - 0.141: 59 0.141 - 0.189: 3 0.189 - 0.236: 1 Chirality restraints: 2164 Sorted by residual: chirality pdb=" CB ILE F 29 " pdb=" CA ILE F 29 " pdb=" CG1 ILE F 29 " pdb=" CG2 ILE F 29 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.24 2.00e-01 2.50e+01 1.39e+00 chirality pdb=" CG LEU A 48 " pdb=" CB LEU A 48 " pdb=" CD1 LEU A 48 " pdb=" CD2 LEU A 48 " both_signs ideal model delta sigma weight residual False -2.59 -2.41 -0.18 2.00e-01 2.50e+01 7.82e-01 chirality pdb=" CA GLN K 205 " pdb=" N GLN K 205 " pdb=" C GLN K 205 " pdb=" CB GLN K 205 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.92e-01 ... (remaining 2161 not shown) Planarity restraints: 1475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG J 136 " -0.005 2.00e-02 2.50e+03 1.17e-02 4.10e+00 pdb=" N9 DG J 136 " 0.004 2.00e-02 2.50e+03 pdb=" C8 DG J 136 " -0.002 2.00e-02 2.50e+03 pdb=" N7 DG J 136 " 0.003 2.00e-02 2.50e+03 pdb=" C5 DG J 136 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG J 136 " 0.029 2.00e-02 2.50e+03 pdb=" O6 DG J 136 " -0.026 2.00e-02 2.50e+03 pdb=" N1 DG J 136 " 0.005 2.00e-02 2.50e+03 pdb=" C2 DG J 136 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG J 136 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DG J 136 " -0.005 2.00e-02 2.50e+03 pdb=" C4 DG J 136 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS B 31 " 0.029 5.00e-02 4.00e+02 4.32e-02 2.98e+00 pdb=" N PRO B 32 " -0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 32 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO B 32 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C1' DT I 105 " -0.020 2.00e-02 2.50e+03 1.03e-02 2.63e+00 pdb=" N1 DT I 105 " 0.022 2.00e-02 2.50e+03 pdb=" C2 DT I 105 " 0.001 2.00e-02 2.50e+03 pdb=" O2 DT I 105 " 0.006 2.00e-02 2.50e+03 pdb=" N3 DT I 105 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DT I 105 " -0.004 2.00e-02 2.50e+03 pdb=" O4 DT I 105 " -0.008 2.00e-02 2.50e+03 pdb=" C5 DT I 105 " -0.002 2.00e-02 2.50e+03 pdb=" C7 DT I 105 " 0.007 2.00e-02 2.50e+03 pdb=" C6 DT I 105 " 0.000 2.00e-02 2.50e+03 ... (remaining 1472 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1616 2.76 - 3.29: 11748 3.29 - 3.83: 23869 3.83 - 4.36: 25926 4.36 - 4.90: 38626 Nonbonded interactions: 101785 Sorted by model distance: nonbonded pdb=" OD1 ASN K 21 " pdb=" OH TYR K 40 " model vdw 2.221 2.440 nonbonded pdb=" O ILE E 62 " pdb=" NE2 GLN E 93 " model vdw 2.225 2.520 nonbonded pdb=" OG1 THR K 78 " pdb=" O ASN K 81 " model vdw 2.232 2.440 nonbonded pdb=" N4 DC I 64 " pdb=" N6 DA I 65 " model vdw 2.236 3.200 nonbonded pdb=" O ILE A 119 " pdb=" OG SER B 47 " model vdw 2.280 2.440 ... (remaining 101780 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = (chain 'A' and (resid 46 through 49 or (resid 50 and (name N or name CA or name \ C or name O or name CB )) or resid 51 through 132)) selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and (resid 16 through 74 or (resid 75 and (name N or name CA or name \ C or name O or name CB )) or resid 76 through 99 or (resid 100 and (name N or na \ me CA or name C or name O or name CB )) or resid 101 through 116)) selection = (chain 'G' and (resid 16 through 113 or (resid 114 and (name N or name CA or nam \ e C or name O or name CB )) or resid 115 through 116)) } ncs_group { reference = (chain 'D' and (resid 35 through 37 or (resid 38 and (name N or name CA or name \ C or name O or name CB )) or resid 39 through 127)) selection = (chain 'H' and (resid 35 through 107 or (resid 108 and (name N or name CA or nam \ e C or name O or name CB )) or resid 109 through 127)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.550 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.150 Construct map_model_manager: 0.010 Extract box with map and model: 2.770 Check model and map are aligned: 0.190 Set scattering table: 0.110 Process input model: 39.160 Find NCS groups from input model: 0.480 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.890 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.360 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6821 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 : 0.003 0.047 13074 Z= 0.169 Angle : 0.583 8.215 18784 Z= 0.349 Chirality : 0.035 0.236 2164 Planarity : 0.003 0.043 1475 Dihedral : 26.959 145.718 5259 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 12.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.31 % Favored : 96.69 % Rotamer Outliers : 0.14 % 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: 0.16 (0.28), residues: 875 helix: 1.26 (0.23), residues: 518 sheet: -0.56 (0.99), residues: 29 loop : -1.76 (0.31), residues: 328 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 201 time to evaluate : 1.149 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 201 average time/residue: 0.2942 time to fit residues: 79.8964 Evaluate side-chains 155 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3162 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 10.0000 chunk 85 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 5.9990 chunk 57 optimal weight: 10.0000 chunk 45 optimal weight: 0.7980 chunk 88 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 65 optimal weight: 4.9990 chunk 102 optimal weight: 40.0000 overall best weight: 2.7588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 85 GLN A 93 GLN A 113 HIS ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 98 GLN E 55 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 115 ASN ** K 77 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 145 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.059 13074 Z= 0.267 Angle : 0.594 7.151 18784 Z= 0.344 Chirality : 0.036 0.189 2164 Planarity : 0.006 0.070 1475 Dihedral : 30.949 147.993 3599 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 15.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 3.60 % 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: -0.00 (0.28), residues: 875 helix: 1.09 (0.23), residues: 523 sheet: -0.70 (0.88), residues: 33 loop : -1.79 (0.32), residues: 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 190 time to evaluate : 1.014 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 26 outliers final: 20 residues processed: 205 average time/residue: 0.3036 time to fit residues: 82.7411 Evaluate side-chains 179 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 159 time to evaluate : 1.025 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1481 time to fit residues: 6.1820 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 85 optimal weight: 10.0000 chunk 69 optimal weight: 0.6980 chunk 28 optimal weight: 9.9990 chunk 102 optimal weight: 0.8980 chunk 111 optimal weight: 4.9990 chunk 91 optimal weight: 10.0000 chunk 101 optimal weight: 9.9990 chunk 35 optimal weight: 0.9990 chunk 82 optimal weight: 10.0000 overall best weight: 1.7186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 90 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN K 145 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7142 moved from start: 0.2803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 13074 Z= 0.201 Angle : 0.555 8.059 18784 Z= 0.322 Chirality : 0.035 0.145 2164 Planarity : 0.004 0.044 1475 Dihedral : 30.927 147.094 3599 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 15.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.54 % Favored : 96.46 % Rotamer Outliers : 2.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.28), residues: 875 helix: 1.13 (0.23), residues: 521 sheet: -0.70 (0.84), residues: 33 loop : -1.77 (0.32), residues: 321 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 202 time to evaluate : 0.952 Fit side-chains revert: symmetry clash outliers start: 15 outliers final: 5 residues processed: 207 average time/residue: 0.3147 time to fit residues: 86.5302 Evaluate side-chains 182 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 177 time to evaluate : 1.030 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.2077 time to fit residues: 2.7867 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 20.0000 chunk 11 optimal weight: 4.9990 chunk 49 optimal weight: 0.0170 chunk 69 optimal weight: 2.9990 chunk 103 optimal weight: 40.0000 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 30.0000 chunk 29 optimal weight: 10.0000 chunk 90 optimal weight: 7.9990 overall best weight: 4.0026 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 93 GLN G 39 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 90 ASN G 115 ASN K 145 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7352 moved from start: 0.4601 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.070 13074 Z= 0.345 Angle : 0.659 10.535 18784 Z= 0.377 Chirality : 0.038 0.174 2164 Planarity : 0.006 0.053 1475 Dihedral : 31.569 148.498 3599 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.66 % Favored : 96.34 % Rotamer Outliers : 4.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.38 (0.28), residues: 875 helix: 0.71 (0.22), residues: 529 sheet: -0.15 (0.82), residues: 37 loop : -1.98 (0.31), residues: 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 246 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 211 time to evaluate : 1.035 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 35 outliers final: 20 residues processed: 225 average time/residue: 0.3320 time to fit residues: 97.6096 Evaluate side-chains 204 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 184 time to evaluate : 1.060 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.1265 time to fit residues: 5.6871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 5.9990 chunk 1 optimal weight: 2.9990 chunk 81 optimal weight: 10.0000 chunk 45 optimal weight: 4.9990 chunk 93 optimal weight: 10.0000 chunk 75 optimal weight: 10.0000 chunk 0 optimal weight: 9.9990 chunk 55 optimal weight: 0.6980 chunk 98 optimal weight: 30.0000 chunk 27 optimal weight: 7.9990 chunk 36 optimal weight: 10.0000 overall best weight: 4.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 93 GLN G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN K 145 ASN ** K 205 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.5582 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.067 13074 Z= 0.369 Angle : 0.666 10.949 18784 Z= 0.384 Chirality : 0.039 0.177 2164 Planarity : 0.006 0.045 1475 Dihedral : 31.777 148.452 3599 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 21.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.46 % Favored : 95.54 % Rotamer Outliers : 4.15 % 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: -0.42 (0.28), residues: 875 helix: 0.74 (0.22), residues: 528 sheet: -0.10 (0.85), residues: 37 loop : -2.10 (0.32), residues: 310 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 241 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 211 time to evaluate : 1.026 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 30 outliers final: 19 residues processed: 226 average time/residue: 0.3197 time to fit residues: 95.8683 Evaluate side-chains 196 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 177 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 0 residues processed: 19 average time/residue: 0.1113 time to fit residues: 5.2970 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 10.0000 chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 5.9990 chunk 26 optimal weight: 8.9990 chunk 109 optimal weight: 4.9990 chunk 90 optimal weight: 10.0000 chunk 50 optimal weight: 0.7980 chunk 9 optimal weight: 6.9990 chunk 36 optimal weight: 0.2980 chunk 57 optimal weight: 8.9990 chunk 105 optimal weight: 6.9990 overall best weight: 2.6184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 90 ASN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN K 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.053 13074 Z= 0.269 Angle : 0.640 10.361 18784 Z= 0.367 Chirality : 0.037 0.165 2164 Planarity : 0.005 0.053 1475 Dihedral : 31.706 148.148 3599 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 18.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.69 % Favored : 95.31 % Rotamer Outliers : 2.21 % 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: -0.21 (0.28), residues: 875 helix: 0.84 (0.22), residues: 546 sheet: 1.05 (1.25), residues: 17 loop : -2.01 (0.31), residues: 312 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 213 time to evaluate : 1.131 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 11 residues processed: 218 average time/residue: 0.3506 time to fit residues: 101.5817 Evaluate side-chains 207 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 196 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 11 outliers final: 0 residues processed: 11 average time/residue: 0.1151 time to fit residues: 3.6015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.8980 chunk 62 optimal weight: 8.9990 chunk 79 optimal weight: 10.0000 chunk 61 optimal weight: 9.9990 chunk 92 optimal weight: 8.9990 chunk 108 optimal weight: 4.9990 chunk 68 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 1.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 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 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.5706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 13074 Z= 0.207 Angle : 0.612 8.796 18784 Z= 0.352 Chirality : 0.036 0.150 2164 Planarity : 0.005 0.047 1475 Dihedral : 31.527 148.237 3599 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.05 (0.28), residues: 875 helix: 1.10 (0.23), residues: 540 sheet: 0.08 (1.02), residues: 27 loop : -1.94 (0.32), residues: 308 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 218 time to evaluate : 1.084 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 6 residues processed: 219 average time/residue: 0.2976 time to fit residues: 88.3174 Evaluate side-chains 206 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 200 time to evaluate : 1.156 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1180 time to fit residues: 2.6744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 74 optimal weight: 10.0000 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 85 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 104 optimal weight: 8.9990 chunk 95 optimal weight: 10.0000 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN K 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7309 moved from start: 0.5611 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 13074 Z= 0.187 Angle : 0.608 8.918 18784 Z= 0.347 Chirality : 0.036 0.180 2164 Planarity : 0.004 0.050 1475 Dihedral : 31.332 147.982 3599 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 16.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.23 % Favored : 95.77 % Rotamer Outliers : 1.24 % 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: 0.07 (0.28), residues: 875 helix: 1.13 (0.23), residues: 539 sheet: -0.05 (0.98), residues: 27 loop : -1.94 (0.32), residues: 309 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 215 time to evaluate : 1.022 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 5 residues processed: 217 average time/residue: 0.2986 time to fit residues: 87.4499 Evaluate side-chains 202 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1168 time to fit residues: 2.4311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 9.9990 chunk 104 optimal weight: 10.0000 chunk 61 optimal weight: 0.0570 chunk 44 optimal weight: 0.9980 chunk 79 optimal weight: 10.0000 chunk 31 optimal weight: 0.9990 chunk 91 optimal weight: 10.0000 chunk 95 optimal weight: 10.0000 chunk 66 optimal weight: 1.9990 chunk 107 optimal weight: 30.0000 chunk 65 optimal weight: 2.9990 overall best weight: 1.4104 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 93 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN K 205 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5735 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.043 13074 Z= 0.210 Angle : 0.634 11.423 18784 Z= 0.355 Chirality : 0.036 0.205 2164 Planarity : 0.005 0.072 1475 Dihedral : 31.319 148.042 3599 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 17.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer Outliers : 0.97 % 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: -0.01 (0.28), residues: 875 helix: 1.12 (0.23), residues: 537 sheet: -1.10 (0.91), residues: 30 loop : -1.96 (0.31), residues: 308 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 204 time to evaluate : 1.046 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 206 average time/residue: 0.2951 time to fit residues: 82.9395 Evaluate side-chains 199 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 197 time to evaluate : 1.037 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1141 time to fit residues: 1.6521 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 0.8980 chunk 74 optimal weight: 10.0000 chunk 112 optimal weight: 0.6980 chunk 103 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 9 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 54 optimal weight: 0.6980 chunk 71 optimal weight: 30.0000 chunk 95 optimal weight: 10.0000 chunk 27 optimal weight: 4.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN K 205 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7322 moved from start: 0.5844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.050 13074 Z= 0.215 Angle : 0.642 11.308 18784 Z= 0.361 Chirality : 0.036 0.284 2164 Planarity : 0.005 0.079 1475 Dihedral : 31.310 148.137 3599 Min Nonbonded Distance : 2.116 Molprobity Statistics. All-atom Clashscore : 17.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.91 % Favored : 95.09 % Rotamer Outliers : 0.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.04 (0.28), residues: 875 helix: 1.09 (0.23), residues: 538 sheet: -0.97 (0.98), residues: 30 loop : -1.98 (0.32), residues: 307 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1750 Ramachandran restraints generated. 875 Oldfield, 0 Emsley, 875 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 197 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 197 average time/residue: 0.2901 time to fit residues: 78.3903 Evaluate side-chains 197 residues out of total 764 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 194 time to evaluate : 1.187 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1199 time to fit residues: 2.0119 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 10.0000 chunk 13 optimal weight: 0.8980 chunk 24 optimal weight: 9.9990 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 5.9990 chunk 92 optimal weight: 10.0000 chunk 11 optimal weight: 5.9990 chunk 16 optimal weight: 0.9990 chunk 78 optimal weight: 8.9990 chunk 5 optimal weight: 0.0470 chunk 64 optimal weight: 9.9990 overall best weight: 2.7884 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 66 ASN E 93 GLN ** G 39 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 42 GLN ** G 83 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 115 ASN ** K 39 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** K 205 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4163 r_free = 0.4163 target = 0.114335 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3484 r_free = 0.3484 target = 0.076373 restraints weight = 35471.175| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3527 r_free = 0.3527 target = 0.078658 restraints weight = 18299.874| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 48)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.080086 restraints weight = 12871.686| |-----------------------------------------------------------------------------| r_work (final): 0.3514 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7778 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.044 13074 Z= 0.277 Angle : 0.669 11.076 18784 Z= 0.375 Chirality : 0.037 0.213 2164 Planarity : 0.005 0.087 1475 Dihedral : 31.544 148.879 3599 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 20.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 0.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.28), residues: 875 helix: 0.99 (0.23), residues: 539 sheet: -0.78 (1.20), residues: 20 loop : -2.06 (0.31), residues: 316 =============================================================================== Job complete usr+sys time: 2306.75 seconds wall clock time: 42 minutes 56.03 seconds (2576.03 seconds total)