Starting phenix.real_space_refine on Thu Jun 12 20:15:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8sn5_40613/06_2025/8sn5_40613.cif Found real_map, /net/cci-nas-00/data/ceres_data/8sn5_40613/06_2025/8sn5_40613.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8sn5_40613/06_2025/8sn5_40613.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8sn5_40613/06_2025/8sn5_40613.map" model { file = "/net/cci-nas-00/data/ceres_data/8sn5_40613/06_2025/8sn5_40613.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8sn5_40613/06_2025/8sn5_40613.cif" } resolution = 3.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } 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= 0.003 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 15 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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 32.772 74.839 47.610 1.00 92.05 S ATOM 12446 SG CYS K 51 33.544 71.534 45.841 1.00 78.30 S ATOM 12470 SG CYS K 54 32.537 74.397 43.794 1.00100.28 S ATOM 12187 SG CYS K 16 22.380 68.849 53.466 1.00109.61 S ATOM 12205 SG CYS K 19 20.326 66.237 55.227 1.00105.23 S ATOM 12335 SG CYS K 36 23.285 67.916 57.089 1.00 94.72 S ATOM 12357 SG CYS K 39 24.037 65.484 54.484 1.00 92.21 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: 8.80, per 1000 atoms: 0.60 Number of scatterers: 14600 At special positions: 0 Unit cell: (108.896, 134.128, 127.488, 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: 3.53 Conformation dependent library (CDL) restraints added in 1.3 seconds 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 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " 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: 48 helices and 13 sheets defined 63.6% alpha, 5.3% beta 135 base pairs and 233 stacking pairs defined. Time for finding SS restraints: 6.78 Creating SS restraints... Processing helix chain 'A' and resid 44 through 55 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.502A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (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: 3.794A 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: 3.921A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.822A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.776A 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 removed outlier: 4.203A pdb=" N ALA C 21 " --> pdb=" O ARG C 17 " (cutoff:3.500A) Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.476A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.813A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.725A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.708A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 Processing helix chain 'E' and resid 85 through 114 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 49 through 76 removed outlier: 3.803A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.726A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 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: 3.571A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.543A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.571A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 10 through 15 removed outlier: 3.619A pdb=" N GLN K 15 " --> pdb=" O LEU K 11 " (cutoff:3.500A) Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.596A 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 90 removed outlier: 3.702A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 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: 3.773A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 145 removed outlier: 4.256A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 39 No H-bonds generated for 'chain 'M' and resid 37 through 39' Processing helix chain 'M' and resid 56 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.679A 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: 3.738A 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 97 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.809A 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: 6.826A 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: 7.004A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.679A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28 removed outlier: 4.096A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB4, first strand: chain 'M' and resid 12 through 16 removed outlier: 3.623A pdb=" N VAL M 5 " --> pdb=" O ILE M 13 " (cutoff:3.500A) removed outlier: 4.045A pdb=" N LEU M 15 " --> pdb=" O ILE M 3 " (cutoff:3.500A) removed outlier: 3.862A pdb=" N ILE M 3 " --> pdb=" O LEU M 15 " (cutoff:3.500A) removed outlier: 8.316A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.175A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 5.970A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 7.140A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N ARG M 42 " --> pdb=" O VAL M 70 " (cutoff:3.500A) 501 hydrogen bonds defined for protein. 1464 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 233 stacking parallelities Total time for adding SS restraints: 5.31 Time building geometry restraints manager: 4.27 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: 3384 1.34 - 1.45: 4369 1.45 - 1.57: 7084 1.57 - 1.69: 586 1.69 - 1.81: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.456 -0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CA ILE B 29 " pdb=" CB ILE B 29 " ideal model delta sigma weight residual 1.540 1.525 0.015 1.36e-02 5.41e+03 1.26e+00 bond pdb=" CB LYS M 48 " pdb=" CG LYS M 48 " ideal model delta sigma weight residual 1.520 1.552 -0.032 3.00e-02 1.11e+03 1.17e+00 bond pdb=" C VAL K 24 " pdb=" N GLU K 25 " ideal model delta sigma weight residual 1.331 1.353 -0.022 2.07e-02 2.33e+03 1.15e+00 bond pdb=" C3' DA J -73 " pdb=" C2' DA J -73 " ideal model delta sigma weight residual 1.525 1.543 -0.018 2.00e-02 2.50e+03 8.29e-01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.54: 21557 1.54 - 3.07: 551 3.07 - 4.61: 41 4.61 - 6.14: 16 6.14 - 7.68: 6 Bond angle restraints: 22171 Sorted by residual: angle pdb=" N TRP L 141 " pdb=" CA TRP L 141 " pdb=" CB TRP L 141 " ideal model delta sigma weight residual 110.12 115.65 -5.53 1.47e+00 4.63e-01 1.41e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.89 -6.35 1.91e+00 2.74e-01 1.10e+01 angle pdb=" CB LYS M 48 " pdb=" CG LYS M 48 " pdb=" CD LYS M 48 " ideal model delta sigma weight residual 111.30 118.73 -7.43 2.30e+00 1.89e-01 1.04e+01 angle pdb=" C GLU L 140 " pdb=" N TRP L 141 " pdb=" CA TRP L 141 " ideal model delta sigma weight residual 120.28 115.98 4.30 1.34e+00 5.57e-01 1.03e+01 angle pdb=" CA TRP L 141 " pdb=" CB TRP L 141 " pdb=" CG TRP L 141 " ideal model delta sigma weight residual 113.60 118.60 -5.00 1.90e+00 2.77e-01 6.93e+00 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.68: 7298 35.68 - 71.35: 1294 71.35 - 107.03: 17 107.03 - 142.70: 0 142.70 - 178.38: 2 Dihedral angle restraints: 8611 sinusoidal: 5471 harmonic: 3140 Sorted by residual: 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 38.38 -178.38 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 76.32 143.68 1 3.50e+01 8.16e-04 1.42e+01 dihedral pdb=" CA ARG L 131 " pdb=" C ARG L 131 " pdb=" N ASP L 132 " pdb=" CA ASP L 132 " ideal model delta harmonic sigma weight residual -180.00 -162.15 -17.85 0 5.00e+00 4.00e-02 1.27e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 1794 0.031 - 0.061: 526 0.061 - 0.092: 118 0.092 - 0.123: 66 0.123 - 0.153: 12 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.88e-01 chirality pdb=" CA GLN A 125 " pdb=" N GLN A 125 " pdb=" C GLN A 125 " pdb=" CB GLN A 125 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.78e-01 chirality pdb=" CA GLU K 25 " pdb=" N GLU K 25 " pdb=" C GLU K 25 " pdb=" CB GLU K 25 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.52e-01 ... (remaining 2513 not shown) Planarity restraints: 1796 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 141 " 0.030 2.00e-02 2.50e+03 2.98e-02 2.23e+01 pdb=" CG TRP L 141 " -0.081 2.00e-02 2.50e+03 pdb=" CD1 TRP L 141 " 0.037 2.00e-02 2.50e+03 pdb=" CD2 TRP L 141 " 0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP L 141 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 141 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 141 " 0.009 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 141 " 0.001 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 141 " 0.004 2.00e-02 2.50e+03 pdb=" CH2 TRP L 141 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " -0.022 2.00e-02 2.50e+03 9.23e-03 2.34e+00 pdb=" N9 DA I -35 " 0.018 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " -0.008 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " 0.005 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " 0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -54 " 0.020 2.00e-02 2.50e+03 9.03e-03 2.24e+00 pdb=" N9 DA I -54 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DA I -54 " -0.000 2.00e-02 2.50e+03 pdb=" N7 DA I -54 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DA I -54 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -54 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -54 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DA I -54 " -0.003 2.00e-02 2.50e+03 pdb=" C2 DA I -54 " -0.000 2.00e-02 2.50e+03 pdb=" N3 DA I -54 " -0.004 2.00e-02 2.50e+03 pdb=" C4 DA I -54 " -0.002 2.00e-02 2.50e+03 ... (remaining 1793 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.68: 413 2.68 - 3.24: 13032 3.24 - 3.79: 26278 3.79 - 4.35: 32109 4.35 - 4.90: 47543 Nonbonded interactions: 119375 Sorted by model distance: nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.131 2.496 nonbonded pdb=" OG SER A 57 " pdb=" OE1 GLU A 59 " model vdw 2.178 3.040 nonbonded pdb=" OG SER L 91 " pdb=" OE1 GLN L 92 " model vdw 2.221 3.040 nonbonded pdb=" OD1 ASP L 130 " pdb=" NZ LYS L 133 " model vdw 2.237 3.120 nonbonded pdb=" OE2 GLU A 94 " pdb=" NE2 GLN G 104 " model vdw 2.243 3.120 ... (remaining 119370 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: 1.090 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: 0.580 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 42.540 Find NCS groups from input model: 0.350 Set up NCS constraints: 0.080 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:3.000 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.910 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8374 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 15482 Z= 0.152 Angle : 0.574 7.753 22186 Z= 0.329 Chirality : 0.035 0.153 2516 Planarity : 0.004 0.037 1794 Dihedral : 25.638 178.379 6577 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 9.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 0.11 % Allowed : 0.22 % Favored : 99.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.26 (0.27), residues: 1057 helix: 2.63 (0.21), residues: 646 sheet: 0.85 (0.75), residues: 47 loop : -0.56 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.081 0.005 TRP L 141 HIS 0.005 0.001 HIS D 109 PHE 0.006 0.001 PHE D 70 TYR 0.018 0.001 TYR H 40 ARG 0.006 0.000 ARG L 131 Details of bonding type rmsd link_TRANS : bond 0.00088 ( 2) link_TRANS : angle 0.68680 ( 6) hydrogen bonds : bond 0.10388 ( 848) hydrogen bonds : angle 3.98729 ( 2154) metal coordination : bond 0.02151 ( 8) metal coordination : angle 3.91026 ( 9) covalent geometry : bond 0.00328 (15472) covalent geometry : angle 0.56875 (22171) *********************** 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 284 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 284 time to evaluate : 1.145 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 60 LEU cc_start: 0.9152 (mt) cc_final: 0.8940 (mt) REVERT: C 39 TYR cc_start: 0.8837 (m-80) cc_final: 0.8516 (m-80) REVERT: D 108 LYS cc_start: 0.8234 (ttpt) cc_final: 0.8001 (mtmt) REVERT: H 35 GLU cc_start: 0.8641 (mp0) cc_final: 0.8421 (mp0) REVERT: H 89 ILE cc_start: 0.9224 (mt) cc_final: 0.9005 (mt) REVERT: K 13 GLU cc_start: 0.8434 (tp30) cc_final: 0.8139 (tm-30) REVERT: L 60 TYR cc_start: 0.7143 (t80) cc_final: 0.6810 (t80) outliers start: 0 outliers final: 0 residues processed: 284 average time/residue: 0.3289 time to fit residues: 126.3865 Evaluate side-chains 226 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 226 time to evaluate : 1.145 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 1.9990 chunk 97 optimal weight: 4.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.9980 chunk 52 optimal weight: 0.0070 chunk 101 optimal weight: 6.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 1.9990 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 7.9990 overall best weight: 0.7600 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 38 ASN K 81 GLN K 83 HIS ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 46 GLN M 2 GLN M 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3696 r_free = 0.3696 target = 0.121298 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3020 r_free = 0.3020 target = 0.080647 restraints weight = 38775.486| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.083034 restraints weight = 26833.971| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3042 r_free = 0.3042 target = 0.082409 restraints weight = 19658.668| |-----------------------------------------------------------------------------| r_work (final): 0.3009 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3009 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3009 r_free = 0.3009 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3006 r_free = 0.3006 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3006 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8394 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 15482 Z= 0.162 Angle : 0.602 11.511 22186 Z= 0.337 Chirality : 0.036 0.161 2516 Planarity : 0.004 0.043 1794 Dihedral : 28.845 178.604 4413 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 8.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.13 % Favored : 96.87 % Rotamer: Outliers : 1.30 % Allowed : 13.20 % Favored : 85.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.23 (0.27), residues: 1057 helix: 2.61 (0.21), residues: 653 sheet: 0.57 (0.70), residues: 50 loop : -0.61 (0.33), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.066 0.004 TRP L 141 HIS 0.006 0.001 HIS L 75 PHE 0.014 0.001 PHE L 62 TYR 0.015 0.002 TYR L 74 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00085 ( 2) link_TRANS : angle 0.37143 ( 6) hydrogen bonds : bond 0.04379 ( 848) hydrogen bonds : angle 3.39731 ( 2154) metal coordination : bond 0.01553 ( 8) metal coordination : angle 6.13744 ( 9) covalent geometry : bond 0.00359 (15472) covalent geometry : angle 0.58897 (22171) *********************** 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 257 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 246 time to evaluate : 1.093 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9175 (t) cc_final: 0.7929 (t) REVERT: A 59 GLU cc_start: 0.8912 (pm20) cc_final: 0.8458 (pm20) REVERT: A 120 MET cc_start: 0.8142 (mtt) cc_final: 0.7853 (mtt) REVERT: A 125 GLN cc_start: 0.7927 (OUTLIER) cc_final: 0.7339 (pm20) REVERT: D 88 THR cc_start: 0.9392 (m) cc_final: 0.8957 (p) REVERT: D 108 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8093 (mtmt) REVERT: F 88 TYR cc_start: 0.8731 (m-80) cc_final: 0.8493 (m-80) REVERT: H 35 GLU cc_start: 0.8936 (mp0) cc_final: 0.8649 (mp0) REVERT: L 60 TYR cc_start: 0.7372 (t80) cc_final: 0.6973 (t80) REVERT: L 88 ILE cc_start: 0.8593 (mp) cc_final: 0.8381 (mp) outliers start: 11 outliers final: 8 residues processed: 251 average time/residue: 0.3015 time to fit residues: 105.3524 Evaluate side-chains 231 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 222 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 45 TYR Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 121 optimal weight: 6.9990 chunk 128 optimal weight: 0.0870 chunk 50 optimal weight: 1.9990 chunk 102 optimal weight: 0.0470 chunk 42 optimal weight: 0.5980 chunk 35 optimal weight: 0.5980 chunk 126 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 66 optimal weight: 0.9980 chunk 104 optimal weight: 2.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.4656 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 68 GLN G 38 ASN H 47 GLN K 32 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 55 HIS M 25 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.122507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3170 r_free = 0.3170 target = 0.089030 restraints weight = 64297.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.091003 restraints weight = 62599.541| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.091873 restraints weight = 31439.739| |-----------------------------------------------------------------------------| r_work (final): 0.3128 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3128 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.39 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3128 r_free = 0.3128 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3128 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8283 moved from start: 0.1626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15482 Z= 0.145 Angle : 0.574 12.258 22186 Z= 0.324 Chirality : 0.035 0.146 2516 Planarity : 0.004 0.044 1794 Dihedral : 28.911 178.726 4413 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 8.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 1.41 % Allowed : 14.61 % Favored : 83.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.18 (0.26), residues: 1057 helix: 2.56 (0.21), residues: 654 sheet: 0.83 (0.69), residues: 49 loop : -0.66 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 141 HIS 0.003 0.001 HIS K 65 PHE 0.013 0.001 PHE L 62 TYR 0.014 0.001 TYR E 99 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd link_TRANS : bond 0.00009 ( 2) link_TRANS : angle 0.32681 ( 6) hydrogen bonds : bond 0.04036 ( 848) hydrogen bonds : angle 3.25468 ( 2154) metal coordination : bond 0.01282 ( 8) metal coordination : angle 5.33982 ( 9) covalent geometry : bond 0.00314 (15472) covalent geometry : angle 0.56405 (22171) *********************** 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 251 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 239 time to evaluate : 1.128 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9062 (t) cc_final: 0.7805 (t) REVERT: A 59 GLU cc_start: 0.8758 (pm20) cc_final: 0.8136 (pm20) REVERT: A 120 MET cc_start: 0.8196 (mtt) cc_final: 0.7906 (mtt) REVERT: A 123 ASP cc_start: 0.8773 (m-30) cc_final: 0.8536 (m-30) REVERT: A 125 GLN cc_start: 0.7881 (OUTLIER) cc_final: 0.7203 (pm20) REVERT: B 63 GLU cc_start: 0.8280 (mt-10) cc_final: 0.8039 (mt-10) REVERT: D 88 THR cc_start: 0.9160 (m) cc_final: 0.8773 (p) REVERT: D 108 LYS cc_start: 0.8274 (ttpt) cc_final: 0.8021 (mtmt) REVERT: G 118 LYS cc_start: 0.8144 (tmtt) cc_final: 0.7891 (tmtt) REVERT: H 35 GLU cc_start: 0.8772 (mp0) cc_final: 0.8519 (mp0) REVERT: K 20 MET cc_start: 0.7546 (mmp) cc_final: 0.7319 (mmp) REVERT: L 60 TYR cc_start: 0.7338 (t80) cc_final: 0.7029 (t80) REVERT: L 88 ILE cc_start: 0.8355 (OUTLIER) cc_final: 0.8109 (mp) outliers start: 12 outliers final: 6 residues processed: 242 average time/residue: 0.3086 time to fit residues: 103.8415 Evaluate side-chains 223 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 215 time to evaluate : 1.113 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 105 optimal weight: 4.9990 chunk 18 optimal weight: 0.2980 chunk 52 optimal weight: 0.6980 chunk 72 optimal weight: 5.9990 chunk 90 optimal weight: 4.9990 chunk 6 optimal weight: 0.9980 chunk 103 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 60 optimal weight: 0.1980 chunk 98 optimal weight: 4.9990 chunk 121 optimal weight: 3.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 93 GLN E 68 GLN K 32 ASN K 41 GLN L 34 GLN L 46 GLN ** L 55 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** M 25 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.119059 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.084590 restraints weight = 56632.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.086767 restraints weight = 60263.109| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3105 r_free = 0.3105 target = 0.086949 restraints weight = 34554.893| |-----------------------------------------------------------------------------| r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3053 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.43 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3053 r_free = 0.3053 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3053 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.1899 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15482 Z= 0.191 Angle : 0.609 11.242 22186 Z= 0.339 Chirality : 0.036 0.169 2516 Planarity : 0.004 0.048 1794 Dihedral : 29.065 178.576 4413 Min Nonbonded Distance : 2.094 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.49 % Allowed : 16.67 % Favored : 80.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.27), residues: 1057 helix: 2.51 (0.21), residues: 653 sheet: 0.77 (0.67), residues: 48 loop : -0.73 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP L 141 HIS 0.004 0.001 HIS D 109 PHE 0.014 0.001 PHE L 62 TYR 0.036 0.002 TYR L 134 ARG 0.006 0.000 ARG G 71 Details of bonding type rmsd link_TRANS : bond 0.00128 ( 2) link_TRANS : angle 0.39327 ( 6) hydrogen bonds : bond 0.04657 ( 848) hydrogen bonds : angle 3.41478 ( 2154) metal coordination : bond 0.01795 ( 8) metal coordination : angle 5.92361 ( 9) covalent geometry : bond 0.00437 (15472) covalent geometry : angle 0.59711 (22171) *********************** 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 249 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 227 time to evaluate : 1.123 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9075 (t) cc_final: 0.7793 (t) REVERT: A 59 GLU cc_start: 0.8941 (pm20) cc_final: 0.8238 (pm20) REVERT: A 125 GLN cc_start: 0.7897 (OUTLIER) cc_final: 0.7153 (pm20) REVERT: B 63 GLU cc_start: 0.8349 (mt-10) cc_final: 0.8115 (mt-10) REVERT: B 88 TYR cc_start: 0.7647 (m-80) cc_final: 0.7297 (m-80) REVERT: D 33 ARG cc_start: 0.7654 (mtp-110) cc_final: 0.7442 (mtp-110) REVERT: D 108 LYS cc_start: 0.8379 (ttpt) cc_final: 0.8074 (mtmt) REVERT: F 84 MET cc_start: 0.8690 (mmm) cc_final: 0.8457 (mmm) REVERT: F 88 TYR cc_start: 0.8660 (m-80) cc_final: 0.8370 (m-80) REVERT: H 35 GLU cc_start: 0.8791 (mp0) cc_final: 0.8512 (mp0) REVERT: H 51 ASP cc_start: 0.8404 (OUTLIER) cc_final: 0.8159 (t0) REVERT: K 68 ARG cc_start: 0.6915 (mtm110) cc_final: 0.6487 (mtm110) REVERT: L 60 TYR cc_start: 0.7475 (t80) cc_final: 0.7143 (t80) REVERT: L 88 ILE cc_start: 0.8404 (OUTLIER) cc_final: 0.8188 (mp) outliers start: 22 outliers final: 15 residues processed: 232 average time/residue: 0.2949 time to fit residues: 95.6669 Evaluate side-chains 231 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 213 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 93 optimal weight: 4.9990 chunk 79 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 125 optimal weight: 8.9990 chunk 47 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 2 optimal weight: 0.9990 chunk 112 optimal weight: 8.9990 chunk 45 optimal weight: 0.0980 chunk 25 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN L 55 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.118493 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.081346 restraints weight = 52401.215| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083233 restraints weight = 37906.869| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.082612 restraints weight = 34522.150| |-----------------------------------------------------------------------------| r_work (final): 0.2993 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2993 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.15 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2993 r_free = 0.2993 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2993 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8399 moved from start: 0.2141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 15482 Z= 0.187 Angle : 0.611 11.800 22186 Z= 0.342 Chirality : 0.036 0.165 2516 Planarity : 0.004 0.050 1794 Dihedral : 29.077 179.082 4413 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 9.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 2.60 % Allowed : 18.40 % Favored : 79.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.93 (0.27), residues: 1057 helix: 2.40 (0.21), residues: 660 sheet: 0.34 (0.68), residues: 48 loop : -0.84 (0.33), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.041 0.003 TRP L 141 HIS 0.008 0.001 HIS K 65 PHE 0.014 0.001 PHE L 62 TYR 0.018 0.002 TYR H 40 ARG 0.005 0.000 ARG G 71 Details of bonding type rmsd link_TRANS : bond 0.00119 ( 2) link_TRANS : angle 0.41327 ( 6) hydrogen bonds : bond 0.04588 ( 848) hydrogen bonds : angle 3.37082 ( 2154) metal coordination : bond 0.01978 ( 8) metal coordination : angle 5.67824 ( 9) covalent geometry : bond 0.00427 (15472) covalent geometry : angle 0.60068 (22171) *********************** 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 249 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 1.120 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9112 (t) cc_final: 0.7810 (t) REVERT: A 59 GLU cc_start: 0.8994 (pm20) cc_final: 0.8059 (pm20) REVERT: A 125 GLN cc_start: 0.7858 (OUTLIER) cc_final: 0.7111 (pm20) REVERT: B 63 GLU cc_start: 0.8387 (mt-10) cc_final: 0.8098 (mt-10) REVERT: B 88 TYR cc_start: 0.8347 (m-80) cc_final: 0.7950 (m-80) REVERT: D 33 ARG cc_start: 0.7663 (mtp-110) cc_final: 0.7192 (mtm110) REVERT: D 108 LYS cc_start: 0.8404 (ttpt) cc_final: 0.8083 (mtpt) REVERT: E 39 HIS cc_start: 0.8328 (t-90) cc_final: 0.8071 (t-90) REVERT: F 88 TYR cc_start: 0.8815 (m-80) cc_final: 0.7153 (m-10) REVERT: H 35 GLU cc_start: 0.8894 (mp0) cc_final: 0.8547 (mp0) REVERT: H 51 ASP cc_start: 0.8517 (OUTLIER) cc_final: 0.8282 (t0) REVERT: H 83 TYR cc_start: 0.7568 (m-10) cc_final: 0.7142 (m-10) REVERT: K 41 GLN cc_start: 0.9372 (OUTLIER) cc_final: 0.8700 (tp40) REVERT: L 31 PHE cc_start: 0.8175 (m-80) cc_final: 0.7500 (t80) REVERT: L 88 ILE cc_start: 0.8536 (OUTLIER) cc_final: 0.8316 (mp) outliers start: 23 outliers final: 14 residues processed: 232 average time/residue: 0.2932 time to fit residues: 95.8498 Evaluate side-chains 234 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 216 time to evaluate : 1.213 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 70 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 56 optimal weight: 1.9990 chunk 25 optimal weight: 4.9990 chunk 96 optimal weight: 3.9990 chunk 99 optimal weight: 5.9990 chunk 39 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 85 optimal weight: 6.9990 chunk 51 optimal weight: 2.9990 chunk 118 optimal weight: 0.9980 chunk 98 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.116339 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3032 r_free = 0.3032 target = 0.081176 restraints weight = 54349.536| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.083538 restraints weight = 58170.718| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3047 r_free = 0.3047 target = 0.083426 restraints weight = 35829.858| |-----------------------------------------------------------------------------| r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2997 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8419 moved from start: 0.2492 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 15482 Z= 0.238 Angle : 0.662 12.226 22186 Z= 0.364 Chirality : 0.038 0.161 2516 Planarity : 0.004 0.051 1794 Dihedral : 29.195 179.092 4413 Min Nonbonded Distance : 2.100 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.61 % Favored : 96.39 % Rotamer: Outliers : 2.92 % Allowed : 19.05 % Favored : 78.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.62 (0.26), residues: 1057 helix: 2.16 (0.20), residues: 659 sheet: 0.25 (0.69), residues: 48 loop : -0.97 (0.32), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP L 141 HIS 0.011 0.001 HIS K 65 PHE 0.018 0.002 PHE L 62 TYR 0.021 0.002 TYR H 40 ARG 0.005 0.000 ARG H 31 Details of bonding type rmsd link_TRANS : bond 0.00198 ( 2) link_TRANS : angle 0.36376 ( 6) hydrogen bonds : bond 0.05318 ( 848) hydrogen bonds : angle 3.60178 ( 2154) metal coordination : bond 0.02640 ( 8) metal coordination : angle 6.25487 ( 9) covalent geometry : bond 0.00553 (15472) covalent geometry : angle 0.65026 (22171) *********************** 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 245 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 219 time to evaluate : 1.130 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9102 (t) cc_final: 0.7829 (t) REVERT: A 59 GLU cc_start: 0.8924 (pm20) cc_final: 0.8010 (pm20) REVERT: A 90 MET cc_start: 0.8720 (mmp) cc_final: 0.8446 (tpp) REVERT: A 125 GLN cc_start: 0.8066 (OUTLIER) cc_final: 0.7302 (pm20) REVERT: B 63 GLU cc_start: 0.8396 (mt-10) cc_final: 0.8174 (mt-10) REVERT: D 33 ARG cc_start: 0.7772 (mtp-110) cc_final: 0.7239 (mtm110) REVERT: D 108 LYS cc_start: 0.8479 (ttpt) cc_final: 0.8175 (mtpt) REVERT: F 88 TYR cc_start: 0.9024 (m-80) cc_final: 0.8657 (m-10) REVERT: H 35 GLU cc_start: 0.8821 (mp0) cc_final: 0.8482 (mp0) REVERT: H 51 ASP cc_start: 0.8497 (OUTLIER) cc_final: 0.8276 (t0) REVERT: K 41 GLN cc_start: 0.9324 (OUTLIER) cc_final: 0.8661 (tp40) REVERT: K 68 ARG cc_start: 0.6813 (mtm110) cc_final: 0.6324 (mtm110) REVERT: K 84 TYR cc_start: 0.7685 (m-80) cc_final: 0.6729 (m-80) REVERT: L 31 PHE cc_start: 0.8151 (m-80) cc_final: 0.7877 (m-80) REVERT: L 88 ILE cc_start: 0.8518 (OUTLIER) cc_final: 0.8294 (mp) outliers start: 26 outliers final: 18 residues processed: 233 average time/residue: 0.2900 time to fit residues: 94.9401 Evaluate side-chains 231 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 209 time to evaluate : 1.206 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 115 THR Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain K residue 76 LEU Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 36 THR Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.5980 chunk 123 optimal weight: 0.9990 chunk 52 optimal weight: 0.6980 chunk 128 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 44 optimal weight: 0.7980 chunk 118 optimal weight: 0.9980 chunk 111 optimal weight: 4.9990 chunk 0 optimal weight: 5.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 93 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.118326 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3049 r_free = 0.3049 target = 0.082127 restraints weight = 57806.612| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3082 r_free = 0.3082 target = 0.085588 restraints weight = 46213.488| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3071 r_free = 0.3071 target = 0.084882 restraints weight = 26145.639| |-----------------------------------------------------------------------------| r_work (final): 0.3027 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3032 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3032 r_free = 0.3032 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3032 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8356 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 15482 Z= 0.163 Angle : 0.620 12.423 22186 Z= 0.342 Chirality : 0.036 0.163 2516 Planarity : 0.004 0.051 1794 Dihedral : 29.090 179.968 4413 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 9.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.32 % Favored : 96.68 % Rotamer: Outliers : 3.03 % Allowed : 19.37 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.78 (0.27), residues: 1057 helix: 2.32 (0.21), residues: 660 sheet: 0.13 (0.70), residues: 48 loop : -0.97 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.057 0.004 TRP L 141 HIS 0.009 0.001 HIS K 65 PHE 0.014 0.001 PHE L 62 TYR 0.021 0.002 TYR L 134 ARG 0.006 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00055 ( 2) link_TRANS : angle 0.31460 ( 6) hydrogen bonds : bond 0.04465 ( 848) hydrogen bonds : angle 3.28485 ( 2154) metal coordination : bond 0.01914 ( 8) metal coordination : angle 5.53310 ( 9) covalent geometry : bond 0.00366 (15472) covalent geometry : angle 0.61017 (22171) *********************** 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 255 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 228 time to evaluate : 1.174 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9114 (t) cc_final: 0.8319 (t) REVERT: A 59 GLU cc_start: 0.8841 (pm20) cc_final: 0.7822 (pm20) REVERT: A 125 GLN cc_start: 0.7817 (OUTLIER) cc_final: 0.7054 (pm20) REVERT: B 63 GLU cc_start: 0.8402 (mt-10) cc_final: 0.8060 (mt-10) REVERT: D 33 ARG cc_start: 0.7787 (mtp-110) cc_final: 0.7566 (mtm110) REVERT: D 108 LYS cc_start: 0.8352 (ttpt) cc_final: 0.8023 (mtpt) REVERT: E 61 LEU cc_start: 0.9437 (OUTLIER) cc_final: 0.9126 (mm) REVERT: F 88 TYR cc_start: 0.8925 (m-80) cc_final: 0.8599 (m-10) REVERT: G 24 GLN cc_start: 0.8898 (mm-40) cc_final: 0.8686 (mm-40) REVERT: H 35 GLU cc_start: 0.8917 (mp0) cc_final: 0.8551 (mp0) REVERT: H 51 ASP cc_start: 0.8493 (OUTLIER) cc_final: 0.8271 (t0) REVERT: K 21 GLU cc_start: 0.7672 (mm-30) cc_final: 0.7439 (mm-30) REVERT: K 23 LEU cc_start: 0.7851 (mt) cc_final: 0.7576 (mp) REVERT: K 41 GLN cc_start: 0.9321 (OUTLIER) cc_final: 0.8739 (tp40) REVERT: K 84 TYR cc_start: 0.7695 (m-80) cc_final: 0.6743 (m-80) REVERT: L 31 PHE cc_start: 0.8200 (m-80) cc_final: 0.7874 (m-80) REVERT: L 88 ILE cc_start: 0.8509 (OUTLIER) cc_final: 0.8292 (mp) REVERT: L 144 LYS cc_start: 0.8681 (pttp) cc_final: 0.8465 (pttp) REVERT: M 1 MET cc_start: 0.5250 (tmm) cc_final: 0.4617 (tpt) outliers start: 27 outliers final: 16 residues processed: 238 average time/residue: 0.2860 time to fit residues: 96.3002 Evaluate side-chains 241 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 27 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 19 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 27 optimal weight: 0.9990 chunk 17 optimal weight: 8.9990 chunk 123 optimal weight: 0.0870 chunk 42 optimal weight: 0.9990 chunk 126 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 25 optimal weight: 0.0020 chunk 77 optimal weight: 3.9990 overall best weight: 0.5968 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 75 HIS K 41 GLN K 69 ASN ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3680 r_free = 0.3680 target = 0.120019 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.085242 restraints weight = 56141.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3112 r_free = 0.3112 target = 0.087578 restraints weight = 58280.375| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3119 r_free = 0.3119 target = 0.087792 restraints weight = 32790.490| |-----------------------------------------------------------------------------| r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3072 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3072 r_free = 0.3072 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 = 0.3072 r_free = 0.3072 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3072 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8337 moved from start: 0.2553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 15482 Z= 0.153 Angle : 0.622 13.098 22186 Z= 0.342 Chirality : 0.035 0.166 2516 Planarity : 0.004 0.050 1794 Dihedral : 29.068 179.438 4413 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 9.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.60 % Allowed : 21.10 % Favored : 76.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.82 (0.27), residues: 1057 helix: 2.40 (0.21), residues: 659 sheet: -0.14 (0.69), residues: 42 loop : -0.97 (0.32), residues: 356 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.090 0.005 TRP L 141 HIS 0.009 0.001 HIS K 65 PHE 0.017 0.001 PHE L 62 TYR 0.029 0.002 TYR L 145 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00046 ( 2) link_TRANS : angle 0.18396 ( 6) hydrogen bonds : bond 0.04235 ( 848) hydrogen bonds : angle 3.28119 ( 2154) metal coordination : bond 0.01761 ( 8) metal coordination : angle 5.29066 ( 9) covalent geometry : bond 0.00336 (15472) covalent geometry : angle 0.61324 (22171) *********************** 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 249 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 226 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9057 (t) cc_final: 0.8265 (t) REVERT: A 59 GLU cc_start: 0.8807 (pm20) cc_final: 0.7658 (pm20) REVERT: A 123 ASP cc_start: 0.8896 (m-30) cc_final: 0.8640 (m-30) REVERT: A 125 GLN cc_start: 0.7919 (OUTLIER) cc_final: 0.7221 (pm20) REVERT: B 63 GLU cc_start: 0.8364 (mt-10) cc_final: 0.8089 (mt-10) REVERT: B 88 TYR cc_start: 0.8532 (m-10) cc_final: 0.7445 (m-10) REVERT: D 108 LYS cc_start: 0.8303 (ttpt) cc_final: 0.7991 (mtmt) REVERT: E 61 LEU cc_start: 0.9399 (OUTLIER) cc_final: 0.9123 (mm) REVERT: G 24 GLN cc_start: 0.8763 (mm-40) cc_final: 0.8543 (mm-40) REVERT: H 35 GLU cc_start: 0.8781 (mp0) cc_final: 0.8494 (mp0) REVERT: H 40 TYR cc_start: 0.9184 (m-80) cc_final: 0.8668 (m-80) REVERT: K 23 LEU cc_start: 0.7708 (mt) cc_final: 0.7445 (mp) REVERT: K 41 GLN cc_start: 0.9287 (OUTLIER) cc_final: 0.8670 (tp40) REVERT: K 68 ARG cc_start: 0.6856 (mtm110) cc_final: 0.6271 (mtm110) REVERT: K 84 TYR cc_start: 0.7639 (m-80) cc_final: 0.6703 (m-80) REVERT: L 31 PHE cc_start: 0.8096 (m-80) cc_final: 0.7814 (m-80) REVERT: L 88 ILE cc_start: 0.8305 (OUTLIER) cc_final: 0.7993 (mp) REVERT: M 1 MET cc_start: 0.4763 (tmm) cc_final: 0.4166 (tpt) outliers start: 23 outliers final: 16 residues processed: 238 average time/residue: 0.2869 time to fit residues: 97.3763 Evaluate side-chains 236 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 216 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 82 optimal weight: 4.9990 chunk 117 optimal weight: 1.9990 chunk 73 optimal weight: 6.9990 chunk 17 optimal weight: 0.0670 chunk 40 optimal weight: 1.9990 chunk 23 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 94 optimal weight: 4.9990 chunk 49 optimal weight: 0.2980 chunk 37 optimal weight: 0.0470 chunk 84 optimal weight: 5.9990 overall best weight: 0.8820 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 75 HIS ** 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 = 0.3668 r_free = 0.3668 target = 0.119224 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.2990 r_free = 0.2990 target = 0.078984 restraints weight = 43295.758| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3007 r_free = 0.3007 target = 0.080227 restraints weight = 25692.303| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3001 r_free = 0.3001 target = 0.080137 restraints weight = 24043.440| |-----------------------------------------------------------------------------| r_work (final): 0.2969 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2969 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.02 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2969 r_free = 0.2969 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.2969 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8430 moved from start: 0.2606 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 15482 Z= 0.168 Angle : 0.647 13.337 22186 Z= 0.354 Chirality : 0.036 0.211 2516 Planarity : 0.004 0.049 1794 Dihedral : 29.091 179.029 4413 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 2.81 % Allowed : 21.00 % Favored : 76.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.27), residues: 1057 helix: 2.34 (0.21), residues: 660 sheet: 0.07 (0.70), residues: 48 loop : -0.98 (0.32), residues: 349 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.105 0.006 TRP L 141 HIS 0.009 0.001 HIS K 65 PHE 0.011 0.001 PHE L 62 TYR 0.028 0.002 TYR L 145 ARG 0.006 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00064 ( 2) link_TRANS : angle 0.21268 ( 6) hydrogen bonds : bond 0.04433 ( 848) hydrogen bonds : angle 3.33548 ( 2154) metal coordination : bond 0.01842 ( 8) metal coordination : angle 5.47489 ( 9) covalent geometry : bond 0.00379 (15472) covalent geometry : angle 0.63793 (22171) *********************** 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 248 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 223 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9121 (t) cc_final: 0.8379 (t) REVERT: A 59 GLU cc_start: 0.8815 (pm20) cc_final: 0.7677 (pm20) REVERT: A 123 ASP cc_start: 0.8896 (m-30) cc_final: 0.8631 (m-30) REVERT: A 125 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7225 (pm20) REVERT: B 63 GLU cc_start: 0.8422 (mt-10) cc_final: 0.8149 (mt-10) REVERT: B 88 TYR cc_start: 0.8566 (m-10) cc_final: 0.7309 (m-10) REVERT: D 59 MET cc_start: 0.8575 (tpp) cc_final: 0.7958 (tpp) REVERT: D 108 LYS cc_start: 0.8405 (ttpt) cc_final: 0.8096 (mtpt) REVERT: E 61 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9102 (mm) REVERT: G 24 GLN cc_start: 0.8841 (mm-40) cc_final: 0.8601 (mm-40) REVERT: H 35 GLU cc_start: 0.8866 (mp0) cc_final: 0.8524 (mp0) REVERT: H 40 TYR cc_start: 0.9247 (m-80) cc_final: 0.8740 (m-80) REVERT: H 51 ASP cc_start: 0.8468 (OUTLIER) cc_final: 0.8235 (t0) REVERT: K 23 LEU cc_start: 0.7866 (mt) cc_final: 0.7609 (mp) REVERT: K 41 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8577 (tp40) REVERT: K 84 TYR cc_start: 0.7719 (m-80) cc_final: 0.6744 (m-80) REVERT: L 31 PHE cc_start: 0.8232 (m-80) cc_final: 0.7918 (m-80) REVERT: L 88 ILE cc_start: 0.8433 (OUTLIER) cc_final: 0.8200 (mp) REVERT: M 1 MET cc_start: 0.5176 (tmm) cc_final: 0.4622 (tpt) outliers start: 25 outliers final: 16 residues processed: 233 average time/residue: 0.2901 time to fit residues: 96.0190 Evaluate side-chains 236 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 215 time to evaluate : 1.259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 45 optimal weight: 0.0870 chunk 101 optimal weight: 5.9990 chunk 115 optimal weight: 9.9990 chunk 33 optimal weight: 0.7980 chunk 120 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 34 optimal weight: 0.9990 chunk 62 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.9990 overall best weight: 0.6962 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** 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 = 0.3682 r_free = 0.3682 target = 0.120171 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 26)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.085134 restraints weight = 42479.091| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3091 r_free = 0.3091 target = 0.085864 restraints weight = 45181.094| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 24)----------------| | r_work = 0.3094 r_free = 0.3094 target = 0.085939 restraints weight = 45080.304| |-----------------------------------------------------------------------------| r_work (final): 0.3058 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3058 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3058 r_free = 0.3058 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 = 0.3058 r_free = 0.3058 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3058 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8353 moved from start: 0.2686 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 15482 Z= 0.160 Angle : 0.652 13.720 22186 Z= 0.358 Chirality : 0.036 0.258 2516 Planarity : 0.004 0.052 1794 Dihedral : 29.089 179.076 4413 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.08 % Favored : 95.92 % Rotamer: Outliers : 2.49 % Allowed : 21.43 % Favored : 76.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.27), residues: 1057 helix: 2.31 (0.21), residues: 661 sheet: -0.42 (0.68), residues: 42 loop : -0.99 (0.32), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.092 0.005 TRP L 141 HIS 0.009 0.001 HIS K 65 PHE 0.009 0.001 PHE L 62 TYR 0.022 0.002 TYR E 99 ARG 0.007 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00047 ( 2) link_TRANS : angle 0.16318 ( 6) hydrogen bonds : bond 0.04368 ( 848) hydrogen bonds : angle 3.36067 ( 2154) metal coordination : bond 0.01778 ( 8) metal coordination : angle 5.21310 ( 9) covalent geometry : bond 0.00357 (15472) covalent geometry : angle 0.64376 (22171) ********************** 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 247 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 225 time to evaluate : 1.234 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 57 SER cc_start: 0.9057 (t) cc_final: 0.8311 (t) REVERT: A 59 GLU cc_start: 0.8793 (pm20) cc_final: 0.7677 (pm20) REVERT: A 123 ASP cc_start: 0.8874 (m-30) cc_final: 0.8616 (m-30) REVERT: A 125 GLN cc_start: 0.7902 (OUTLIER) cc_final: 0.7236 (pm20) REVERT: B 88 TYR cc_start: 0.8557 (m-10) cc_final: 0.7356 (m-10) REVERT: D 108 LYS cc_start: 0.8329 (ttpt) cc_final: 0.8047 (mtpt) REVERT: E 61 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9135 (mm) REVERT: H 35 GLU cc_start: 0.8794 (mp0) cc_final: 0.8500 (mp0) REVERT: H 40 TYR cc_start: 0.9226 (m-80) cc_final: 0.8805 (m-80) REVERT: K 23 LEU cc_start: 0.7717 (mt) cc_final: 0.7478 (mp) REVERT: K 41 GLN cc_start: 0.9316 (OUTLIER) cc_final: 0.8723 (tp40) REVERT: K 68 ARG cc_start: 0.6672 (mtm110) cc_final: 0.5759 (mtm110) REVERT: K 84 TYR cc_start: 0.7625 (m-80) cc_final: 0.6682 (m-80) REVERT: L 4 LYS cc_start: 0.9061 (ptmt) cc_final: 0.8745 (pttt) REVERT: L 31 PHE cc_start: 0.8028 (m-80) cc_final: 0.7780 (m-80) REVERT: L 88 ILE cc_start: 0.8327 (OUTLIER) cc_final: 0.8029 (mp) REVERT: M 1 MET cc_start: 0.4880 (tmm) cc_final: 0.4351 (tpt) outliers start: 22 outliers final: 17 residues processed: 235 average time/residue: 0.2802 time to fit residues: 94.3029 Evaluate side-chains 241 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 220 time to evaluate : 1.268 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 46 VAL Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 81 VAL Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 61 LEU Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 16 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 115 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain L residue 26 VAL Chi-restraints excluded: chain L residue 88 ILE Chi-restraints excluded: chain M residue 68 HIS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 50 optimal weight: 0.0770 chunk 110 optimal weight: 3.9990 chunk 111 optimal weight: 8.9990 chunk 36 optimal weight: 5.9990 chunk 83 optimal weight: 5.9990 chunk 115 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 chunk 80 optimal weight: 3.9990 chunk 108 optimal weight: 4.9990 chunk 30 optimal weight: 0.9990 overall best weight: 1.9344 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 32 ASN ** K 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3707 r_free = 0.3707 target = 0.121115 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3225 r_free = 0.3225 target = 0.090777 restraints weight = 71062.280| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 26)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.091760 restraints weight = 71710.593| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3215 r_free = 0.3215 target = 0.093609 restraints weight = 32839.959| |-----------------------------------------------------------------------------| r_work (final): 0.3138 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3137 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3137 r_free = 0.3137 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.03 number of occupancies < 0.1: 4 | |-----------------------------------------------------------------------------| r_final: 0.3137 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2846 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.074 15482 Z= 0.257 Angle : 0.721 12.995 22186 Z= 0.394 Chirality : 0.040 0.224 2516 Planarity : 0.005 0.046 1794 Dihedral : 29.261 178.271 4413 Min Nonbonded Distance : 2.115 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.27 % Allowed : 22.19 % Favored : 75.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.43 (0.26), residues: 1057 helix: 2.08 (0.21), residues: 657 sheet: -0.08 (0.71), residues: 48 loop : -1.12 (0.32), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.085 0.005 TRP L 141 HIS 0.010 0.001 HIS K 65 PHE 0.013 0.002 PHE L 62 TYR 0.032 0.002 TYR H 83 ARG 0.004 0.000 ARG D 86 Details of bonding type rmsd link_TRANS : bond 0.00215 ( 2) link_TRANS : angle 0.26639 ( 6) hydrogen bonds : bond 0.05465 ( 848) hydrogen bonds : angle 3.72767 ( 2154) metal coordination : bond 0.02648 ( 8) metal coordination : angle 6.22388 ( 9) covalent geometry : bond 0.00597 (15472) covalent geometry : angle 0.71015 (22171) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4639.54 seconds wall clock time: 80 minutes 59.65 seconds (4859.65 seconds total)