Starting phenix.real_space_refine (version: 1.21rc1) on Sat Apr 22 09:41:02 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/04_2023/7eg6_31106.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/04_2023/7eg6_31106.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/04_2023/7eg6_31106.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/04_2023/7eg6_31106.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/04_2023/7eg6_31106.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7eg6_31106/04_2023/7eg6_31106.pdb" } resolution = 3.1 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 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 292 5.49 5 S 12 5.16 5 C 6692 2.51 5 N 2277 2.21 5 O 2845 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "M ASP 668": "OD1" <-> "OD2" Residue "M ASP 670": "OD1" <-> "OD2" Residue "M ARG 676": "NH1" <-> "NH2" Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 94": "OE1" <-> "OE2" Residue "A PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 24": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "B TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 73": "OE1" <-> "OE2" Residue "D TYR 80": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 102": "OE1" <-> "OE2" Residue "E TYR 41": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 50": "OE1" <-> "OE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 51": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "F TYR 88": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 100": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 56": "OE1" <-> "OE2" Residue "H TYR 34": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H ASP 48": "OD1" <-> "OD2" Residue "H GLU 68": "OE1" <-> "OE2" Residue "H GLU 73": "OE1" <-> "OE2" Residue "H GLU 102": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-4938/modules/chem_data/mon_lib" Total number of atoms: 12118 Number of models: 1 Model: "" Number of chains: 11 Chain: "M" Number of atoms: 159 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 159 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Chain: "A" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 800 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 778 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 778 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2978 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2978 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3008 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3008 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Time building chain proxies: 6.87, per 1000 atoms: 0.57 Number of scatterers: 12118 At special positions: 0 Unit cell: (83.7876, 120.31, 129.978, 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 12 16.00 P 292 15.00 O 2845 8.00 N 2277 7.00 C 6692 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: 5.78 Conformation dependent library (CDL) restraints added in 1.1 seconds 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1458 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 10 sheets defined 72.0% alpha, 2.8% beta 144 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 5.07 Creating SS restraints... Processing helix chain 'M' and resid 665 through 680 removed outlier: 3.794A pdb=" N ASP M 670 " --> pdb=" O ASP M 666 " (cutoff:3.500A) removed outlier: 3.671A pdb=" N THR M 671 " --> pdb=" O LYS M 667 " (cutoff:3.500A) removed outlier: 3.882A pdb=" N ARG M 676 " --> pdb=" O ARG M 672 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.585A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 25 through 29 removed outlier: 3.544A pdb=" N ILE B 29 " --> pdb=" O ILE B 26 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.503A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.655A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.555A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.640A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.561A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.514A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.878A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.603A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 72 removed outlier: 4.443A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.552A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 removed outlier: 3.841A pdb=" N ALA H 121 " --> pdb=" O LYS H 117 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.880A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.307A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.972A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.119A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 410 hydrogen bonds defined for protein. 1215 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 4.32 Time building geometry restraints manager: 6.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2035 1.33 - 1.45: 4332 1.45 - 1.56: 5953 1.56 - 1.68: 582 1.68 - 1.80: 22 Bond restraints: 12924 Sorted by residual: bond pdb=" C1' DG I 3 " pdb=" N9 DG I 3 " ideal model delta sigma weight residual 1.460 1.383 0.077 2.00e-02 2.50e+03 1.48e+01 bond pdb=" C1' DA I 147 " pdb=" N9 DA I 147 " ideal model delta sigma weight residual 1.460 1.393 0.067 2.00e-02 2.50e+03 1.12e+01 bond pdb=" C1' DA J 3 " pdb=" N9 DA J 3 " ideal model delta sigma weight residual 1.460 1.400 0.060 2.00e-02 2.50e+03 9.15e+00 bond pdb=" C ILE G 79 " pdb=" N PRO G 80 " ideal model delta sigma weight residual 1.335 1.365 -0.030 1.28e-02 6.10e+03 5.64e+00 bond pdb=" C ILE C 79 " pdb=" N PRO C 80 " ideal model delta sigma weight residual 1.333 1.366 -0.033 1.44e-02 4.82e+03 5.18e+00 ... (remaining 12919 not shown) Histogram of bond angle deviations from ideal: 98.15 - 105.18: 1289 105.18 - 112.22: 7171 112.22 - 119.25: 3665 119.25 - 126.29: 5698 126.29 - 133.32: 892 Bond angle restraints: 18715 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 113.10 108.20 4.90 9.70e-01 1.06e+00 2.55e+01 angle pdb=" N ARG M 676 " pdb=" CA ARG M 676 " pdb=" C ARG M 676 " ideal model delta sigma weight residual 111.36 107.26 4.10 1.09e+00 8.42e-01 1.42e+01 angle pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sigma weight residual 120.20 125.64 -5.44 1.50e+00 4.44e-01 1.32e+01 angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.09 123.87 -3.78 1.25e+00 6.40e-01 9.16e+00 angle pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sigma weight residual 120.20 124.65 -4.45 1.50e+00 4.44e-01 8.80e+00 ... (remaining 18710 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 29.95: 5135 29.95 - 59.89: 1573 59.89 - 89.84: 49 89.84 - 119.78: 0 119.78 - 149.73: 3 Dihedral angle restraints: 6760 sinusoidal: 4502 harmonic: 2258 Sorted by residual: dihedral pdb=" C4' DG J 94 " pdb=" C3' DG J 94 " pdb=" O3' DG J 94 " pdb=" P DG J 95 " ideal model delta sinusoidal sigma weight residual 220.00 70.27 149.73 1 3.50e+01 8.16e-04 1.46e+01 dihedral pdb=" C4' DC J 126 " pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " pdb=" P DC J 127 " ideal model delta sinusoidal sigma weight residual 220.00 79.88 140.12 1 3.50e+01 8.16e-04 1.39e+01 dihedral pdb=" C4' DT J 15 " pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " pdb=" P DC J 16 " ideal model delta sinusoidal sigma weight residual -140.00 -18.31 -121.69 1 3.50e+01 8.16e-04 1.20e+01 ... (remaining 6757 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1496 0.042 - 0.084: 516 0.084 - 0.126: 97 0.126 - 0.168: 27 0.168 - 0.209: 1 Chirality restraints: 2137 Sorted by residual: chirality pdb=" P DG J 95 " pdb=" OP1 DG J 95 " pdb=" OP2 DG J 95 " pdb=" O5' DG J 95 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.21 2.00e-01 2.50e+01 1.10e+00 chirality pdb=" C3' DC J 126 " pdb=" C4' DC J 126 " pdb=" O3' DC J 126 " pdb=" C2' DC J 126 " both_signs ideal model delta sigma weight residual False -2.66 -2.50 -0.16 2.00e-01 2.50e+01 6.51e-01 chirality pdb=" CA VAL G 107 " pdb=" N VAL G 107 " pdb=" C VAL G 107 " pdb=" CB VAL G 107 " both_signs ideal model delta sigma weight residual False 2.44 2.60 -0.16 2.00e-01 2.50e+01 6.39e-01 ... (remaining 2134 not shown) Planarity restraints: 1362 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ILE G 79 " -0.039 5.00e-02 4.00e+02 6.00e-02 5.77e+00 pdb=" N PRO G 80 " 0.104 5.00e-02 4.00e+02 pdb=" CA PRO G 80 " -0.031 5.00e-02 4.00e+02 pdb=" CD PRO G 80 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C MET E 120 " -0.039 5.00e-02 4.00e+02 5.94e-02 5.64e+00 pdb=" N PRO E 121 " 0.103 5.00e-02 4.00e+02 pdb=" CA PRO E 121 " -0.030 5.00e-02 4.00e+02 pdb=" CD PRO E 121 " -0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ILE C 79 " 0.039 5.00e-02 4.00e+02 5.85e-02 5.48e+00 pdb=" N PRO C 80 " -0.101 5.00e-02 4.00e+02 pdb=" CA PRO C 80 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO C 80 " 0.032 5.00e-02 4.00e+02 ... (remaining 1359 not shown) Histogram of nonbonded interaction distances: 2.35 - 2.86: 3622 2.86 - 3.37: 9941 3.37 - 3.88: 24177 3.88 - 4.39: 27558 4.39 - 4.90: 38877 Nonbonded interactions: 104175 Sorted by model distance: nonbonded pdb=" O THR G 16 " pdb=" OG SER G 19 " model vdw 2.348 2.440 nonbonded pdb=" OE1 GLU A 73 " pdb=" ND2 ASN B 25 " model vdw 2.357 2.520 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.359 2.440 nonbonded pdb=" OH TYR G 39 " pdb=" OE1 GLU H 68 " model vdw 2.374 2.440 nonbonded pdb=" O LEU E 92 " pdb=" OG SER E 96 " model vdw 2.374 2.440 ... (remaining 104170 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 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and (resid 20 through 22 or (resid 23 and (name N or name CA or name \ C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 20 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.950 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 14.730 Check model and map are aligned: 0.000 Set scattering table: 0.000 Process input model: 39.010 Find NCS groups from input model: 0.520 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:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 60.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8478 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 : 0.007 0.077 12924 Z= 0.418 Angle : 0.733 8.319 18715 Z= 0.452 Chirality : 0.043 0.209 2137 Planarity : 0.006 0.060 1362 Dihedral : 27.636 149.731 5302 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 1.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.92 % Favored : 99.08 % 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: -1.78 (0.24), residues: 761 helix: -0.88 (0.17), residues: 551 sheet: None (None), residues: 0 loop : -1.60 (0.33), residues: 210 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 180 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 180 time to evaluate : 0.990 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 180 average time/residue: 0.3587 time to fit residues: 83.1130 Evaluate side-chains 154 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 154 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 85 optimal weight: 3.9990 chunk 76 optimal weight: 1.9990 chunk 42 optimal weight: 0.6980 chunk 26 optimal weight: 0.9980 chunk 51 optimal weight: 0.8980 chunk 40 optimal weight: 0.7980 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 0.4980 chunk 58 optimal weight: 0.7980 chunk 91 optimal weight: 1.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 39 HIS A 55 GLN A 68 GLN A 76 GLN ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN C 104 GLN D 79 HIS D 92 GLN E 68 GLN E 125 GLN F 93 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8458 moved from start: 0.1530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.033 12924 Z= 0.236 Angle : 0.545 5.795 18715 Z= 0.333 Chirality : 0.033 0.136 2137 Planarity : 0.004 0.048 1362 Dihedral : 31.158 149.382 3802 Min Nonbonded Distance : 2.240 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.79 % Favored : 99.21 % 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: 1.33 (0.28), residues: 761 helix: 1.61 (0.21), residues: 561 sheet: None (None), residues: 0 loop : -1.20 (0.35), residues: 200 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 165 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 164 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 164 average time/residue: 0.3106 time to fit residues: 67.6240 Evaluate side-chains 151 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 151 time to evaluate : 1.004 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 50 optimal weight: 0.9990 chunk 28 optimal weight: 0.0010 chunk 76 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 25 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 81 optimal weight: 1.9990 chunk 31 optimal weight: 0.9990 chunk 73 optimal weight: 5.9990 chunk 90 optimal weight: 2.9990 overall best weight: 1.1994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN B 75 HIS B 93 GLN C 38 ASN C 104 GLN F 93 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8483 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.033 12924 Z= 0.324 Angle : 0.565 7.254 18715 Z= 0.342 Chirality : 0.036 0.134 2137 Planarity : 0.004 0.039 1362 Dihedral : 31.370 148.886 3802 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 5.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.31 % Favored : 98.69 % 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: 2.29 (0.30), residues: 761 helix: 2.39 (0.22), residues: 562 sheet: None (None), residues: 0 loop : -1.13 (0.35), residues: 199 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.866 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.3111 time to fit residues: 61.7982 Evaluate side-chains 145 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 145 time to evaluate : 0.954 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0217 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 69 optimal weight: 1.9990 chunk 47 optimal weight: 1.9990 chunk 10 optimal weight: 0.0370 chunk 43 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 92 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 48 optimal weight: 0.8980 chunk 87 optimal weight: 7.9990 chunk 26 optimal weight: 0.7980 chunk 81 optimal weight: 1.9990 overall best weight: 0.9460 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 104 GLN D 81 ASN E 68 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.034 12924 Z= 0.268 Angle : 0.546 7.293 18715 Z= 0.331 Chirality : 0.034 0.127 2137 Planarity : 0.004 0.037 1362 Dihedral : 31.308 148.292 3802 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.18 % Favored : 98.82 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.74 (0.30), residues: 761 helix: 2.73 (0.22), residues: 562 sheet: None (None), residues: 0 loop : -1.02 (0.36), residues: 199 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 154 time to evaluate : 1.013 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 4 outliers final: 0 residues processed: 156 average time/residue: 0.3098 time to fit residues: 64.8717 Evaluate side-chains 149 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.888 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0476 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 55 optimal weight: 1.9990 chunk 1 optimal weight: 0.7980 chunk 72 optimal weight: 1.9990 chunk 40 optimal weight: 0.5980 chunk 83 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 49 optimal weight: 1.9990 chunk 87 optimal weight: 7.9990 chunk 24 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 68 GLN F 93 GLN G 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 12924 Z= 0.235 Angle : 0.536 6.995 18715 Z= 0.326 Chirality : 0.033 0.126 2137 Planarity : 0.004 0.036 1362 Dihedral : 31.292 147.870 3802 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 5.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 2.87 (0.30), residues: 761 helix: 2.81 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -0.96 (0.37), residues: 196 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 150 time to evaluate : 1.021 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 150 average time/residue: 0.3132 time to fit residues: 63.7184 Evaluate side-chains 149 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.938 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1432 time to fit residues: 1.3108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 87 optimal weight: 7.9990 chunk 19 optimal weight: 0.0970 chunk 57 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 81 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 32 optimal weight: 0.9990 chunk 51 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.035 12924 Z= 0.203 Angle : 0.528 6.915 18715 Z= 0.322 Chirality : 0.033 0.129 2137 Planarity : 0.004 0.041 1362 Dihedral : 31.223 147.600 3802 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 5.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.45 % Favored : 98.55 % 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: 3.06 (0.30), residues: 761 helix: 2.96 (0.22), residues: 563 sheet: None (None), residues: 0 loop : -0.91 (0.37), residues: 198 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 156 average time/residue: 0.2995 time to fit residues: 62.8210 Evaluate side-chains 152 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.007 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1120 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 11 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 82 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 chunk 60 optimal weight: 0.6980 chunk 59 optimal weight: 0.7980 chunk 44 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 58 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN G 73 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8452 moved from start: 0.2189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.039 12924 Z= 0.239 Angle : 0.535 7.191 18715 Z= 0.324 Chirality : 0.033 0.123 2137 Planarity : 0.004 0.036 1362 Dihedral : 31.234 147.057 3802 Min Nonbonded Distance : 2.164 Molprobity Statistics. All-atom Clashscore : 5.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 3.07 (0.30), residues: 761 helix: 2.94 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -0.82 (0.38), residues: 196 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 152 average time/residue: 0.3166 time to fit residues: 64.2143 Evaluate side-chains 149 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1282 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 29 optimal weight: 1.9990 chunk 19 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 61 optimal weight: 0.9980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 9 optimal weight: 0.0980 chunk 76 optimal weight: 2.9990 chunk 88 optimal weight: 5.9990 chunk 93 optimal weight: 1.9990 chunk 85 optimal weight: 3.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN E 68 GLN F 75 HIS G 73 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8448 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12924 Z= 0.230 Angle : 0.534 6.964 18715 Z= 0.325 Chirality : 0.033 0.124 2137 Planarity : 0.004 0.036 1362 Dihedral : 31.183 146.886 3802 Min Nonbonded Distance : 2.175 Molprobity Statistics. All-atom Clashscore : 5.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % Rotamer Outliers : 0.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.17 (0.30), residues: 761 helix: 3.00 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -0.79 (0.38), residues: 196 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 151 time to evaluate : 0.886 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 153 average time/residue: 0.3184 time to fit residues: 65.3527 Evaluate side-chains 149 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1450 time to fit residues: 1.4564 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 90 optimal weight: 2.9990 chunk 93 optimal weight: 1.9990 chunk 54 optimal weight: 0.9990 chunk 39 optimal weight: 0.4980 chunk 71 optimal weight: 0.4980 chunk 27 optimal weight: 0.8980 chunk 81 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 59 optimal weight: 0.9980 chunk 95 optimal weight: 1.9990 chunk 58 optimal weight: 0.6980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN F 93 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8445 moved from start: 0.2423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12924 Z= 0.227 Angle : 0.535 6.583 18715 Z= 0.325 Chirality : 0.033 0.125 2137 Planarity : 0.004 0.035 1362 Dihedral : 31.132 146.554 3802 Min Nonbonded Distance : 2.178 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 3.20 (0.30), residues: 761 helix: 3.02 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -0.73 (0.38), residues: 196 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 153 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 153 time to evaluate : 1.027 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 153 average time/residue: 0.3013 time to fit residues: 62.1362 Evaluate side-chains 148 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.939 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1409 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 45 optimal weight: 0.1980 chunk 66 optimal weight: 0.9990 chunk 100 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 8 optimal weight: 0.0370 chunk 61 optimal weight: 0.6980 chunk 49 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 85 optimal weight: 4.9990 chunk 24 optimal weight: 0.7980 overall best weight: 0.5458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN ** G 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 64 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8420 moved from start: 0.2617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12924 Z= 0.199 Angle : 0.531 7.063 18715 Z= 0.322 Chirality : 0.032 0.126 2137 Planarity : 0.004 0.036 1362 Dihedral : 30.963 146.254 3802 Min Nonbonded Distance : 2.193 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.58 % Favored : 98.42 % 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: 3.27 (0.30), residues: 761 helix: 3.05 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -0.62 (0.39), residues: 196 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1522 Ramachandran restraints generated. 761 Oldfield, 0 Emsley, 761 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 160 time to evaluate : 1.030 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.2981 time to fit residues: 64.3572 Evaluate side-chains 152 residues out of total 651 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 152 time to evaluate : 0.949 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.1019 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 101 random chunks: chunk 73 optimal weight: 5.9990 chunk 11 optimal weight: 0.9990 chunk 22 optimal weight: 1.9990 chunk 80 optimal weight: 1.9990 chunk 33 optimal weight: 0.0370 chunk 82 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 14 optimal weight: 0.5980 chunk 70 optimal weight: 1.9990 chunk 4 optimal weight: 0.7980 chunk 57 optimal weight: 0.5980 overall best weight: 0.6058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 76 GLN C 104 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3501 r_free = 0.3501 target = 0.084583 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2912 r_free = 0.2912 target = 0.057177 restraints weight = 33592.916| |-----------------------------------------------------------------------------| r_work (start): 0.2871 rms_B_bonded: 2.18 r_work: 0.2686 rms_B_bonded: 4.09 restraints_weight: 0.5000 r_work (final): 0.2686 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8745 moved from start: 0.2685 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.034 12924 Z= 0.208 Angle : 0.535 7.697 18715 Z= 0.324 Chirality : 0.032 0.125 2137 Planarity : 0.004 0.037 1362 Dihedral : 31.004 145.783 3802 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.71 % Favored : 98.29 % 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: 3.31 (0.30), residues: 761 helix: 3.07 (0.22), residues: 565 sheet: None (None), residues: 0 loop : -0.62 (0.39), residues: 196 =============================================================================== Job complete usr+sys time: 2332.70 seconds wall clock time: 42 minutes 48.02 seconds (2568.02 seconds total)