Starting phenix.real_space_refine (version: dev) on Mon Feb 20 02:08:24 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/02_2023/7on1_12993.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/02_2023/7on1_12993.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/02_2023/7on1_12993.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/02_2023/7on1_12993.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/02_2023/7on1_12993.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7on1_12993/02_2023/7on1_12993.pdb" } resolution = 3.35 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= 0.001 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 35 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "C TYR 297": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "b GLU 75": "OE1" <-> "OE2" Residue "d TYR 46": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e TYR 140": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e GLU 141": "OE1" <-> "OE2" Residue "e TYR 145": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "e ASP 150": "OD1" <-> "OD2" Residue "e ASP 167": "OD1" <-> "OD2" Residue "f ASP 86": "OD1" <-> "OD2" Residue "g TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "g GLU 63": "OE1" <-> "OE2" Residue "g GLU 66": "OE1" <-> "OE2" Residue "h TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "h ASP 55": "OD1" <-> "OD2" Residue "h GLU 80": "OE1" <-> "OE2" Residue "c TYR 52": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "c GLU 63": "OE1" <-> "OE2" Residue "c ASP 92": "OD1" <-> "OD2" Residue "a ASP 150": "OD1" <-> "OD2" Residue "a GLU 164": "OE1" <-> "OE2" Residue "a ASP 173": "OD1" <-> "OD2" Residue "a ASP 175": "OD1" <-> "OD2" Residue "a GLU 191": "OE1" <-> "OE2" Residue "a GLU 199": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 11150 Number of models: 1 Model: "" Number of chains: 12 Chain: "C" Number of atoms: 169 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 169 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 2 Chain: "b" Number of atoms: 625 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 625 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Unresolved non-hydrogen bonds: 2 Unresolved non-hydrogen angles: 3 Unresolved non-hydrogen dihedrals: 1 Unresolved non-hydrogen chiralities: 1 Chain: "d" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 735 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "e" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "f" Number of atoms: 627 Number of conformers: 1 Conformer: "" Number of residues, atoms: 79, 627 Classifications: {'peptide': 79} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 77} Chain: "g" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 745 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 4, 'TRANS': 92} Chain: "h" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 729 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: "c" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 742 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 92} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 2 Unresolved non-hydrogen chiralities: 1 Chain: "I" Number of atoms: 2509 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2509 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "J" Number of atoms: 2534 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 2534 Classifications: {'DNA': 123} Link IDs: {'rna3p': 122} Chain: "a" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 781 Classifications: {'peptide': 97} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 2, 'TRANS': 94} Unresolved non-hydrogen bonds: 13 Unresolved non-hydrogen angles: 16 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "D" Number of atoms: 173 Number of conformers: 1 Conformer: "" Number of residues, atoms: 21, 173 Classifications: {'peptide': 21} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 1, 'TRANS': 19} Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 2 Time building chain proxies: 6.48, per 1000 atoms: 0.58 Number of scatterers: 11150 At special positions: 0 Unit cell: (120.7, 115.6, 107.1, 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 10 16.00 P 246 15.00 O 2586 8.00 N 2069 7.00 C 6239 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: 5.93 Conformation dependent library (CDL) restraints added in 1.0 seconds 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 7 sheets defined 71.6% alpha, 2.1% beta 109 base pairs and 199 stacking pairs defined. Time for finding SS restraints: 4.75 Creating SS restraints... Processing helix chain 'C' and resid 296 through 300 Processing helix chain 'b' and resid 25 through 30 removed outlier: 3.717A pdb=" N ILE b 30 " --> pdb=" O ILE b 27 " (cutoff:3.500A) Processing helix chain 'b' and resid 31 through 43 Processing helix chain 'b' and resid 50 through 77 removed outlier: 3.909A pdb=" N GLU b 54 " --> pdb=" O LEU b 50 " (cutoff:3.500A) removed outlier: 3.627A pdb=" N ALA b 77 " --> pdb=" O TYR b 73 " (cutoff:3.500A) Processing helix chain 'b' and resid 83 through 94 removed outlier: 3.690A pdb=" N VAL b 87 " --> pdb=" O THR b 83 " (cutoff:3.500A) Processing helix chain 'd' and resid 41 through 53 Processing helix chain 'd' and resid 59 through 88 removed outlier: 3.550A pdb=" N MET d 63 " --> pdb=" O SER d 59 " (cutoff:3.500A) removed outlier: 3.773A pdb=" N ASN d 88 " --> pdb=" O LEU d 84 " (cutoff:3.500A) Processing helix chain 'd' and resid 94 through 106 Processing helix chain 'd' and resid 107 through 128 removed outlier: 4.043A pdb=" N HIS d 113 " --> pdb=" O GLU d 109 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N SER d 128 " --> pdb=" O LYS d 124 " (cutoff:3.500A) Processing helix chain 'e' and resid 134 through 148 Processing helix chain 'e' and resid 154 through 169 removed outlier: 3.922A pdb=" N PHE e 158 " --> pdb=" O SER e 154 " (cutoff:3.500A) Processing helix chain 'e' and resid 180 through 208 removed outlier: 3.521A pdb=" N MET e 184 " --> pdb=" O SER e 180 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N ALA e 208 " --> pdb=" O LEU e 204 " (cutoff:3.500A) Processing helix chain 'e' and resid 214 through 226 removed outlier: 4.082A pdb=" N GLY e 226 " --> pdb=" O ARG e 222 " (cutoff:3.500A) Processing helix chain 'f' and resid 26 through 30 removed outlier: 3.640A pdb=" N GLY f 29 " --> pdb=" O ASN f 26 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N ILE f 30 " --> pdb=" O ILE f 27 " (cutoff:3.500A) No H-bonds generated for 'chain 'f' and resid 26 through 30' Processing helix chain 'f' and resid 31 through 43 removed outlier: 3.727A pdb=" N ILE f 35 " --> pdb=" O THR f 31 " (cutoff:3.500A) Processing helix chain 'f' and resid 50 through 77 removed outlier: 4.361A pdb=" N GLU f 54 " --> pdb=" O LEU f 50 " (cutoff:3.500A) removed outlier: 3.688A pdb=" N ALA f 77 " --> pdb=" O TYR f 73 " (cutoff:3.500A) Processing helix chain 'f' and resid 83 through 95 removed outlier: 3.519A pdb=" N VAL f 87 " --> pdb=" O THR f 83 " (cutoff:3.500A) Processing helix chain 'g' and resid 18 through 23 Processing helix chain 'g' and resid 29 through 38 Processing helix chain 'g' and resid 48 through 75 removed outlier: 3.682A pdb=" N ASN g 75 " --> pdb=" O ALA g 71 " (cutoff:3.500A) Processing helix chain 'g' and resid 81 through 91 Processing helix chain 'g' and resid 92 through 99 Processing helix chain 'h' and resid 41 through 53 removed outlier: 3.751A pdb=" N ILE h 45 " --> pdb=" O TYR h 41 " (cutoff:3.500A) Processing helix chain 'h' and resid 59 through 88 removed outlier: 3.588A pdb=" N ASN h 88 " --> pdb=" O LEU h 84 " (cutoff:3.500A) Processing helix chain 'h' and resid 94 through 106 removed outlier: 3.586A pdb=" N ILE h 98 " --> pdb=" O SER h 94 " (cutoff:3.500A) Processing helix chain 'h' and resid 107 through 126 removed outlier: 3.507A pdb=" N SER h 116 " --> pdb=" O LYS h 112 " (cutoff:3.500A) Processing helix chain 'c' and resid 18 through 24 Processing helix chain 'c' and resid 29 through 38 Processing helix chain 'c' and resid 47 through 75 removed outlier: 4.523A pdb=" N VAL c 51 " --> pdb=" O SER c 47 " (cutoff:3.500A) removed outlier: 3.742A pdb=" N ASN c 75 " --> pdb=" O ALA c 71 " (cutoff:3.500A) Processing helix chain 'c' and resid 81 through 91 Processing helix chain 'c' and resid 92 through 99 Processing helix chain 'a' and resid 134 through 148 Processing helix chain 'a' and resid 154 through 168 removed outlier: 3.679A pdb=" N PHE a 158 " --> pdb=" O SER a 154 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N GLU a 168 " --> pdb=" O GLU a 164 " (cutoff:3.500A) Processing helix chain 'a' and resid 179 through 208 removed outlier: 3.523A pdb=" N ALA a 208 " --> pdb=" O LEU a 204 " (cutoff:3.500A) Processing helix chain 'a' and resid 214 through 226 removed outlier: 3.564A pdb=" N MET a 218 " --> pdb=" O MET a 214 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N GLY a 226 " --> pdb=" O ARG a 222 " (cutoff:3.500A) Processing helix chain 'D' and resid 296 through 300 Processing sheet with id=AA1, first strand: chain 'b' and resid 46 through 47 removed outlier: 7.617A pdb=" N ARG b 46 " --> pdb=" O ILE a 213 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'b' and resid 81 through 82 Processing sheet with id=AA3, first strand: chain 'b' and resid 97 through 99 removed outlier: 6.722A pdb=" N THR b 97 " --> pdb=" O THR g 103 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'd' and resid 92 through 93 Processing sheet with id=AA5, first strand: chain 'e' and resid 177 through 178 removed outlier: 6.946A pdb=" N ARG e 177 " --> pdb=" O VAL f 82 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'f' and resid 98 through 99 Processing sheet with id=AA7, first strand: chain 'g' and resid 79 through 80 390 hydrogen bonds defined for protein. 1152 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 283 hydrogen bonds 550 hydrogen bond angles 0 basepair planarities 109 basepair parallelities 199 stacking parallelities Total time for adding SS restraints: 4.09 Time building geometry restraints manager: 6.21 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: 2072 1.33 - 1.45: 3752 1.45 - 1.57: 5509 1.57 - 1.69: 490 1.69 - 1.80: 20 Bond restraints: 11843 Sorted by residual: bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.457 -0.035 3.00e-02 1.11e+03 1.38e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.452 -0.030 3.00e-02 1.11e+03 1.03e+00 bond pdb=" C3' DC J 53 " pdb=" C2' DC J 53 " ideal model delta sigma weight residual 1.525 1.544 -0.019 2.00e-02 2.50e+03 8.70e-01 bond pdb=" N LYS c 76 " pdb=" CA LYS c 76 " ideal model delta sigma weight residual 1.457 1.469 -0.012 1.29e-02 6.01e+03 8.61e-01 bond pdb=" C3' DT I 1 " pdb=" C2' DT I 1 " ideal model delta sigma weight residual 1.525 1.542 -0.017 2.00e-02 2.50e+03 7.18e-01 ... (remaining 11838 not shown) Histogram of bond angle deviations from ideal: 99.32 - 106.25: 1591 106.25 - 113.18: 6372 113.18 - 120.11: 4380 120.11 - 127.03: 4134 127.03 - 133.96: 579 Bond angle restraints: 17056 Sorted by residual: angle pdb=" N LYS f 32 " pdb=" CA LYS f 32 " pdb=" C LYS f 32 " ideal model delta sigma weight residual 109.81 116.33 -6.52 2.21e+00 2.05e-01 8.71e+00 angle pdb=" C ASN g 75 " pdb=" N LYS g 76 " pdb=" CA LYS g 76 " ideal model delta sigma weight residual 122.46 125.27 -2.81 1.41e+00 5.03e-01 3.96e+00 angle pdb=" C ASN d 88 " pdb=" N LYS d 89 " pdb=" CA LYS d 89 " ideal model delta sigma weight residual 122.46 125.26 -2.80 1.41e+00 5.03e-01 3.94e+00 angle pdb=" CA LYS b 32 " pdb=" C LYS b 32 " pdb=" N PRO b 33 " ideal model delta sigma weight residual 118.44 121.54 -3.10 1.59e+00 3.96e-01 3.79e+00 angle pdb=" CA LYS f 32 " pdb=" C LYS f 32 " pdb=" N PRO f 33 " ideal model delta sigma weight residual 118.44 121.51 -3.07 1.59e+00 3.96e-01 3.73e+00 ... (remaining 17051 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 5211 35.74 - 71.48: 1050 71.48 - 107.22: 12 107.22 - 142.96: 0 142.96 - 178.70: 2 Dihedral angle restraints: 6275 sinusoidal: 4010 harmonic: 2265 Sorted by residual: dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual -140.00 38.70 -178.70 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 36.57 -176.57 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CB LYS d 50 " pdb=" CG LYS d 50 " pdb=" CD LYS d 50 " pdb=" CE LYS d 50 " ideal model delta sinusoidal sigma weight residual 180.00 122.95 57.05 3 1.50e+01 4.44e-03 9.42e+00 ... (remaining 6272 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 1505 0.028 - 0.056: 326 0.056 - 0.084: 75 0.084 - 0.112: 36 0.112 - 0.140: 13 Chirality restraints: 1955 Sorted by residual: chirality pdb=" CA LYS f 32 " pdb=" N LYS f 32 " pdb=" C LYS f 32 " pdb=" CB LYS f 32 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.87e-01 chirality pdb=" CA ILE c 81 " pdb=" N ILE c 81 " pdb=" C ILE c 81 " pdb=" CB ILE c 81 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.88e-01 chirality pdb=" CA ILE h 58 " pdb=" N ILE h 58 " pdb=" C ILE h 58 " pdb=" CB ILE h 58 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.58e-01 ... (remaining 1952 not shown) Planarity restraints: 1299 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS f 32 " -0.031 5.00e-02 4.00e+02 4.68e-02 3.51e+00 pdb=" N PRO f 33 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO f 33 " -0.023 5.00e-02 4.00e+02 pdb=" CD PRO f 33 " -0.027 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS b 32 " -0.019 5.00e-02 4.00e+02 2.80e-02 1.25e+00 pdb=" N PRO b 33 " 0.048 5.00e-02 4.00e+02 pdb=" CA PRO b 33 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO b 33 " -0.016 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE g 81 " 0.018 5.00e-02 4.00e+02 2.69e-02 1.16e+00 pdb=" N PRO g 82 " -0.047 5.00e-02 4.00e+02 pdb=" CA PRO g 82 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO g 82 " 0.015 5.00e-02 4.00e+02 ... (remaining 1296 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.68: 301 2.68 - 3.23: 9377 3.23 - 3.79: 19631 3.79 - 4.34: 24425 4.34 - 4.90: 36170 Nonbonded interactions: 89904 Sorted by model distance: nonbonded pdb=" O2 DC I -20 " pdb=" N2 DG J 20 " model vdw 2.120 2.496 nonbonded pdb=" N2 DG I -60 " pdb=" O2 DC J 60 " model vdw 2.149 2.496 nonbonded pdb=" O2 DC I -21 " pdb=" N2 DG J 21 " model vdw 2.179 2.496 nonbonded pdb=" OG1 THR e 171 " pdb=" OD1 ASP e 173 " model vdw 2.226 2.440 nonbonded pdb=" OG SER e 148 " pdb=" OD1 ASP e 150 " model vdw 2.292 2.440 ... (remaining 89899 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 'C' selection = (chain 'D' and (resid 284 through 285 or (resid 286 and (name N or name CA or na \ me C or name O or name CB )) or resid 287 through 304)) } ncs_group { reference = chain 'a' selection = chain 'e' } ncs_group { reference = chain 'b' selection = (chain 'f' and (resid 25 through 54 or (resid 55 and (name N or name CA or name \ C or name O or name CB )) or resid 56 through 103)) } ncs_group { reference = chain 'c' selection = (chain 'g' and (resid 17 through 112 or (resid 113 and (name N or name CA or nam \ e C or name O or name CB )))) } ncs_group { reference = (chain 'd' and ((resid 35 through 36 and (name N or name CA or name C or name O \ or name CB )) or resid 37 through 128)) selection = (chain 'h' 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 128)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 246 5.49 5 S 10 5.16 5 C 6239 2.51 5 N 2069 2.21 5 O 2586 1.98 5 sf(0) = scattering factor at diffraction angle 0. 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: 0.010 Normalize map: mean=0, sd=1: 1.670 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.070 Construct map_model_manager: 0.000 Extract box with map and model: 7.630 Check model and map are aligned: 0.160 Process input model: 36.680 Find NCS groups from input model: 0.440 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.110 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:2.910 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.730 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 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 : 0.002 0.035 11843 Z= 0.130 Angle : 0.466 6.522 17056 Z= 0.298 Chirality : 0.029 0.140 1955 Planarity : 0.003 0.047 1299 Dihedral : 26.279 178.699 4809 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % Rotamer Outliers : 0.00 % 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: -0.25 (0.27), residues: 757 helix: 0.58 (0.21), residues: 525 sheet: None (None), residues: 0 loop : -1.82 (0.32), residues: 232 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.938 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.3780 time to fit residues: 90.3126 Evaluate side-chains 141 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.910 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 40 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 38 optimal weight: 2.9990 chunk 75 optimal weight: 5.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 6.9990 chunk 56 optimal weight: 3.9990 chunk 87 optimal weight: 0.6980 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN e 187 GLN e 219 GLN e 227 GLN f 76 HIS h 51 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8779 moved from start: 0.3390 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.058 11843 Z= 0.415 Angle : 0.636 6.426 17056 Z= 0.365 Chirality : 0.039 0.149 1955 Planarity : 0.005 0.042 1299 Dihedral : 30.120 173.837 3327 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.64 % Favored : 97.36 % Rotamer Outliers : 1.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.30), residues: 757 helix: 1.70 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.64 (0.36), residues: 223 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 153 time to evaluate : 0.916 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 157 average time/residue: 0.3840 time to fit residues: 75.7119 Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1676 time to fit residues: 2.7366 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 0.9980 chunk 72 optimal weight: 6.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 0.6980 chunk 77 optimal weight: 5.9990 chunk 86 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 70 optimal weight: 4.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN d 88 ASN c 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8703 moved from start: 0.3303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11843 Z= 0.185 Angle : 0.498 5.607 17056 Z= 0.297 Chirality : 0.032 0.130 1955 Planarity : 0.003 0.041 1299 Dihedral : 29.893 175.266 3327 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % Rotamer Outliers : 1.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.89 (0.31), residues: 757 helix: 2.33 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.51 (0.36), residues: 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 153 time to evaluate : 0.934 Fit side-chains outliers start: 7 outliers final: 3 residues processed: 154 average time/residue: 0.3602 time to fit residues: 70.5893 Evaluate side-chains 147 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 144 time to evaluate : 0.881 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2640 time to fit residues: 2.1484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 65 optimal weight: 5.9990 chunk 45 optimal weight: 0.9990 chunk 9 optimal weight: 7.9990 chunk 41 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 chunk 92 optimal weight: 3.9990 chunk 83 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 5.9990 overall best weight: 2.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN d 51 GLN c 101 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8793 moved from start: 0.3938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.050 11843 Z= 0.336 Angle : 0.578 5.747 17056 Z= 0.338 Chirality : 0.036 0.142 1955 Planarity : 0.004 0.043 1299 Dihedral : 30.152 173.584 3327 Min Nonbonded Distance : 2.058 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 1.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.96 (0.31), residues: 757 helix: 2.35 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.43 (0.38), residues: 222 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 157 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 145 time to evaluate : 0.886 Fit side-chains outliers start: 12 outliers final: 9 residues processed: 150 average time/residue: 0.3646 time to fit residues: 69.4875 Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 140 time to evaluate : 0.855 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.2273 time to fit residues: 3.9426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 4.9990 chunk 1 optimal weight: 0.9980 chunk 69 optimal weight: 6.9990 chunk 38 optimal weight: 0.9990 chunk 79 optimal weight: 4.9990 chunk 64 optimal weight: 5.9990 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 chunk 31 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11843 Z= 0.195 Angle : 0.509 5.622 17056 Z= 0.304 Chirality : 0.032 0.134 1955 Planarity : 0.004 0.042 1299 Dihedral : 29.975 174.640 3327 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer Outliers : 1.09 % 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: 2.26 (0.31), residues: 757 helix: 2.60 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 223 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 147 time to evaluate : 0.965 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 150 average time/residue: 0.3639 time to fit residues: 69.4780 Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 144 time to evaluate : 1.055 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.3677 time to fit residues: 3.5325 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 5.9990 chunk 18 optimal weight: 5.9990 chunk 54 optimal weight: 0.3980 chunk 22 optimal weight: 4.9990 chunk 92 optimal weight: 2.9990 chunk 77 optimal weight: 5.9990 chunk 43 optimal weight: 2.9990 chunk 7 optimal weight: 4.9990 chunk 30 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 89 optimal weight: 0.9980 overall best weight: 2.0786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8794 moved from start: 0.4155 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.048 11843 Z= 0.323 Angle : 0.576 5.757 17056 Z= 0.337 Chirality : 0.036 0.140 1955 Planarity : 0.004 0.043 1299 Dihedral : 30.155 173.443 3327 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 1.41 % 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: 2.13 (0.31), residues: 757 helix: 2.50 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.44 (0.38), residues: 223 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 145 time to evaluate : 1.010 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 149 average time/residue: 0.3420 time to fit residues: 64.9807 Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 143 time to evaluate : 0.831 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.1769 time to fit residues: 2.5197 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 3.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 78 optimal weight: 4.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 2.9990 chunk 57 optimal weight: 0.9990 chunk 56 optimal weight: 0.5980 chunk 42 optimal weight: 0.7980 chunk 36 optimal weight: 1.9990 chunk 55 optimal weight: 0.5980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.3904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11843 Z= 0.178 Angle : 0.501 5.689 17056 Z= 0.300 Chirality : 0.032 0.132 1955 Planarity : 0.003 0.042 1299 Dihedral : 29.946 174.922 3327 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 7.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.06 % Favored : 98.94 % Rotamer Outliers : 0.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.43 (0.31), residues: 757 helix: 2.74 (0.22), residues: 532 sheet: None (None), residues: 0 loop : -1.35 (0.38), residues: 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 147 time to evaluate : 1.079 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 148 average time/residue: 0.3478 time to fit residues: 65.9217 Evaluate side-chains 145 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 143 time to evaluate : 0.861 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1061 time to fit residues: 1.4486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 0.9990 chunk 18 optimal weight: 5.9990 chunk 17 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 chunk 45 optimal weight: 0.6980 chunk 8 optimal weight: 2.9990 chunk 72 optimal weight: 6.9990 chunk 84 optimal weight: 8.9990 chunk 88 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8732 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11843 Z= 0.205 Angle : 0.516 7.135 17056 Z= 0.306 Chirality : 0.032 0.131 1955 Planarity : 0.004 0.043 1299 Dihedral : 29.972 174.353 3327 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.78 % 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: 2.49 (0.31), residues: 757 helix: 2.77 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.30 (0.39), residues: 223 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 143 time to evaluate : 0.999 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 145 average time/residue: 0.3570 time to fit residues: 66.7021 Evaluate side-chains 144 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 142 time to evaluate : 0.946 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1179 time to fit residues: 1.5442 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 3.9990 chunk 88 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 3.9990 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 chunk 85 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 91 optimal weight: 0.9980 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 296 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8730 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11843 Z= 0.204 Angle : 0.519 6.953 17056 Z= 0.307 Chirality : 0.032 0.131 1955 Planarity : 0.004 0.043 1299 Dihedral : 29.944 174.338 3327 Min Nonbonded Distance : 2.122 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer Outliers : 0.94 % 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: 2.54 (0.31), residues: 757 helix: 2.80 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.26 (0.39), residues: 223 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 141 time to evaluate : 0.969 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 143 average time/residue: 0.3521 time to fit residues: 64.8995 Evaluate side-chains 143 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 140 time to evaluate : 0.980 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2850 time to fit residues: 2.2329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 0.6980 chunk 43 optimal weight: 5.9990 chunk 63 optimal weight: 6.9990 chunk 95 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 76 optimal weight: 5.9990 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 0.0010 chunk 46 optimal weight: 0.8980 chunk 60 optimal weight: 1.9990 chunk 81 optimal weight: 5.9990 overall best weight: 0.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 moved from start: 0.3974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.043 11843 Z= 0.190 Angle : 0.515 7.259 17056 Z= 0.304 Chirality : 0.032 0.130 1955 Planarity : 0.004 0.043 1299 Dihedral : 29.936 174.417 3327 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer Outliers : 0.00 % 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: 2.57 (0.31), residues: 757 helix: 2.81 (0.22), residues: 534 sheet: None (None), residues: 0 loop : -1.23 (0.40), residues: 223 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1514 Ramachandran restraints generated. 757 Oldfield, 0 Emsley, 757 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 143 time to evaluate : 1.027 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 143 average time/residue: 0.3511 time to fit residues: 63.9456 Evaluate side-chains 141 residues out of total 659 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 141 time to evaluate : 0.862 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0190 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 0.8980 chunk 70 optimal weight: 5.9990 chunk 11 optimal weight: 4.9990 chunk 21 optimal weight: 0.7980 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 9 optimal weight: 8.9990 chunk 14 optimal weight: 3.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 0.7980 overall best weight: 1.4782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3642 r_free = 0.3642 target = 0.118794 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2963 r_free = 0.2963 target = 0.076535 restraints weight = 19714.108| |-----------------------------------------------------------------------------| r_work (start): 0.2929 rms_B_bonded: 1.57 r_work: 0.2767 rms_B_bonded: 3.23 restraints_weight: 0.5000 r_work: 0.2634 rms_B_bonded: 4.99 restraints_weight: 0.2500 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8979 moved from start: 0.4111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 11843 Z= 0.253 Angle : 0.546 6.603 17056 Z= 0.320 Chirality : 0.034 0.133 1955 Planarity : 0.004 0.043 1299 Dihedral : 30.014 173.830 3327 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.43 % Favored : 96.57 % Rotamer Outliers : 0.16 % 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: 2.50 (0.31), residues: 757 helix: 2.75 (0.22), residues: 535 sheet: None (None), residues: 0 loop : -1.24 (0.40), residues: 222 =============================================================================== Job complete usr+sys time: 2312.38 seconds wall clock time: 42 minutes 42.93 seconds (2562.93 seconds total)