Starting phenix.real_space_refine on Thu Aug 6 07:49:53 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, restraint, /net/cci-nas-00/data/ceres_data/8sn4_40612/08_2026/8sn4_40612.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn4_40612/08_2026/8sn4_40612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/8sn4_40612/08_2026/8sn4_40612.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn4_40612/08_2026/8sn4_40612.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8sn4_40612/08_2026/8sn4_40612.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn4_40612/08_2026/8sn4_40612.map" restraint_files = "/net/cci-nas-00/data/ceres_data/8sn4_40612/08_2026/8sn4_40612.cif" default_restraint = "/net/cci-nas-00/data/ceres_data/8sn4_40612/08_2026/8sn4_40612.cif" } resolution = 3.7 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= 0.000 sd= 0.004 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: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8269 2.51 5 N 2713 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.2rc3-6140/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 14600 Number of models: 1 Model: "" Number of chains: 14 Chain: "A" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "B" Number of atoms: 661 Number of conformers: 1 Conformer: "" Number of residues, atoms: 83, 661 Classifications: {'peptide': 83} Link IDs: {'PTRANS': 1, 'TRANS': 81} Chain: "C" Number of atoms: 827 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 827 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 740 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 740 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 99, 815 Classifications: {'peptide': 99} Link IDs: {'PTRANS': 4, 'TRANS': 94} Chain: "F" Number of atoms: 653 Number of conformers: 1 Conformer: "" Number of residues, atoms: 82, 653 Classifications: {'peptide': 82} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 80} Chain: "G" Number of atoms: 836 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 836 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 743 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Conformer: "B" Number of residues, atoms: 93, 731 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} bond proxies already assigned to first conformer: 728 Chain: "I" Number of atoms: 2996 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 2996 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "J" Number of atoms: 3031 Number of conformers: 1 Conformer: "" Number of residues, atoms: 147, 3031 Classifications: {'DNA': 147} Link IDs: {'rna3p': 146} Chain: "K" Number of atoms: 691 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} Conformer: "B" Number of residues, atoms: 85, 687 Classifications: {'peptide': 85} Link IDs: {'PTRANS': 6, 'TRANS': 78} bond proxies already assigned to first conformer: 698 Chain: "L" Number of atoms: 1188 Number of conformers: 1 Conformer: "" Number of residues, atoms: 148, 1188 Classifications: {'peptide': 148} Modifications used: {'COO': 1} Link IDs: {'PCIS': 1, 'PTRANS': 14, 'TRANS': 132} Chain: "M" Number of atoms: 602 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 602 Classifications: {'peptide': 76} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' ZN': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} List of CYS excluded from plausible disulfide bonds: (reason: may participate in coordination) ATOM 12296 SG CYS K 31 33.347 72.273 47.031 1.00 86.22 S ATOM 12446 SG CYS K 51 34.177 68.839 45.573 1.00 81.44 S ATOM 12470 SG CYS K 54 33.180 71.557 43.284 1.00 91.27 S ATOM 12187 SG CYS K 16 23.217 66.833 52.909 1.00107.40 S ATOM 12205 SG CYS K 19 21.018 64.361 54.707 1.00109.20 S ATOM 12335 SG CYS K 36 24.056 65.730 56.569 1.00 99.38 S ATOM 12357 SG CYS K 39 24.585 63.331 53.903 1.00 91.82 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 2.66, per 1000 atoms: 0.18 Number of scatterers: 14600 At special positions: 0 Unit cell: (111.552, 131.472, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3289 8.00 N 2713 7.00 C 8269 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 - 3.00 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 Links applied TRANS " SER C 11 " - " SER D 123 " " SER G 11 " - " SER H 123 " Time building additional restraints: 0.77 Conformation dependent library (CDL) restraints added in 320.3 milliseconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" ND1 HIS K 33 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 63.5% alpha, 5.2% beta 135 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 1.63 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.624A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.634A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.864A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.996A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.664A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.642A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 83 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.624A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.709A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.766A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.835A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.512A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.744A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.536A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.581A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.730A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.933A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.567A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.509A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.581A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 147 removed outlier: 4.138A pdb=" N ILE L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN L 143 " --> pdb=" O ARG L 139 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.926A 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: 3.521A 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 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.910A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (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 101 through 102 removed outlier: 6.378A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.165A 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 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.578A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB3, first strand: chain 'M' and resid 12 through 16 removed outlier: 9.416A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 1.84 Time building geometry restraints manager: 1.10 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3478 1.34 - 1.46: 4329 1.46 - 1.58: 7030 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.516 1.545 -0.029 8.00e-03 1.56e+04 1.35e+01 bond pdb=" C3' DG J 21 " pdb=" C2' DG J 21 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.06e+01 bond pdb=" C3' DT J -17 " pdb=" C2' DT J -17 " ideal model delta sigma weight residual 1.516 1.542 -0.026 8.00e-03 1.56e+04 1.04e+01 bond pdb=" C3' DT I 30 " pdb=" C2' DT I 30 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.75e+00 bond pdb=" C3' DC I 22 " pdb=" C2' DC I 22 " ideal model delta sigma weight residual 1.516 1.541 -0.025 8.00e-03 1.56e+04 9.63e+00 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21315 1.85 - 3.69: 824 3.69 - 5.54: 25 5.54 - 7.39: 5 7.39 - 9.23: 2 Bond angle restraints: 22171 Sorted by residual: angle pdb=" O4' DA I -35 " pdb=" C4' DA I -35 " pdb=" C3' DA I -35 " ideal model delta sigma weight residual 106.00 103.13 2.87 6.00e-01 2.78e+00 2.29e+01 angle pdb=" N3 DT J 9 " pdb=" C4 DT J 9 " pdb=" O4 DT J 9 " ideal model delta sigma weight residual 119.90 122.56 -2.66 6.00e-01 2.78e+00 1.97e+01 angle pdb=" O4' DT I -26 " pdb=" C4' DT I -26 " pdb=" C3' DT I -26 " ideal model delta sigma weight residual 106.00 103.36 2.64 6.00e-01 2.78e+00 1.93e+01 angle pdb=" N3 DT J -24 " pdb=" C4 DT J -24 " pdb=" O4 DT J -24 " ideal model delta sigma weight residual 119.90 122.53 -2.63 6.00e-01 2.78e+00 1.91e+01 angle pdb=" N3 DT I 1 " pdb=" C4 DT I 1 " pdb=" O4 DT I 1 " ideal model delta sigma weight residual 119.90 122.50 -2.60 6.00e-01 2.78e+00 1.88e+01 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 7271 35.62 - 71.24: 1314 71.24 - 106.86: 24 106.86 - 142.48: 0 142.48 - 178.10: 2 Dihedral angle restraints: 8611 sinusoidal: 5471 harmonic: 3140 Sorted by residual: dihedral pdb=" CA ASP L 29 " pdb=" C ASP L 29 " pdb=" N MET L 30 " pdb=" CA MET L 30 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.10 -178.10 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 74.08 145.92 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2011 0.052 - 0.105: 447 0.105 - 0.157: 56 0.157 - 0.209: 1 0.209 - 0.262: 1 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CB ILE L 137 " pdb=" CA ILE L 137 " pdb=" CG1 ILE L 137 " pdb=" CG2 ILE L 137 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ARG L 136 " pdb=" N ARG L 136 " pdb=" C ARG L 136 " pdb=" CB ARG L 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2513 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 33 " 0.017 2.00e-02 2.50e+03 1.41e-02 4.96e+00 pdb=" CG TRP L 33 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 33 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP L 33 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 33 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 33 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 33 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO K 38 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 43 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.025 5.00e-02 4.00e+02 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 421 2.69 - 3.24: 13054 3.24 - 3.79: 26064 3.79 - 4.35: 32194 4.35 - 4.90: 47740 Nonbonded interactions: 119473 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.136 2.496 nonbonded pdb=" O ASP L 87 " pdb=" OG SER L 91 " model vdw 2.213 3.040 nonbonded pdb=" ND2 ASN A 108 " pdb=" O GLY B 42 " model vdw 2.222 3.120 nonbonded pdb=" OG SER D 64 " pdb=" O GLY F 101 " model vdw 2.230 3.040 nonbonded pdb=" OG SER L 91 " pdb=" OE1 GLN L 92 " model vdw 2.237 3.040 ... (remaining 119468 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' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } 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=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.940 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: 0.140 Check model and map are aligned: 0.040 Set scattering table: 0.020 Process input model: 12.960 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.030 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:0.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.300 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8541 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 0.051 15482 Z= 0.469 Angle : 0.707 9.232 22186 Z= 0.608 Chirality : 0.043 0.262 2516 Planarity : 0.004 0.049 1794 Dihedral : 25.751 178.102 6577 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.84 (0.26), residues: 1057 helix: 2.28 (0.21), residues: 643 sheet: 1.82 (0.76), residues: 48 loop : -0.85 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 136 TYR 0.022 0.001 TYR H 40 PHE 0.009 0.001 PHE D 65 TRP 0.038 0.003 TRP L 33 HIS 0.007 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00518 / 0.47 (15472) covalent geometry : angle 0.70327 / 0.61 (22171) hydrogen bonds : bond 0.10682 / 7.33 ( 842) hydrogen bonds : angle 4.11058 / 2.82 ( 2133) metal coordination : bond 0.01850 / 0.92 ( 8) metal coordination : angle 3.84400 / 1.99 ( 9) link_TRANS : bond 0.00188 / 0.09 ( 2) link_TRANS : angle 0.45399 / 0.24 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8469 (m110) cc_final: 0.8113 (m110) REVERT: C 11 SER cc_start: 0.8505 (t) cc_final: 0.8201 (p) REVERT: D 40 TYR cc_start: 0.9159 (m-80) cc_final: 0.8378 (m-80) REVERT: D 51 ASP cc_start: 0.7967 (p0) cc_final: 0.7741 (p0) REVERT: F 74 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7889 (tm-30) REVERT: L 7 ASN cc_start: 0.9107 (m-40) cc_final: 0.8813 (m110) REVERT: M 1 MET cc_start: 0.8023 (tmm) cc_final: 0.7346 (tmm) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.1191 time to fit residues: 35.5753 Evaluate side-chains 165 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 165 time to evaluate : 0.257 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 98 optimal weight: 9.9990 chunk 107 optimal weight: 6.9990 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 1.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 9.9990 chunk 122 optimal weight: 20.0000 chunk 91 optimal weight: 10.0000 chunk 55 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 overall best weight: 2.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** M 2 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3676 r_free = 0.3676 target = 0.136561 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.2841 r_free = 0.2841 target = 0.080329 restraints weight = 41015.907| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.081753 restraints weight = 23604.361| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2872 r_free = 0.2872 target = 0.081952 restraints weight = 16065.564| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.2873 r_free = 0.2873 target = 0.082019 restraints weight = 16233.137| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 26)----------------| | r_work = 0.2880 r_free = 0.2880 target = 0.082415 restraints weight = 15650.900| |-----------------------------------------------------------------------------| r_work (final): 0.2834 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2779 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2779 r_free = 0.2779 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2775 r_free = 0.2775 target_work(ls_wunit_k1) = 0.075 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 8 (10 function evaluations) r_final: 0.2775 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8778 moved from start: 0.1346 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 15482 Z= 0.318 Angle : 0.789 13.184 22186 Z= 0.431 Chirality : 0.051 0.307 2516 Planarity : 0.006 0.068 1794 Dihedral : 29.216 173.433 4413 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.71 % Allowed : 11.15 % Favored : 86.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.29 (0.26), residues: 1057 helix: 1.78 (0.20), residues: 649 sheet: 1.72 (0.75), residues: 53 loop : -1.06 (0.31), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 72 TYR 0.029 0.003 TYR H 83 PHE 0.016 0.003 PHE D 70 TRP 0.025 0.004 TRP L 33 HIS 0.008 0.002 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00736 / 0.32 (15472) covalent geometry : angle 0.77935 / 0.43 (22171) hydrogen bonds : bond 0.07093 / 4.75 ( 842) hydrogen bonds : angle 3.87517 / 2.70 ( 2133) metal coordination : bond 0.01566 / 0.70 ( 8) metal coordination : angle 6.16018 / 2.88 ( 9) link_TRANS : bond 0.00250 / 0.12 ( 2) link_TRANS : angle 0.43624 / 0.19 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 184 time to evaluate : 0.328 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8443 (m110) cc_final: 0.8203 (m110) REVERT: C 61 GLU cc_start: 0.9181 (tp30) cc_final: 0.8687 (tp30) REVERT: D 51 ASP cc_start: 0.7954 (p0) cc_final: 0.7699 (p0) REVERT: F 73 THR cc_start: 0.9484 (t) cc_final: 0.9209 (m) REVERT: F 74 GLU cc_start: 0.8245 (tm-30) cc_final: 0.7798 (tm-30) REVERT: H 68 ASP cc_start: 0.9175 (t70) cc_final: 0.8909 (t0) REVERT: L 4 LYS cc_start: 0.9176 (mttp) cc_final: 0.8967 (ptpt) REVERT: L 7 ASN cc_start: 0.9618 (m-40) cc_final: 0.9349 (m110) REVERT: L 63 LYS cc_start: 0.8889 (mttp) cc_final: 0.8684 (mttp) REVERT: M 1 MET cc_start: 0.8384 (tmm) cc_final: 0.7612 (tmm) REVERT: M 4 PHE cc_start: 0.8989 (m-10) cc_final: 0.8717 (m-10) outliers start: 25 outliers final: 20 residues processed: 197 average time/residue: 0.1215 time to fit residues: 34.0732 Evaluate side-chains 192 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 172 time to evaluate : 0.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 110 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 33 optimal weight: 1.9990 chunk 105 optimal weight: 2.9990 chunk 100 optimal weight: 6.9990 chunk 39 optimal weight: 0.9990 chunk 101 optimal weight: 4.9990 chunk 77 optimal weight: 9.9990 chunk 35 optimal weight: 0.6980 chunk 48 optimal weight: 0.6980 chunk 38 optimal weight: 0.9990 chunk 49 optimal weight: 0.7980 chunk 102 optimal weight: 9.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... B 75 HIS E 108 ASN M 2 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3712 r_free = 0.3712 target = 0.139572 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091113 restraints weight = 37090.227| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3010 r_free = 0.3010 target = 0.090597 restraints weight = 22701.663| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3019 r_free = 0.3019 target = 0.091461 restraints weight = 19244.304| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.092207 restraints weight = 15327.411| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3030 r_free = 0.3030 target = 0.092307 restraints weight = 14777.195| |-----------------------------------------------------------------------------| r_work (final): 0.2980 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2984 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.34 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2984 r_free = 0.2984 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2984 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8573 moved from start: 0.1349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 15482 Z= 0.160 Angle : 0.630 10.425 22186 Z= 0.361 Chirality : 0.043 0.243 2516 Planarity : 0.005 0.049 1794 Dihedral : 29.144 176.768 4413 Min Nonbonded Distance : 2.055 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.18 % Favored : 97.82 % Rotamer: Outliers : 2.06 % Allowed : 14.61 % Favored : 83.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.69 (0.26), residues: 1057 helix: 2.20 (0.20), residues: 648 sheet: 1.79 (0.78), residues: 53 loop : -1.11 (0.30), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.023 0.002 TYR H 40 PHE 0.013 0.001 PHE L 50 TRP 0.039 0.004 TRP L 141 HIS 0.003 0.001 HIS B 75 Details of bonding type rmsd/Z covalent geometry : bond 0.00306 / 0.16 (15472) covalent geometry : angle 0.62197 / 0.36 (22171) hydrogen bonds : bond 0.05440 / 3.64 ( 842) hydrogen bonds : angle 3.39419 / 2.36 ( 2133) metal coordination : bond 0.00630 / 0.26 ( 8) metal coordination : angle 5.11645 / 2.47 ( 9) link_TRANS : bond 0.00126 / 0.06 ( 2) link_TRANS : angle 0.30105 / 0.14 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 182 time to evaluate : 0.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8819 (pm20) cc_final: 0.8531 (pm20) REVERT: B 25 ASN cc_start: 0.8406 (m110) cc_final: 0.8160 (m110) REVERT: C 61 GLU cc_start: 0.9146 (tp30) cc_final: 0.8647 (tp30) REVERT: D 40 TYR cc_start: 0.9267 (m-80) cc_final: 0.8502 (m-80) REVERT: D 51 ASP cc_start: 0.8061 (p0) cc_final: 0.7828 (p0) REVERT: F 73 THR cc_start: 0.9486 (t) cc_final: 0.9229 (m) REVERT: F 74 GLU cc_start: 0.8192 (tm-30) cc_final: 0.7721 (tm-30) REVERT: G 13 LYS cc_start: 0.8821 (mmtt) cc_final: 0.8561 (mmtt) REVERT: H 68 ASP cc_start: 0.9200 (t70) cc_final: 0.8906 (t0) REVERT: H 83 TYR cc_start: 0.8659 (m-10) cc_final: 0.8008 (m-10) REVERT: L 7 ASN cc_start: 0.9415 (m-40) cc_final: 0.9181 (m110) REVERT: M 1 MET cc_start: 0.8086 (tmm) cc_final: 0.7189 (tmm) outliers start: 19 outliers final: 14 residues processed: 190 average time/residue: 0.1236 time to fit residues: 33.4833 Evaluate side-chains 181 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 167 time to evaluate : 0.457 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 58 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 48 optimal weight: 0.7980 chunk 73 optimal weight: 20.0000 chunk 7 optimal weight: 1.9990 chunk 102 optimal weight: 8.9990 chunk 60 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 24 optimal weight: 0.8980 chunk 128 optimal weight: 20.0000 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... K 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3711 r_free = 0.3711 target = 0.139418 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 65)----------------| | r_work = 0.2864 r_free = 0.2864 target = 0.080830 restraints weight = 48092.405| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 49)----------------| | r_work = 0.2902 r_free = 0.2902 target = 0.083136 restraints weight = 25360.966| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 53)----------------| | r_work = 0.2928 r_free = 0.2928 target = 0.084666 restraints weight = 17435.775| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.085510 restraints weight = 14321.804| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 29)----------------| | r_work = 0.2948 r_free = 0.2948 target = 0.085924 restraints weight = 13013.733| |-----------------------------------------------------------------------------| r_work (final): 0.2913 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2862 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2862 r_free = 0.2862 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (8 function evaluations) r_final: 0.2862 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8710 moved from start: 0.1466 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15482 Z= 0.157 Angle : 0.628 10.198 22186 Z= 0.357 Chirality : 0.043 0.265 2516 Planarity : 0.005 0.054 1794 Dihedral : 29.201 176.503 4413 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.92 % Allowed : 15.91 % Favored : 81.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.77 (0.26), residues: 1057 helix: 2.31 (0.20), residues: 650 sheet: 1.44 (0.78), residues: 53 loop : -1.10 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.029 0.002 TYR H 40 PHE 0.017 0.001 PHE L 50 TRP 0.067 0.005 TRP L 33 HIS 0.007 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00304 / 0.16 (15472) covalent geometry : angle 0.62085 / 0.36 (22171) hydrogen bonds : bond 0.05189 / 3.50 ( 842) hydrogen bonds : angle 3.33574 / 2.33 ( 2133) metal coordination : bond 0.00651 / 0.29 ( 8) metal coordination : angle 4.79510 / 2.34 ( 9) link_TRANS : bond 0.00111 / 0.05 ( 2) link_TRANS : angle 0.23767 / 0.10 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 176 time to evaluate : 0.281 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 59 GLU cc_start: 0.8756 (pm20) cc_final: 0.8513 (pm20) REVERT: B 25 ASN cc_start: 0.8404 (m110) cc_final: 0.8163 (m110) REVERT: C 61 GLU cc_start: 0.9137 (tp30) cc_final: 0.8648 (tp30) REVERT: D 40 TYR cc_start: 0.9249 (m-80) cc_final: 0.8603 (m-80) REVERT: D 51 ASP cc_start: 0.7960 (p0) cc_final: 0.7745 (p0) REVERT: F 73 THR cc_start: 0.9475 (t) cc_final: 0.9216 (m) REVERT: F 74 GLU cc_start: 0.8155 (tm-30) cc_final: 0.7655 (tm-30) REVERT: H 68 ASP cc_start: 0.9154 (t70) cc_final: 0.8864 (t0) REVERT: L 7 ASN cc_start: 0.9575 (m-40) cc_final: 0.9332 (m110) REVERT: L 30 MET cc_start: 0.8171 (tpp) cc_final: 0.7810 (tpt) REVERT: L 74 TYR cc_start: 0.7734 (t80) cc_final: 0.7488 (t80) REVERT: M 1 MET cc_start: 0.8527 (tmm) cc_final: 0.7675 (tmm) outliers start: 27 outliers final: 22 residues processed: 187 average time/residue: 0.1114 time to fit residues: 29.7087 Evaluate side-chains 190 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 168 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 46 optimal weight: 0.9980 chunk 4 optimal weight: 0.4980 chunk 78 optimal weight: 10.0000 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 20.0000 chunk 98 optimal weight: 9.9990 chunk 54 optimal weight: 0.7980 chunk 126 optimal weight: 9.9990 chunk 60 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 21 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.139772 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 59)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.084142 restraints weight = 40562.016| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.2927 r_free = 0.2927 target = 0.085074 restraints weight = 23414.799| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.2942 r_free = 0.2942 target = 0.086054 restraints weight = 16712.934| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.2944 r_free = 0.2944 target = 0.086145 restraints weight = 15246.774| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 28)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.086169 restraints weight = 14155.787| |-----------------------------------------------------------------------------| r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2867 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.01 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2867 r_free = 0.2867 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2867 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1538 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 15482 Z= 0.147 Angle : 0.617 9.629 22186 Z= 0.351 Chirality : 0.042 0.258 2516 Planarity : 0.005 0.047 1794 Dihedral : 29.224 176.760 4413 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.49 % Allowed : 17.86 % Favored : 79.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.82 (0.26), residues: 1057 helix: 2.35 (0.21), residues: 650 sheet: 1.40 (0.77), residues: 53 loop : -1.09 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 86 TYR 0.028 0.002 TYR H 40 PHE 0.018 0.001 PHE L 50 TRP 0.062 0.004 TRP L 33 HIS 0.011 0.001 HIS K 83 Details of bonding type rmsd/Z covalent geometry : bond 0.00276 / 0.15 (15472) covalent geometry : angle 0.61017 / 0.35 (22171) hydrogen bonds : bond 0.04985 / 3.37 ( 842) hydrogen bonds : angle 3.27753 / 2.29 ( 2133) metal coordination : bond 0.00725 / 0.34 ( 8) metal coordination : angle 4.68320 / 2.31 ( 9) link_TRANS : bond 0.00101 / 0.05 ( 2) link_TRANS : angle 0.20108 / 0.08 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 170 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8545 (m110) cc_final: 0.8268 (m110) REVERT: C 61 GLU cc_start: 0.9117 (tp30) cc_final: 0.8643 (tp30) REVERT: C 74 LYS cc_start: 0.8805 (mmmt) cc_final: 0.8479 (mttm) REVERT: D 40 TYR cc_start: 0.9250 (m-80) cc_final: 0.8615 (m-80) REVERT: D 51 ASP cc_start: 0.7996 (p0) cc_final: 0.7759 (p0) REVERT: F 73 THR cc_start: 0.9489 (t) cc_final: 0.9244 (m) REVERT: F 74 GLU cc_start: 0.8142 (tm-30) cc_final: 0.7623 (tm-30) REVERT: H 68 ASP cc_start: 0.9160 (t70) cc_final: 0.8867 (t0) REVERT: L 4 LYS cc_start: 0.8957 (ptpt) cc_final: 0.8393 (pttm) REVERT: L 7 ASN cc_start: 0.9618 (m-40) cc_final: 0.9333 (m110) REVERT: L 30 MET cc_start: 0.8325 (tpp) cc_final: 0.8070 (tpt) REVERT: M 1 MET cc_start: 0.8412 (tmm) cc_final: 0.7490 (tmm) outliers start: 23 outliers final: 19 residues processed: 182 average time/residue: 0.1354 time to fit residues: 35.0924 Evaluate side-chains 184 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 165 time to evaluate : 0.285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 107 optimal weight: 0.1980 chunk 63 optimal weight: 5.9990 chunk 39 optimal weight: 0.5980 chunk 9 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 122 optimal weight: 0.1980 chunk 32 optimal weight: 1.9990 chunk 103 optimal weight: 7.9990 chunk 110 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.5582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3730 r_free = 0.3730 target = 0.140979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.094616 restraints weight = 40632.409| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3080 r_free = 0.3080 target = 0.095443 restraints weight = 28313.848| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3081 r_free = 0.3081 target = 0.095519 restraints weight = 28496.677| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.096099 restraints weight = 17115.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.097081 restraints weight = 14864.157| |-----------------------------------------------------------------------------| r_work (final): 0.3028 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3043 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3043 r_free = 0.3043 target_work(ls_wunit_k1) = 0.091 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.3043 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.1596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 15482 Z= 0.139 Angle : 0.604 9.435 22186 Z= 0.344 Chirality : 0.041 0.258 2516 Planarity : 0.005 0.044 1794 Dihedral : 29.254 176.814 4413 Min Nonbonded Distance : 2.049 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.60 % Allowed : 17.97 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.88 (0.26), residues: 1057 helix: 2.44 (0.21), residues: 650 sheet: 1.33 (0.78), residues: 48 loop : -1.10 (0.30), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.032 0.002 TYR H 83 PHE 0.019 0.001 PHE L 50 TRP 0.040 0.003 TRP L 33 HIS 0.004 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00249 / 0.14 (15472) covalent geometry : angle 0.59674 / 0.34 (22171) hydrogen bonds : bond 0.04755 / 3.23 ( 842) hydrogen bonds : angle 3.21844 / 2.25 ( 2133) metal coordination : bond 0.00823 / 0.39 ( 8) metal coordination : angle 4.65342 / 2.33 ( 9) link_TRANS : bond 0.00083 / 0.04 ( 2) link_TRANS : angle 0.17227 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 175 time to evaluate : 0.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8399 (m110) cc_final: 0.8128 (m110) REVERT: C 61 GLU cc_start: 0.9125 (tp30) cc_final: 0.8633 (tp30) REVERT: C 74 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8481 (mttm) REVERT: D 40 TYR cc_start: 0.9271 (m-80) cc_final: 0.8554 (m-80) REVERT: D 51 ASP cc_start: 0.8051 (p0) cc_final: 0.7847 (p0) REVERT: F 73 THR cc_start: 0.9513 (t) cc_final: 0.9261 (m) REVERT: F 74 GLU cc_start: 0.8185 (tm-30) cc_final: 0.7652 (tm-30) REVERT: H 68 ASP cc_start: 0.9158 (t70) cc_final: 0.8822 (t0) REVERT: K 83 HIS cc_start: 0.7969 (t-90) cc_final: 0.7266 (t70) REVERT: L 4 LYS cc_start: 0.8718 (ptpt) cc_final: 0.8075 (pttm) REVERT: L 7 ASN cc_start: 0.9366 (m-40) cc_final: 0.9146 (m110) REVERT: M 1 MET cc_start: 0.7869 (tmm) cc_final: 0.7020 (tmm) outliers start: 24 outliers final: 21 residues processed: 186 average time/residue: 0.1137 time to fit residues: 30.1771 Evaluate side-chains 191 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 170 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 136 ARG Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 94 optimal weight: 9.9990 chunk 81 optimal weight: 10.0000 chunk 62 optimal weight: 0.6980 chunk 23 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3722 r_free = 0.3722 target = 0.140289 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.095008 restraints weight = 42416.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3075 r_free = 0.3075 target = 0.095320 restraints weight = 30867.762| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095308 restraints weight = 31741.422| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3090 r_free = 0.3090 target = 0.096490 restraints weight = 17594.203| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3100 r_free = 0.3100 target = 0.097367 restraints weight = 14976.604| |-----------------------------------------------------------------------------| r_work (final): 0.3024 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2980 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2980 r_free = 0.2980 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2980 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 15482 Z= 0.153 Angle : 0.615 9.116 22186 Z= 0.346 Chirality : 0.042 0.265 2516 Planarity : 0.005 0.046 1794 Dihedral : 29.317 176.407 4413 Min Nonbonded Distance : 2.046 Molprobity Statistics. All-atom Clashscore : 7.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.81 % Allowed : 19.05 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.82 (0.26), residues: 1057 helix: 2.37 (0.21), residues: 651 sheet: 1.20 (0.77), residues: 48 loop : -1.08 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 86 TYR 0.047 0.002 TYR F 88 PHE 0.019 0.001 PHE L 50 TRP 0.030 0.002 TRP L 33 HIS 0.002 0.001 HIS L 32 Details of bonding type rmsd/Z covalent geometry : bond 0.00301 / 0.15 (15472) covalent geometry : angle 0.60776 / 0.35 (22171) hydrogen bonds : bond 0.04902 / 3.32 ( 842) hydrogen bonds : angle 3.25373 / 2.28 ( 2133) metal coordination : bond 0.00845 / 0.40 ( 8) metal coordination : angle 4.68157 / 2.33 ( 9) link_TRANS : bond 0.00078 / 0.04 ( 2) link_TRANS : angle 0.19377 / 0.07 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 170 time to evaluate : 0.300 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8448 (m110) cc_final: 0.8190 (m110) REVERT: C 61 GLU cc_start: 0.9140 (tp30) cc_final: 0.8630 (tp30) REVERT: C 74 LYS cc_start: 0.8873 (mmmt) cc_final: 0.8481 (mttm) REVERT: D 40 TYR cc_start: 0.9271 (m-80) cc_final: 0.8613 (m-80) REVERT: D 51 ASP cc_start: 0.8066 (p0) cc_final: 0.7853 (p0) REVERT: D 71 GLU cc_start: 0.7750 (mm-30) cc_final: 0.7518 (mm-30) REVERT: F 73 THR cc_start: 0.9531 (t) cc_final: 0.9288 (m) REVERT: F 74 GLU cc_start: 0.8193 (tm-30) cc_final: 0.7655 (tm-30) REVERT: H 68 ASP cc_start: 0.9192 (t70) cc_final: 0.8865 (t0) REVERT: K 83 HIS cc_start: 0.7969 (t-90) cc_final: 0.7182 (t70) REVERT: L 4 LYS cc_start: 0.8642 (ptpt) cc_final: 0.8004 (pttm) REVERT: L 7 ASN cc_start: 0.9376 (m-40) cc_final: 0.9151 (m110) REVERT: M 1 MET cc_start: 0.7860 (tmm) cc_final: 0.6987 (tmm) outliers start: 26 outliers final: 24 residues processed: 184 average time/residue: 0.1247 time to fit residues: 32.6247 Evaluate side-chains 192 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 168 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9980 chunk 64 optimal weight: 0.7980 chunk 68 optimal weight: 0.2980 chunk 45 optimal weight: 0.7980 chunk 120 optimal weight: 3.9990 chunk 116 optimal weight: 5.9990 chunk 28 optimal weight: 0.7980 chunk 127 optimal weight: 8.9990 chunk 4 optimal weight: 0.7980 chunk 100 optimal weight: 4.9990 chunk 94 optimal weight: 9.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3729 r_free = 0.3729 target = 0.140876 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.2919 r_free = 0.2919 target = 0.084852 restraints weight = 45752.249| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2941 r_free = 0.2941 target = 0.085968 restraints weight = 22936.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.086297 restraints weight = 15313.362| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.2953 r_free = 0.2953 target = 0.086734 restraints weight = 15224.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 31)----------------| | r_work = 0.2955 r_free = 0.2955 target = 0.086877 restraints weight = 13430.284| |-----------------------------------------------------------------------------| r_work (final): 0.2849 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2915 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2915 r_free = 0.2915 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (5 function evaluations) r_final: 0.2915 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8676 moved from start: 0.1738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 15482 Z= 0.142 Angle : 0.611 9.421 22186 Z= 0.344 Chirality : 0.041 0.261 2516 Planarity : 0.005 0.046 1794 Dihedral : 29.337 176.656 4413 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 2.60 % Allowed : 19.26 % Favored : 78.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.85 (0.26), residues: 1057 helix: 2.40 (0.20), residues: 651 sheet: 1.14 (0.77), residues: 48 loop : -1.06 (0.31), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG L 136 TYR 0.038 0.002 TYR F 88 PHE 0.020 0.001 PHE L 50 TRP 0.043 0.003 TRP L 33 HIS 0.005 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (15472) covalent geometry : angle 0.60344 / 0.34 (22171) hydrogen bonds : bond 0.04784 / 3.25 ( 842) hydrogen bonds : angle 3.20719 / 2.25 ( 2133) metal coordination : bond 0.00907 / 0.44 ( 8) metal coordination : angle 4.70827 / 2.37 ( 9) link_TRANS : bond 0.00072 / 0.04 ( 2) link_TRANS : angle 0.15107 / 0.06 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 0.329 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8477 (m110) cc_final: 0.8211 (m110) REVERT: C 61 GLU cc_start: 0.9148 (tp30) cc_final: 0.8676 (tp30) REVERT: C 74 LYS cc_start: 0.8872 (mmmt) cc_final: 0.8468 (mttm) REVERT: D 40 TYR cc_start: 0.9267 (m-80) cc_final: 0.8617 (m-80) REVERT: D 51 ASP cc_start: 0.8085 (p0) cc_final: 0.7863 (p0) REVERT: D 71 GLU cc_start: 0.7766 (mm-30) cc_final: 0.7538 (mm-30) REVERT: F 73 THR cc_start: 0.9548 (t) cc_final: 0.9245 (m) REVERT: F 74 GLU cc_start: 0.8195 (tm-30) cc_final: 0.7635 (tm-30) REVERT: H 47 GLN cc_start: 0.8598 (tt0) cc_final: 0.8245 (mt0) REVERT: H 68 ASP cc_start: 0.9183 (t70) cc_final: 0.8904 (t0) REVERT: K 83 HIS cc_start: 0.7762 (t-90) cc_final: 0.7061 (t70) REVERT: L 4 LYS cc_start: 0.8835 (ptpt) cc_final: 0.8239 (pttm) REVERT: L 7 ASN cc_start: 0.9610 (m-40) cc_final: 0.9316 (m110) REVERT: M 1 MET cc_start: 0.8456 (tmm) cc_final: 0.7543 (tmm) outliers start: 24 outliers final: 23 residues processed: 186 average time/residue: 0.1338 time to fit residues: 35.4667 Evaluate side-chains 192 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 0.373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 6.9990 chunk 72 optimal weight: 20.0000 chunk 35 optimal weight: 0.9980 chunk 39 optimal weight: 0.6980 chunk 87 optimal weight: 20.0000 chunk 13 optimal weight: 0.6980 chunk 50 optimal weight: 0.6980 chunk 9 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 4 optimal weight: 0.5980 chunk 43 optimal weight: 0.7980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3731 r_free = 0.3731 target = 0.141033 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.090845 restraints weight = 35434.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.091585 restraints weight = 21422.234| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.092022 restraints weight = 17311.708| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 23)----------------| | r_work = 0.3043 r_free = 0.3043 target = 0.092488 restraints weight = 14699.298| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.092675 restraints weight = 13727.505| |-----------------------------------------------------------------------------| r_work (final): 0.2944 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8555 moved from start: 0.1799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 15482 Z= 0.142 Angle : 0.615 9.384 22186 Z= 0.345 Chirality : 0.041 0.263 2516 Planarity : 0.005 0.046 1794 Dihedral : 29.364 176.623 4413 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 2.60 % Allowed : 19.81 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.84 (0.26), residues: 1057 helix: 2.41 (0.20), residues: 650 sheet: 1.16 (0.77), residues: 48 loop : -1.10 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.049 0.002 TYR F 88 PHE 0.019 0.001 PHE L 50 TRP 0.038 0.002 TRP L 33 HIS 0.004 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00267 / 0.14 (15472) covalent geometry : angle 0.60776 / 0.34 (22171) hydrogen bonds : bond 0.04762 / 3.24 ( 842) hydrogen bonds : angle 3.20308 / 2.24 ( 2133) metal coordination : bond 0.00951 / 0.46 ( 8) metal coordination : angle 4.62648 / 2.33 ( 9) link_TRANS : bond 0.00063 / 0.03 ( 2) link_TRANS : angle 0.13394 / 0.05 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 176 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8501 (m110) cc_final: 0.8229 (m110) REVERT: C 61 GLU cc_start: 0.9112 (tp30) cc_final: 0.8624 (tp30) REVERT: C 74 LYS cc_start: 0.8875 (mmmt) cc_final: 0.8495 (mttm) REVERT: D 40 TYR cc_start: 0.9263 (m-80) cc_final: 0.8552 (m-80) REVERT: D 51 ASP cc_start: 0.8102 (p0) cc_final: 0.7865 (p0) REVERT: D 71 GLU cc_start: 0.7835 (mm-30) cc_final: 0.7596 (mm-30) REVERT: F 74 GLU cc_start: 0.8179 (tm-30) cc_final: 0.7692 (tm-30) REVERT: H 47 GLN cc_start: 0.8620 (tt0) cc_final: 0.8275 (mt0) REVERT: H 68 ASP cc_start: 0.9208 (t70) cc_final: 0.8892 (t0) REVERT: K 83 HIS cc_start: 0.7766 (t-90) cc_final: 0.6965 (t70) REVERT: L 4 LYS cc_start: 0.8503 (ptpt) cc_final: 0.7909 (pttm) REVERT: L 7 ASN cc_start: 0.9383 (m-40) cc_final: 0.9118 (m110) REVERT: L 63 LYS cc_start: 0.9038 (mttp) cc_final: 0.8646 (mttp) REVERT: M 1 MET cc_start: 0.7968 (tmm) cc_final: 0.7125 (tmm) REVERT: M 72 ARG cc_start: 0.7186 (mmm160) cc_final: 0.6932 (mmm160) outliers start: 24 outliers final: 23 residues processed: 188 average time/residue: 0.1334 time to fit residues: 35.5518 Evaluate side-chains 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 174 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 11 LEU Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 112 optimal weight: 0.5980 chunk 18 optimal weight: 0.5980 chunk 81 optimal weight: 10.0000 chunk 97 optimal weight: 9.9990 chunk 111 optimal weight: 3.9990 chunk 104 optimal weight: 0.4980 chunk 114 optimal weight: 5.9990 chunk 42 optimal weight: 1.9990 chunk 121 optimal weight: 3.9990 chunk 86 optimal weight: 9.9990 chunk 66 optimal weight: 0.6980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3723 r_free = 0.3723 target = 0.140436 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2898 r_free = 0.2898 target = 0.083445 restraints weight = 48070.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 28)----------------| | r_work = 0.2926 r_free = 0.2926 target = 0.084863 restraints weight = 24787.671| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.2945 r_free = 0.2945 target = 0.086240 restraints weight = 15580.833| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.2950 r_free = 0.2950 target = 0.086428 restraints weight = 14518.337| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 23)----------------| | r_work = 0.2949 r_free = 0.2949 target = 0.086450 restraints weight = 12980.620| |-----------------------------------------------------------------------------| r_work (final): 0.2892 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2892 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2892 r_free = 0.2892 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2892 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8685 moved from start: 0.1861 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 15482 Z= 0.153 Angle : 0.623 9.344 22186 Z= 0.348 Chirality : 0.041 0.268 2516 Planarity : 0.005 0.047 1794 Dihedral : 29.415 176.398 4413 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.71 % Allowed : 19.70 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.79 (0.26), residues: 1057 helix: 2.38 (0.21), residues: 650 sheet: 1.14 (0.76), residues: 48 loop : -1.14 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.054 0.002 TYR F 88 PHE 0.020 0.001 PHE L 50 TRP 0.041 0.003 TRP L 33 HIS 0.004 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00307 / 0.15 (15472) covalent geometry : angle 0.61628 / 0.35 (22171) hydrogen bonds : bond 0.04907 / 3.34 ( 842) hydrogen bonds : angle 3.22360 / 2.25 ( 2133) metal coordination : bond 0.00952 / 0.46 ( 8) metal coordination : angle 4.63061 / 2.34 ( 9) link_TRANS : bond 0.00063 / 0.03 ( 2) link_TRANS : angle 0.14883 / 0.06 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8469 (m110) cc_final: 0.8224 (m110) REVERT: C 61 GLU cc_start: 0.9151 (tp30) cc_final: 0.8676 (tp30) REVERT: C 74 LYS cc_start: 0.8854 (mmmt) cc_final: 0.8472 (mttm) REVERT: D 40 TYR cc_start: 0.9298 (m-80) cc_final: 0.8591 (m-80) REVERT: D 51 ASP cc_start: 0.8066 (p0) cc_final: 0.7835 (p0) REVERT: D 71 GLU cc_start: 0.7805 (mm-30) cc_final: 0.7599 (mm-30) REVERT: F 74 GLU cc_start: 0.8211 (tm-30) cc_final: 0.7714 (tm-30) REVERT: H 47 GLN cc_start: 0.8600 (tt0) cc_final: 0.8229 (mt0) REVERT: H 68 ASP cc_start: 0.9169 (t70) cc_final: 0.8898 (t0) REVERT: K 83 HIS cc_start: 0.7717 (t-90) cc_final: 0.6954 (t70) REVERT: L 4 LYS cc_start: 0.8783 (ptpt) cc_final: 0.8200 (pttm) REVERT: L 7 ASN cc_start: 0.9593 (m-40) cc_final: 0.9309 (m110) REVERT: L 63 LYS cc_start: 0.8970 (mttp) cc_final: 0.8585 (mttp) REVERT: M 1 MET cc_start: 0.8424 (tmm) cc_final: 0.7515 (tmm) REVERT: M 72 ARG cc_start: 0.7400 (mmm160) cc_final: 0.7119 (mmm160) outliers start: 25 outliers final: 22 residues processed: 186 average time/residue: 0.1356 time to fit residues: 35.7969 Evaluate side-chains 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 174 time to evaluate : 0.368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 11 SER Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 46 GLN Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 23 optimal weight: 0.8980 chunk 103 optimal weight: 2.9990 chunk 128 optimal weight: 8.9990 chunk 49 optimal weight: 0.9990 chunk 71 optimal weight: 1.9990 chunk 113 optimal weight: 10.0000 chunk 24 optimal weight: 0.8980 chunk 87 optimal weight: 20.0000 chunk 123 optimal weight: 7.9990 chunk 127 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3701 r_free = 0.3701 target = 0.138647 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3072 r_free = 0.3072 target = 0.093173 restraints weight = 41891.165| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.092946 restraints weight = 31220.988| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.093051 restraints weight = 32882.291| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 25)----------------| | r_work = 0.3056 r_free = 0.3056 target = 0.094106 restraints weight = 18188.969| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 25)----------------| | r_work = 0.3074 r_free = 0.3074 target = 0.095532 restraints weight = 15371.104| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3014 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3014 r_free = 0.3014 target_work(ls_wunit_k1) = 0.089 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.3014 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8546 moved from start: 0.1936 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 15482 Z= 0.204 Angle : 0.663 9.234 22186 Z= 0.364 Chirality : 0.043 0.284 2516 Planarity : 0.005 0.061 1794 Dihedral : 29.508 175.795 4413 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.60 % Allowed : 20.56 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % 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: 1.62 (0.26), residues: 1057 helix: 2.25 (0.21), residues: 650 sheet: 1.02 (0.76), residues: 48 loop : -1.20 (0.31), residues: 359 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG G 99 TYR 0.063 0.002 TYR F 88 PHE 0.020 0.002 PHE L 50 TRP 0.040 0.002 TRP L 33 HIS 0.005 0.001 HIS L 55 Details of bonding type rmsd/Z covalent geometry : bond 0.00449 / 0.20 (15472) covalent geometry : angle 0.65502 / 0.36 (22171) hydrogen bonds : bond 0.05435 / 3.68 ( 842) hydrogen bonds : angle 3.37663 / 2.37 ( 2133) metal coordination : bond 0.01003 / 0.48 ( 8) metal coordination : angle 5.01556 / 2.52 ( 9) link_TRANS : bond 0.00133 / 0.06 ( 2) link_TRANS : angle 0.23380 / 0.09 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2232.88 seconds wall clock time: 39 minutes 6.26 seconds (2346.26 seconds total)