Starting phenix.real_space_refine on Sun Apr 5 22:09:33 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9zen_74113/04_2026/9zen_74113.cif Found real_map, /net/cci-nas-00/data/ceres_data/9zen_74113/04_2026/9zen_74113.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.17 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9zen_74113/04_2026/9zen_74113.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9zen_74113/04_2026/9zen_74113.map" model { file = "/net/cci-nas-00/data/ceres_data/9zen_74113/04_2026/9zen_74113.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9zen_74113/04_2026/9zen_74113.cif" } resolution = 3.17 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 Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.018 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 288 5.49 5 S 22 5.16 5 C 7718 2.51 5 N 2567 2.21 5 O 3150 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 13745 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" 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: "C" Number of atoms: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "D" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "E" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} 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: 844 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 844 Classifications: {'peptide': 111} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 105} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 14 Unresolved non-hydrogen dihedrals: 10 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 724 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 724 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Chain: "K" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 119, 907 Classifications: {'peptide': 119} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 1, 'TRANS': 117} Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 11 Unresolved non-hydrogen chiralities: 3 Planarities with less than four sites: {'GLU:plan': 1, 'GLN:plan1': 1} Unresolved non-hydrogen planarities: 8 Time building chain proxies: 2.92, per 1000 atoms: 0.21 Number of scatterers: 13745 At special positions: 0 Unit cell: (141.616, 108.682, 116.367, 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 22 16.00 P 288 15.00 O 3150 8.00 N 2567 7.00 C 7718 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=2, symmetry=0 Simple disulfide: pdb=" SG CYS L 22 " - pdb=" SG CYS L 97 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 97 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 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: 0.99 Conformation dependent library (CDL) restraints added in 498.9 milliseconds 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1844 Finding SS restraints... Secondary structure from input PDB file: 34 helices and 12 sheets defined 54.5% alpha, 4.2% beta 139 base pairs and 256 stacking pairs defined. Time for finding SS restraints: 2.19 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.610A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.616A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.295A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 removed outlier: 4.153A pdb=" N VAL A 89 " --> pdb=" O GLN A 85 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N MET A 90 " --> pdb=" O SER A 86 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.584A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.626A 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: 4.155A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.820A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 22 removed outlier: 3.571A pdb=" N GLY C 22 " --> pdb=" O SER C 19 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.613A pdb=" N TYR C 50 " --> pdb=" O GLY C 46 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 89 removed outlier: 3.515A pdb=" N ASN C 89 " --> pdb=" O LEU C 85 " (cutoff:3.500A) Processing helix chain 'C' and resid 92 through 97 removed outlier: 3.806A pdb=" N LEU C 96 " --> pdb=" O GLU C 92 " (cutoff:3.500A) Processing helix chain 'D' and resid 38 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.796A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 125 Processing helix chain 'E' and resid 44 through 57 removed outlier: 3.532A pdb=" N LYS E 56 " --> pdb=" O ARG E 52 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.591A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 4.077A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 4.323A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) removed outlier: 3.714A pdb=" N LYS E 79 " --> pdb=" O ALA E 75 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 4.168A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) removed outlier: 3.868A pdb=" N MET E 90 " --> pdb=" O SER E 86 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.567A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.604A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 77 removed outlier: 4.231A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.836A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.811A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 22 removed outlier: 3.571A pdb=" N GLY G 22 " --> pdb=" O SER G 19 " (cutoff:3.500A) Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 removed outlier: 3.613A pdb=" N TYR G 50 " --> pdb=" O GLY G 46 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 89 removed outlier: 3.515A pdb=" N ASN G 89 " --> pdb=" O LEU G 85 " (cutoff:3.500A) Processing helix chain 'G' and resid 92 through 97 removed outlier: 3.807A pdb=" N LEU G 96 " --> pdb=" O GLU G 92 " (cutoff:3.500A) Processing helix chain 'H' and resid 38 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.796A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 125 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.670A 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 removed outlier: 3.516A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 removed outlier: 6.463A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA5, first strand: chain 'C' and resid 100 through 102 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.722A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 19 through 22 removed outlier: 4.233A pdb=" N LEU L 20 " --> pdb=" O LEU L 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU L 82 " --> pdb=" O LEU L 20 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 36 through 37 Processing sheet with id=AB2, first strand: chain 'K' and resid 19 through 22 removed outlier: 4.232A pdb=" N LEU K 20 " --> pdb=" O LEU K 82 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N LEU K 82 " --> pdb=" O LEU K 20 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 36 through 37 395 hydrogen bonds defined for protein. 1155 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 357 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 139 basepair parallelities 256 stacking parallelities Total time for adding SS restraints: 2.65 Time building geometry restraints manager: 1.41 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: 2889 1.33 - 1.45: 4614 1.45 - 1.58: 6467 1.58 - 1.70: 576 1.70 - 1.82: 36 Bond restraints: 14582 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.485 -0.063 3.00e-02 1.11e+03 4.38e+00 bond pdb=" C3' DG I -30 " pdb=" O3' DG I -30 " ideal model delta sigma weight residual 1.422 1.482 -0.060 3.00e-02 1.11e+03 3.97e+00 bond pdb=" C3' DC I 4 " pdb=" O3' DC I 4 " ideal model delta sigma weight residual 1.422 1.479 -0.057 3.00e-02 1.11e+03 3.65e+00 bond pdb=" C3' DC J -58 " pdb=" O3' DC J -58 " ideal model delta sigma weight residual 1.422 1.476 -0.054 3.00e-02 1.11e+03 3.22e+00 bond pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " ideal model delta sigma weight residual 1.422 1.475 -0.053 3.00e-02 1.11e+03 3.14e+00 ... (remaining 14577 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.98: 20249 1.98 - 3.97: 575 3.97 - 5.95: 76 5.95 - 7.94: 30 7.94 - 9.92: 11 Bond angle restraints: 20941 Sorted by residual: angle pdb=" N GLU E 94 " pdb=" CA GLU E 94 " pdb=" CB GLU E 94 " ideal model delta sigma weight residual 110.28 117.15 -6.87 1.55e+00 4.16e-01 1.97e+01 angle pdb=" N GLU A 94 " pdb=" CA GLU A 94 " pdb=" CB GLU A 94 " ideal model delta sigma weight residual 110.28 117.09 -6.81 1.55e+00 4.16e-01 1.93e+01 angle pdb=" N GLY K 57 " pdb=" CA GLY K 57 " pdb=" C GLY K 57 " ideal model delta sigma weight residual 113.18 122.71 -9.53 2.37e+00 1.78e-01 1.62e+01 angle pdb=" CB LYS D 116 " pdb=" CG LYS D 116 " pdb=" CD LYS D 116 " ideal model delta sigma weight residual 111.30 120.55 -9.25 2.30e+00 1.89e-01 1.62e+01 angle pdb=" CB LYS H 116 " pdb=" CG LYS H 116 " pdb=" CD LYS H 116 " ideal model delta sigma weight residual 111.30 120.54 -9.24 2.30e+00 1.89e-01 1.61e+01 ... (remaining 20936 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.44: 6537 35.44 - 70.88: 1433 70.88 - 106.33: 18 106.33 - 141.77: 4 141.77 - 177.21: 2 Dihedral angle restraints: 7994 sinusoidal: 5120 harmonic: 2874 Sorted by residual: dihedral pdb=" CB CYS L 22 " pdb=" SG CYS L 22 " pdb=" SG CYS L 97 " pdb=" CB CYS L 97 " ideal model delta sinusoidal sigma weight residual 93.00 145.84 -52.84 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 97 " pdb=" CB CYS K 97 " ideal model delta sinusoidal sigma weight residual 93.00 145.84 -52.84 1 1.00e+01 1.00e-02 3.80e+01 dihedral pdb=" CA VAL L 94 " pdb=" C VAL L 94 " pdb=" N TYR L 95 " pdb=" CA TYR L 95 " ideal model delta harmonic sigma weight residual 180.00 151.70 28.30 0 5.00e+00 4.00e-02 3.20e+01 ... (remaining 7991 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.047: 1794 0.047 - 0.093: 451 0.093 - 0.140: 110 0.140 - 0.186: 6 0.186 - 0.233: 5 Chirality restraints: 2366 Sorted by residual: chirality pdb=" CB ILE K 71 " pdb=" CA ILE K 71 " pdb=" CG1 ILE K 71 " pdb=" CG2 ILE K 71 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.35e+00 chirality pdb=" CB ILE L 71 " pdb=" CA ILE L 71 " pdb=" CG1 ILE L 71 " pdb=" CG2 ILE L 71 " both_signs ideal model delta sigma weight residual False 2.64 2.41 0.23 2.00e-01 2.50e+01 1.34e+00 chirality pdb=" CA TYR L 95 " pdb=" N TYR L 95 " pdb=" C TYR L 95 " pdb=" CB TYR L 95 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.10e+00 ... (remaining 2363 not shown) Planarity restraints: 1656 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASP K 108 " 0.015 2.00e-02 2.50e+03 3.08e-02 9.51e+00 pdb=" CG ASP K 108 " -0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP K 108 " 0.020 2.00e-02 2.50e+03 pdb=" OD2 ASP K 108 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP L 108 " -0.015 2.00e-02 2.50e+03 3.06e-02 9.36e+00 pdb=" CG ASP L 108 " 0.053 2.00e-02 2.50e+03 pdb=" OD1 ASP L 108 " -0.019 2.00e-02 2.50e+03 pdb=" OD2 ASP L 108 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP G 72 " 0.013 2.00e-02 2.50e+03 2.62e-02 6.87e+00 pdb=" CG ASP G 72 " -0.045 2.00e-02 2.50e+03 pdb=" OD1 ASP G 72 " 0.017 2.00e-02 2.50e+03 pdb=" OD2 ASP G 72 " 0.016 2.00e-02 2.50e+03 ... (remaining 1653 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 3558 2.83 - 3.35: 11177 3.35 - 3.87: 25240 3.87 - 4.38: 29264 4.38 - 4.90: 42885 Nonbonded interactions: 112124 Sorted by model distance: nonbonded pdb=" OG SER L 17 " pdb=" O MET L 84 " model vdw 2.317 3.040 nonbonded pdb=" OG SER K 17 " pdb=" O MET K 84 " model vdw 2.317 3.040 nonbonded pdb=" NH1 ARG G 32 " pdb=" OP1 DG J -44 " model vdw 2.366 3.120 nonbonded pdb=" O VAL H 48 " pdb=" NH2 ARG K 26 " model vdw 2.399 3.120 nonbonded pdb=" O VAL D 48 " pdb=" NH2 ARG L 26 " model vdw 2.399 3.120 ... (remaining 112119 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = chain 'B' selection = chain 'F' } ncs_group { reference = chain 'C' selection = chain 'G' } ncs_group { reference = chain 'D' selection = chain 'H' } ncs_group { reference = chain 'K' selection = chain 'L' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 2.880 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.060 Process input model: 15.240 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.040 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:1.460 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.090 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8015 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 : 0.005 0.063 14584 Z= 0.215 Angle : 0.824 9.920 20945 Z= 0.464 Chirality : 0.044 0.233 2366 Planarity : 0.007 0.069 1656 Dihedral : 26.981 177.211 6144 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.10 (0.23), residues: 978 helix: -0.27 (0.20), residues: 516 sheet: -3.85 (0.45), residues: 66 loop : -2.43 (0.26), residues: 396 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.018 0.001 ARG H 99 TYR 0.016 0.002 TYR H 121 PHE 0.024 0.002 PHE C 25 TRP 0.007 0.002 TRP K 106 HIS 0.002 0.001 HIS E 113 Details of bonding type rmsd covalent geometry : bond 0.00459 (14582) covalent geometry : angle 0.82418 (20941) SS BOND : bond 0.00098 ( 2) SS BOND : angle 1.69275 ( 4) hydrogen bonds : bond 0.12080 ( 752) hydrogen bonds : angle 4.02542 ( 1869) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 243 time to evaluate : 0.364 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8556 (pp20) cc_final: 0.8340 (pp20) REVERT: C 36 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8709 (mmtt) REVERT: D 115 THR cc_start: 0.8707 (m) cc_final: 0.8499 (m) REVERT: G 36 LYS cc_start: 0.8982 (mmtm) cc_final: 0.8701 (mmtt) REVERT: H 115 THR cc_start: 0.8729 (m) cc_final: 0.8520 (m) REVERT: L 60 ASN cc_start: 0.7889 (t0) cc_final: 0.7669 (t0) REVERT: K 60 ASN cc_start: 0.7878 (t0) cc_final: 0.7658 (t0) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1230 time to fit residues: 41.6371 Evaluate side-chains 207 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 207 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 108 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 1.9990 chunk 62 optimal weight: 0.0980 chunk 51 optimal weight: 2.9990 chunk 117 optimal weight: 0.4980 overall best weight: 0.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN B 25 ASN D 84 ASN F 64 ASN H 84 ASN L 115 GLN K 115 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.125236 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3889 r_free = 0.3889 target = 0.108548 restraints weight = 32557.394| |-----------------------------------------------------------------------------| r_work (start): 0.3832 rms_B_bonded: 1.71 r_work: 0.3759 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3645 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3645 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 14584 Z= 0.159 Angle : 0.567 6.465 20945 Z= 0.335 Chirality : 0.035 0.206 2366 Planarity : 0.004 0.044 1656 Dihedral : 29.907 179.845 4280 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 0.87 % Allowed : 11.91 % Favored : 87.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -0.42 (0.26), residues: 978 helix: 1.59 (0.22), residues: 520 sheet: -3.99 (0.44), residues: 78 loop : -2.19 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 99 TYR 0.007 0.001 TYR G 50 PHE 0.011 0.001 PHE C 25 TRP 0.005 0.001 TRP K 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00340 (14582) covalent geometry : angle 0.56675 (20941) SS BOND : bond 0.00210 ( 2) SS BOND : angle 1.03945 ( 4) hydrogen bonds : bond 0.04297 ( 752) hydrogen bonds : angle 2.65075 ( 1869) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 220 time to evaluate : 0.355 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.8494 (pp20) cc_final: 0.8263 (pp20) REVERT: L 68 ARG cc_start: 0.6005 (ptt-90) cc_final: 0.5429 (ptp90) REVERT: K 60 ASN cc_start: 0.7979 (t0) cc_final: 0.7759 (t0) REVERT: K 68 ARG cc_start: 0.6159 (ptt-90) cc_final: 0.5574 (ptp90) outliers start: 7 outliers final: 7 residues processed: 220 average time/residue: 0.1344 time to fit residues: 40.7821 Evaluate side-chains 219 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 212 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 35 optimal weight: 2.9990 chunk 45 optimal weight: 0.8980 chunk 55 optimal weight: 0.6980 chunk 29 optimal weight: 0.9980 chunk 36 optimal weight: 4.9990 chunk 22 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 116 optimal weight: 0.0270 chunk 67 optimal weight: 0.7980 chunk 105 optimal weight: 6.9990 chunk 72 optimal weight: 6.9990 overall best weight: 0.6838 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4090 r_free = 0.4090 target = 0.125088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3888 r_free = 0.3888 target = 0.108173 restraints weight = 33068.346| |-----------------------------------------------------------------------------| r_work (start): 0.3841 rms_B_bonded: 1.72 r_work: 0.3767 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3652 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8185 moved from start: 0.1277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14584 Z= 0.145 Angle : 0.553 6.168 20945 Z= 0.328 Chirality : 0.034 0.157 2366 Planarity : 0.004 0.043 1656 Dihedral : 29.862 179.249 4280 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.93 % Favored : 94.07 % Rotamer: Outliers : 1.99 % Allowed : 13.40 % Favored : 84.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.22 (0.27), residues: 978 helix: 2.31 (0.22), residues: 520 sheet: -3.91 (0.46), residues: 78 loop : -2.16 (0.28), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.007 0.001 TYR K 96 PHE 0.008 0.001 PHE C 25 TRP 0.008 0.001 TRP L 106 HIS 0.001 0.000 HIS D 49 Details of bonding type rmsd covalent geometry : bond 0.00312 (14582) covalent geometry : angle 0.55260 (20941) SS BOND : bond 0.00254 ( 2) SS BOND : angle 0.43387 ( 4) hydrogen bonds : bond 0.04002 ( 752) hydrogen bonds : angle 2.43575 ( 1869) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 228 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 212 time to evaluate : 0.342 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: F 91 LYS cc_start: 0.9185 (ttpp) cc_final: 0.8978 (ttpp) REVERT: L 68 ARG cc_start: 0.6234 (ptt-90) cc_final: 0.5505 (ptp90) REVERT: K 60 ASN cc_start: 0.7934 (t0) cc_final: 0.7668 (t0) REVERT: K 68 ARG cc_start: 0.6219 (ptt-90) cc_final: 0.5530 (ptp90) outliers start: 16 outliers final: 13 residues processed: 220 average time/residue: 0.1263 time to fit residues: 38.8757 Evaluate side-chains 220 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 207 time to evaluate : 0.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 85 optimal weight: 6.9990 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.0020 chunk 0 optimal weight: 4.9990 chunk 84 optimal weight: 4.9990 chunk 66 optimal weight: 0.7980 chunk 115 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 102 optimal weight: 1.9990 overall best weight: 0.9192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 93 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4075 r_free = 0.4075 target = 0.124376 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3871 r_free = 0.3871 target = 0.107401 restraints weight = 32873.072| |-----------------------------------------------------------------------------| r_work (start): 0.3819 rms_B_bonded: 1.72 r_work: 0.3745 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3631 rms_B_bonded: 4.92 restraints_weight: 0.2500 r_work (final): 0.3631 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8213 moved from start: 0.1617 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 14584 Z= 0.158 Angle : 0.554 6.141 20945 Z= 0.329 Chirality : 0.034 0.157 2366 Planarity : 0.004 0.042 1656 Dihedral : 30.037 178.718 4280 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 4.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.95 % Favored : 93.05 % Rotamer: Outliers : 2.48 % Allowed : 15.14 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.51 (0.28), residues: 978 helix: 2.66 (0.22), residues: 522 sheet: -4.05 (0.45), residues: 78 loop : -2.19 (0.29), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.009 0.001 TYR K 96 PHE 0.013 0.001 PHE C 25 TRP 0.007 0.001 TRP L 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00343 (14582) covalent geometry : angle 0.55412 (20941) SS BOND : bond 0.00100 ( 2) SS BOND : angle 0.73268 ( 4) hydrogen bonds : bond 0.04235 ( 752) hydrogen bonds : angle 2.37199 ( 1869) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 231 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 211 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8317 (t70) cc_final: 0.8113 (t70) REVERT: D 90 THR cc_start: 0.8889 (p) cc_final: 0.8585 (t) REVERT: H 51 ASP cc_start: 0.8369 (t70) cc_final: 0.8164 (t70) REVERT: H 90 THR cc_start: 0.8906 (p) cc_final: 0.8578 (t) REVERT: L 68 ARG cc_start: 0.6246 (ptt-90) cc_final: 0.5559 (ptp90) REVERT: K 60 ASN cc_start: 0.7935 (t0) cc_final: 0.7688 (t0) REVERT: K 68 ARG cc_start: 0.6226 (ptt-90) cc_final: 0.5561 (ptp90) outliers start: 20 outliers final: 14 residues processed: 224 average time/residue: 0.1225 time to fit residues: 38.3808 Evaluate side-chains 222 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 208 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 27 optimal weight: 3.9990 chunk 102 optimal weight: 0.9990 chunk 78 optimal weight: 3.9990 chunk 119 optimal weight: 1.9990 chunk 103 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 110 optimal weight: 1.9990 chunk 5 optimal weight: 0.6980 chunk 89 optimal weight: 2.9990 chunk 88 optimal weight: 4.9990 overall best weight: 1.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN E 93 GLN F 25 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4040 r_free = 0.4040 target = 0.121935 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3830 r_free = 0.3830 target = 0.104869 restraints weight = 33030.411| |-----------------------------------------------------------------------------| r_work (start): 0.3783 rms_B_bonded: 1.70 r_work: 0.3706 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3591 rms_B_bonded: 4.90 restraints_weight: 0.2500 r_work (final): 0.3591 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.1823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14584 Z= 0.190 Angle : 0.589 6.567 20945 Z= 0.346 Chirality : 0.036 0.168 2366 Planarity : 0.004 0.043 1656 Dihedral : 30.268 178.518 4280 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.61 % Allowed : 15.01 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.44 (0.28), residues: 978 helix: 2.66 (0.22), residues: 522 sheet: -4.26 (0.42), residues: 70 loop : -2.33 (0.28), residues: 386 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG H 99 TYR 0.011 0.001 TYR L 96 PHE 0.016 0.001 PHE C 25 TRP 0.006 0.001 TRP K 110 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00420 (14582) covalent geometry : angle 0.58897 (20941) SS BOND : bond 0.00163 ( 2) SS BOND : angle 0.86216 ( 4) hydrogen bonds : bond 0.04793 ( 752) hydrogen bonds : angle 2.47779 ( 1869) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 203 time to evaluate : 0.349 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.8621 (mptt) cc_final: 0.8354 (mptt) REVERT: D 51 ASP cc_start: 0.8457 (t70) cc_final: 0.8257 (t70) REVERT: D 90 THR cc_start: 0.8898 (p) cc_final: 0.8642 (t) REVERT: E 73 GLU cc_start: 0.8540 (pp20) cc_final: 0.8240 (pp20) REVERT: H 90 THR cc_start: 0.8869 (p) cc_final: 0.8596 (t) REVERT: L 68 ARG cc_start: 0.6494 (ptt-90) cc_final: 0.5804 (ptp90) REVERT: K 60 ASN cc_start: 0.7933 (t0) cc_final: 0.7687 (t0) REVERT: K 68 ARG cc_start: 0.6547 (ptt-90) cc_final: 0.5860 (ptp90) outliers start: 21 outliers final: 19 residues processed: 218 average time/residue: 0.1214 time to fit residues: 37.1430 Evaluate side-chains 220 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 201 time to evaluate : 0.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 99 optimal weight: 6.9990 chunk 79 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 64 optimal weight: 0.9990 chunk 91 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 50 optimal weight: 2.9990 chunk 80 optimal weight: 2.9990 chunk 81 optimal weight: 3.9990 chunk 72 optimal weight: 6.9990 chunk 26 optimal weight: 0.6980 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3890 r_free = 0.3890 target = 0.109277 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.093106 restraints weight = 30631.051| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.58 r_work: 0.3497 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.3378 rms_B_bonded: 4.88 restraints_weight: 0.2500 r_work (final): 0.3378 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8305 moved from start: 0.2304 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 14584 Z= 0.281 Angle : 0.674 7.573 20945 Z= 0.391 Chirality : 0.040 0.190 2366 Planarity : 0.005 0.045 1656 Dihedral : 30.882 179.267 4280 Min Nonbonded Distance : 2.408 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.60 % Allowed : 15.88 % Favored : 80.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.02 (0.27), residues: 978 helix: 2.08 (0.22), residues: 542 sheet: -4.35 (0.41), residues: 70 loop : -2.39 (0.29), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG D 99 TYR 0.014 0.002 TYR K 96 PHE 0.021 0.002 PHE G 25 TRP 0.008 0.002 TRP L 110 HIS 0.003 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00633 (14582) covalent geometry : angle 0.67429 (20941) SS BOND : bond 0.00158 ( 2) SS BOND : angle 1.23327 ( 4) hydrogen bonds : bond 0.06174 ( 752) hydrogen bonds : angle 2.75829 ( 1869) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 238 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 209 time to evaluate : 0.343 Fit side-chains REVERT: D 51 ASP cc_start: 0.8459 (t70) cc_final: 0.8242 (t0) REVERT: D 90 THR cc_start: 0.8998 (p) cc_final: 0.8741 (t) REVERT: E 73 GLU cc_start: 0.8537 (pp20) cc_final: 0.8204 (pp20) REVERT: H 90 THR cc_start: 0.9010 (p) cc_final: 0.8737 (t) REVERT: L 3 GLN cc_start: 0.7800 (pm20) cc_final: 0.7562 (pp30) REVERT: L 83 GLN cc_start: 0.7872 (tp-100) cc_final: 0.7470 (tp-100) REVERT: K 3 GLN cc_start: 0.7728 (pm20) cc_final: 0.7528 (pp30) REVERT: K 60 ASN cc_start: 0.8042 (t0) cc_final: 0.7798 (t0) REVERT: K 83 GLN cc_start: 0.7876 (tp-100) cc_final: 0.7483 (tp-100) REVERT: K 94 VAL cc_start: 0.6649 (t) cc_final: 0.6442 (t) outliers start: 29 outliers final: 27 residues processed: 225 average time/residue: 0.1221 time to fit residues: 38.6698 Evaluate side-chains 233 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 206 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 56 LYS Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 23 LEU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 43 VAL Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 5 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 43 VAL Chi-restraints excluded: chain K residue 54 MET Chi-restraints excluded: chain K residue 68 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 115 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 chunk 111 optimal weight: 0.0980 chunk 94 optimal weight: 2.9990 chunk 9 optimal weight: 0.0170 chunk 119 optimal weight: 7.9990 chunk 49 optimal weight: 0.5980 chunk 95 optimal weight: 3.9990 chunk 45 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 87 optimal weight: 4.9990 overall best weight: 0.7020 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS E 93 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3976 r_free = 0.3976 target = 0.114552 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3727 r_free = 0.3727 target = 0.098440 restraints weight = 30409.052| |-----------------------------------------------------------------------------| r_work (start): 0.3684 rms_B_bonded: 1.54 r_work: 0.3582 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.3466 rms_B_bonded: 4.86 restraints_weight: 0.2500 r_work (final): 0.3466 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8198 moved from start: 0.2106 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 14584 Z= 0.151 Angle : 0.575 6.151 20945 Z= 0.337 Chirality : 0.035 0.166 2366 Planarity : 0.004 0.047 1656 Dihedral : 30.151 179.927 4280 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 6.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.44 % Favored : 93.56 % Rotamer: Outliers : 2.61 % Allowed : 18.49 % Favored : 78.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.41 (0.28), residues: 978 helix: 2.58 (0.22), residues: 534 sheet: -4.26 (0.39), residues: 70 loop : -2.41 (0.29), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.007 0.001 TYR L 96 PHE 0.008 0.001 PHE C 25 TRP 0.007 0.001 TRP L 106 HIS 0.002 0.001 HIS H 109 Details of bonding type rmsd covalent geometry : bond 0.00322 (14582) covalent geometry : angle 0.57499 (20941) SS BOND : bond 0.00116 ( 2) SS BOND : angle 0.57670 ( 4) hydrogen bonds : bond 0.04074 ( 752) hydrogen bonds : angle 2.34364 ( 1869) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 201 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 51 ASP cc_start: 0.8370 (t70) cc_final: 0.8155 (t70) REVERT: E 73 GLU cc_start: 0.8473 (pp20) cc_final: 0.8094 (pp20) REVERT: L 68 ARG cc_start: 0.6645 (ptt-90) cc_final: 0.5739 (ptp90) REVERT: K 60 ASN cc_start: 0.7867 (t0) cc_final: 0.7613 (t0) REVERT: K 68 ARG cc_start: 0.6741 (ptt-90) cc_final: 0.5923 (ptp90) outliers start: 21 outliers final: 16 residues processed: 217 average time/residue: 0.1125 time to fit residues: 35.0251 Evaluate side-chains 216 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 200 time to evaluate : 0.326 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 111 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 43 optimal weight: 3.9990 chunk 103 optimal weight: 5.9990 chunk 62 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS E 93 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4049 r_free = 0.4049 target = 0.122535 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3841 r_free = 0.3841 target = 0.105691 restraints weight = 32581.862| |-----------------------------------------------------------------------------| r_work (start): 0.3789 rms_B_bonded: 1.68 r_work: 0.3714 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.3598 rms_B_bonded: 4.87 restraints_weight: 0.2500 r_work (final): 0.3598 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8246 moved from start: 0.2164 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 14584 Z= 0.171 Angle : 0.597 6.924 20945 Z= 0.348 Chirality : 0.035 0.164 2366 Planarity : 0.004 0.045 1656 Dihedral : 30.230 179.338 4280 Min Nonbonded Distance : 2.369 Molprobity Statistics. All-atom Clashscore : 5.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.16 % Favored : 92.84 % Rotamer: Outliers : 2.98 % Allowed : 19.11 % Favored : 77.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.50 (0.28), residues: 978 helix: 2.59 (0.22), residues: 536 sheet: -4.17 (0.40), residues: 70 loop : -2.32 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.008 0.001 TYR L 96 PHE 0.011 0.001 PHE G 25 TRP 0.005 0.001 TRP L 106 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00378 (14582) covalent geometry : angle 0.59693 (20941) SS BOND : bond 0.00166 ( 2) SS BOND : angle 0.54665 ( 4) hydrogen bonds : bond 0.04373 ( 752) hydrogen bonds : angle 2.38171 ( 1869) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 203 time to evaluate : 0.354 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8441 (pp20) cc_final: 0.8078 (pp20) REVERT: L 1 GLU cc_start: 0.6824 (pt0) cc_final: 0.6407 (pt0) REVERT: L 68 ARG cc_start: 0.6635 (ptt-90) cc_final: 0.5746 (ptp90) REVERT: L 84 MET cc_start: 0.7082 (mtp) cc_final: 0.6721 (ttm) REVERT: K 60 ASN cc_start: 0.7934 (t0) cc_final: 0.7703 (t0) REVERT: K 68 ARG cc_start: 0.6639 (ptt-90) cc_final: 0.5816 (ptp90) outliers start: 24 outliers final: 21 residues processed: 219 average time/residue: 0.1170 time to fit residues: 36.4249 Evaluate side-chains 223 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 202 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 5 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 110 optimal weight: 0.9990 chunk 32 optimal weight: 5.9990 chunk 3 optimal weight: 0.7980 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 4.9990 chunk 56 optimal weight: 0.7980 chunk 39 optimal weight: 3.9990 chunk 31 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 overall best weight: 0.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 49 HIS E 93 GLN H 49 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4053 r_free = 0.4053 target = 0.122657 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3844 r_free = 0.3844 target = 0.105139 restraints weight = 33340.380| |-----------------------------------------------------------------------------| r_work (start): 0.3797 rms_B_bonded: 1.72 r_work: 0.3723 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3606 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3606 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8238 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14584 Z= 0.161 Angle : 0.592 6.614 20945 Z= 0.344 Chirality : 0.035 0.165 2366 Planarity : 0.004 0.045 1656 Dihedral : 30.192 179.890 4280 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 2.48 % Allowed : 20.72 % Favored : 76.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.58 (0.28), residues: 978 helix: 2.66 (0.22), residues: 536 sheet: -4.09 (0.40), residues: 70 loop : -2.28 (0.30), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG H 99 TYR 0.007 0.001 TYR G 50 PHE 0.009 0.001 PHE G 25 TRP 0.005 0.001 TRP K 106 HIS 0.002 0.001 HIS C 31 Details of bonding type rmsd covalent geometry : bond 0.00354 (14582) covalent geometry : angle 0.59155 (20941) SS BOND : bond 0.00157 ( 2) SS BOND : angle 0.55394 ( 4) hydrogen bonds : bond 0.04230 ( 752) hydrogen bonds : angle 2.36194 ( 1869) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 202 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8439 (pp20) cc_final: 0.8070 (pp20) REVERT: E 119 ILE cc_start: 0.8316 (mm) cc_final: 0.8007 (mm) REVERT: L 68 ARG cc_start: 0.6600 (OUTLIER) cc_final: 0.5746 (ptp90) REVERT: L 84 MET cc_start: 0.7099 (mtp) cc_final: 0.6705 (ttm) REVERT: K 3 GLN cc_start: 0.7801 (pm20) cc_final: 0.7561 (pp30) REVERT: K 60 ASN cc_start: 0.7923 (t0) cc_final: 0.7710 (t0) REVERT: K 68 ARG cc_start: 0.6720 (ptt-90) cc_final: 0.5914 (ptp90) outliers start: 20 outliers final: 18 residues processed: 215 average time/residue: 0.1195 time to fit residues: 36.4989 Evaluate side-chains 219 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 200 time to evaluate : 0.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 2 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 84 optimal weight: 4.9990 chunk 51 optimal weight: 0.9990 chunk 97 optimal weight: 3.9990 chunk 91 optimal weight: 3.9990 chunk 35 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 0 optimal weight: 4.9990 chunk 86 optimal weight: 5.9990 chunk 66 optimal weight: 0.8980 chunk 26 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN D 49 HIS E 93 GLN H 49 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4057 r_free = 0.4057 target = 0.122866 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3848 r_free = 0.3848 target = 0.105383 restraints weight = 33079.803| |-----------------------------------------------------------------------------| r_work (start): 0.3801 rms_B_bonded: 1.71 r_work: 0.3728 rms_B_bonded: 2.88 restraints_weight: 0.5000 r_work: 0.3612 rms_B_bonded: 4.93 restraints_weight: 0.2500 r_work (final): 0.3612 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8231 moved from start: 0.2227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 14584 Z= 0.162 Angle : 0.602 9.040 20945 Z= 0.349 Chirality : 0.035 0.164 2366 Planarity : 0.004 0.045 1656 Dihedral : 30.161 179.578 4280 Min Nonbonded Distance : 2.332 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.85 % Favored : 93.15 % Rotamer: Outliers : 2.61 % Allowed : 20.10 % Favored : 77.30 % Cbeta Deviations : 0.11 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.63 (0.28), residues: 978 helix: 2.69 (0.22), residues: 536 sheet: -4.02 (0.40), residues: 70 loop : -2.27 (0.29), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 99 TYR 0.007 0.001 TYR C 50 PHE 0.009 0.001 PHE G 25 TRP 0.005 0.001 TRP L 106 HIS 0.002 0.001 HIS G 31 Details of bonding type rmsd covalent geometry : bond 0.00356 (14582) covalent geometry : angle 0.60191 (20941) SS BOND : bond 0.00186 ( 2) SS BOND : angle 0.48744 ( 4) hydrogen bonds : bond 0.04208 ( 752) hydrogen bonds : angle 2.37938 ( 1869) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1956 Ramachandran restraints generated. 978 Oldfield, 0 Emsley, 978 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 200 time to evaluate : 0.362 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: E 73 GLU cc_start: 0.8428 (pp20) cc_final: 0.8042 (pp20) REVERT: E 119 ILE cc_start: 0.8265 (mm) cc_final: 0.7968 (mm) REVERT: L 68 ARG cc_start: 0.6611 (OUTLIER) cc_final: 0.5652 (ptp90) REVERT: L 84 MET cc_start: 0.7061 (mtp) cc_final: 0.6595 (ttm) REVERT: L 101 GLU cc_start: 0.8224 (tt0) cc_final: 0.7996 (tt0) REVERT: K 3 GLN cc_start: 0.7813 (pm20) cc_final: 0.7567 (pp30) REVERT: K 60 ASN cc_start: 0.7942 (t0) cc_final: 0.7690 (t0) REVERT: K 68 ARG cc_start: 0.6763 (ptt-90) cc_final: 0.5780 (ptp90) REVERT: K 84 MET cc_start: 0.7060 (mtp) cc_final: 0.6641 (ttm) outliers start: 21 outliers final: 19 residues processed: 214 average time/residue: 0.1200 time to fit residues: 36.2851 Evaluate side-chains 218 residues out of total 826 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 198 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 19 SER Chi-restraints excluded: chain C residue 76 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 49 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 19 SER Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 114 VAL Chi-restraints excluded: chain L residue 20 LEU Chi-restraints excluded: chain L residue 49 LEU Chi-restraints excluded: chain L residue 54 MET Chi-restraints excluded: chain L residue 68 ARG Chi-restraints excluded: chain K residue 2 VAL Chi-restraints excluded: chain K residue 20 LEU Chi-restraints excluded: chain K residue 54 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 78 optimal weight: 3.9990 chunk 1 optimal weight: 1.9990 chunk 69 optimal weight: 0.6980 chunk 116 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 41 optimal weight: 4.9990 chunk 87 optimal weight: 5.9990 chunk 24 optimal weight: 2.9990 chunk 73 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.109412 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3635 r_free = 0.3635 target = 0.093258 restraints weight = 30696.985| |-----------------------------------------------------------------------------| r_work (start): 0.3589 rms_B_bonded: 1.58 r_work: 0.3480 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3360 rms_B_bonded: 4.91 restraints_weight: 0.2500 r_work (final): 0.3360 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8298 moved from start: 0.2434 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.040 14584 Z= 0.287 Angle : 0.690 7.402 20945 Z= 0.396 Chirality : 0.040 0.184 2366 Planarity : 0.005 0.044 1656 Dihedral : 30.757 179.633 4280 Min Nonbonded Distance : 2.367 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.49 % Favored : 91.51 % Rotamer: Outliers : 3.35 % Allowed : 19.60 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.21 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: 0.24 (0.28), residues: 978 helix: 2.26 (0.22), residues: 542 sheet: -4.23 (0.41), residues: 70 loop : -2.31 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 99 TYR 0.013 0.002 TYR L 39 PHE 0.020 0.002 PHE G 25 TRP 0.006 0.002 TRP K 110 HIS 0.004 0.001 HIS E 39 Details of bonding type rmsd covalent geometry : bond 0.00648 (14582) covalent geometry : angle 0.69026 (20941) SS BOND : bond 0.00260 ( 2) SS BOND : angle 1.10106 ( 4) hydrogen bonds : bond 0.06046 ( 752) hydrogen bonds : angle 2.72010 ( 1869) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3238.73 seconds wall clock time: 55 minutes 53.29 seconds (3353.29 seconds total)