Starting phenix.real_space_refine on Sun Nov 17 17:44:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/11_2024/8sn4_40612.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/11_2024/8sn4_40612.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/11_2024/8sn4_40612.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/11_2024/8sn4_40612.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/11_2024/8sn4_40612.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn4_40612/11_2024/8sn4_40612.cif" } resolution = 3.7 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= 0.004 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Zn 2 6.06 5 P 294 5.49 5 S 33 5.16 5 C 8269 2.51 5 N 2713 2.21 5 O 3289 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 8 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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 33.347 72.273 47.031 1.00 86.22 S ATOM 12446 SG CYS K 51 34.177 68.839 45.573 1.00 81.44 S ATOM 12470 SG CYS K 54 33.180 71.557 43.284 1.00 91.27 S ATOM 12187 SG CYS K 16 23.217 66.833 52.909 1.00107.40 S ATOM 12205 SG CYS K 19 21.018 64.361 54.707 1.00109.20 S ATOM 12335 SG CYS K 36 24.056 65.730 56.569 1.00 99.38 S ATOM 12357 SG CYS K 39 24.585 63.331 53.903 1.00 91.82 S Residues with excluded nonbonded symmetry interactions: 4 residue: pdb=" N LEU M 73 " occ=0.45 ... (6 atoms not shown) pdb=" CD2 LEU M 73 " occ=0.45 residue: pdb=" N ARG M 74 " occ=0.45 ... (9 atoms not shown) pdb=" NH2 ARG M 74 " occ=0.45 residue: pdb=" N GLY M 75 " occ=0.25 ... (2 atoms not shown) pdb=" O GLY M 75 " occ=0.25 residue: pdb=" N GLY M 76 " occ=0.25 ... (3 atoms not shown) pdb=" OXT GLY M 76 " occ=0.25 Time building chain proxies: 9.45, per 1000 atoms: 0.65 Number of scatterers: 14600 At special positions: 0 Unit cell: (111.552, 131.472, 126.16, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Zn 2 29.99 S 33 16.00 P 294 15.00 O 3289 8.00 N 2713 7.00 C 8269 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.74 Conformation dependent library (CDL) restraints added in 1.5 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 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 9 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2028 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 12 sheets defined 63.5% alpha, 5.2% beta 135 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 7.17 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.624A pdb=" N LEU A 48 " --> pdb=" O GLY A 44 " (cutoff:3.500A) removed outlier: 3.553A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.634A pdb=" N PHE A 67 " --> pdb=" O ARG A 63 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.196A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N LYS A 79 " --> pdb=" O ALA A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 Processing helix chain 'B' and resid 24 through 29 removed outlier: 3.864A pdb=" N GLN B 27 " --> pdb=" O ASP B 24 " (cutoff:3.500A) Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.996A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.705A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 46 through 73 removed outlier: 3.664A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.642A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 91 through 97 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 83 Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.624A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 123 removed outlier: 3.709A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 55 removed outlier: 3.766A pdb=" N LEU E 48 " --> pdb=" O GLY E 44 " (cutoff:3.500A) removed outlier: 3.815A pdb=" N ARG E 49 " --> pdb=" O THR E 45 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.835A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.512A pdb=" N VAL E 89 " --> pdb=" O GLN E 85 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 50 through 76 removed outlier: 3.744A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.559A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) removed outlier: 3.522A pdb=" N GLN F 93 " --> pdb=" O ALA F 89 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 27 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 90 removed outlier: 3.536A pdb=" N ASP G 90 " --> pdb=" O ALA G 86 " (cutoff:3.500A) Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.581A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.730A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 122 Processing helix chain 'K' and resid 36 through 47 Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.933A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 4.130A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 91 removed outlier: 3.567A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 removed outlier: 3.509A pdb=" N ARG L 5 " --> pdb=" O MET L 1 " (cutoff:3.500A) Processing helix chain 'L' and resid 86 through 91 Processing helix chain 'L' and resid 98 through 112 Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.581A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 131 through 147 removed outlier: 4.138A pdb=" N ILE L 137 " --> pdb=" O LYS L 133 " (cutoff:3.500A) removed outlier: 4.444A pdb=" N GLN L 143 " --> pdb=" O ARG L 139 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N LYS L 144 " --> pdb=" O GLU L 140 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 55 through 60 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.926A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.521A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.910A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.378A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.165A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.578A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 21 through 24 Processing sheet with id=AB3, first strand: chain 'M' and resid 12 through 16 removed outlier: 9.416A pdb=" N LEU M 67 " --> pdb=" O GLN M 2 " (cutoff:3.500A) removed outlier: 6.828A pdb=" N PHE M 4 " --> pdb=" O LEU M 67 " (cutoff:3.500A) removed outlier: 7.820A pdb=" N LEU M 69 " --> pdb=" O PHE M 4 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N LYS M 6 " --> pdb=" O LEU M 69 " (cutoff:3.500A) removed outlier: 8.222A pdb=" N LEU M 71 " --> pdb=" O LYS M 6 " (cutoff:3.500A) 495 hydrogen bonds defined for protein. 1443 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 5.40 Time building geometry restraints manager: 4.19 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 3478 1.34 - 1.46: 4329 1.46 - 1.58: 7030 1.58 - 1.70: 586 1.70 - 1.82: 49 Bond restraints: 15472 Sorted by residual: bond pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 1.457 1.475 -0.018 1.29e-02 6.01e+03 1.96e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.455 -0.033 3.00e-02 1.11e+03 1.22e+00 bond pdb=" CG LEU E 126 " pdb=" CD1 LEU E 126 " ideal model delta sigma weight residual 1.521 1.487 0.034 3.30e-02 9.18e+02 1.08e+00 bond pdb=" C3' DT J -67 " pdb=" C2' DT J -67 " ideal model delta sigma weight residual 1.525 1.545 -0.020 2.00e-02 2.50e+03 1.04e+00 bond pdb=" CG LEU B 58 " pdb=" CD1 LEU B 58 " ideal model delta sigma weight residual 1.521 1.491 0.030 3.30e-02 9.18e+02 8.48e-01 ... (remaining 15467 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.85: 21747 1.85 - 3.69: 393 3.69 - 5.54: 24 5.54 - 7.39: 5 7.39 - 9.23: 2 Bond angle restraints: 22171 Sorted by residual: angle pdb=" CA ARG L 136 " pdb=" CB ARG L 136 " pdb=" CG ARG L 136 " ideal model delta sigma weight residual 114.10 121.54 -7.44 2.00e+00 2.50e-01 1.39e+01 angle pdb=" C ARG B 23 " pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 121.54 127.70 -6.16 1.91e+00 2.74e-01 1.04e+01 angle pdb=" CA LEU K 49 " pdb=" CB LEU K 49 " pdb=" CG LEU K 49 " ideal model delta sigma weight residual 116.30 125.53 -9.23 3.50e+00 8.16e-02 6.96e+00 angle pdb=" C THR A 80 " pdb=" N ASP A 81 " pdb=" CA ASP A 81 " ideal model delta sigma weight residual 121.54 126.38 -4.84 1.91e+00 2.74e-01 6.43e+00 angle pdb=" CB LYS C 118 " pdb=" CG LYS C 118 " pdb=" CD LYS C 118 " ideal model delta sigma weight residual 111.30 116.81 -5.51 2.30e+00 1.89e-01 5.73e+00 ... (remaining 22166 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.62: 7268 35.62 - 71.24: 1312 71.24 - 106.86: 23 106.86 - 142.48: 0 142.48 - 178.10: 2 Dihedral angle restraints: 8605 sinusoidal: 5467 harmonic: 3138 Sorted by residual: dihedral pdb=" CA ASP L 29 " pdb=" C ASP L 29 " pdb=" N MET L 30 " pdb=" CA MET L 30 " ideal model delta harmonic sigma weight residual -180.00 -160.11 -19.89 0 5.00e+00 4.00e-02 1.58e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.10 -178.10 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 20 " pdb=" C3' DG J 20 " pdb=" O3' DG J 20 " pdb=" P DG J 21 " ideal model delta sinusoidal sigma weight residual 220.00 74.08 145.92 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 8602 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 2231 0.052 - 0.105: 247 0.105 - 0.157: 36 0.157 - 0.209: 1 0.209 - 0.262: 1 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CB ILE L 137 " pdb=" CA ILE L 137 " pdb=" CG1 ILE L 137 " pdb=" CG2 ILE L 137 " both_signs ideal model delta sigma weight residual False 2.64 2.38 0.26 2.00e-01 2.50e+01 1.71e+00 chirality pdb=" CA ARG L 136 " pdb=" N ARG L 136 " pdb=" C ARG L 136 " pdb=" CB ARG L 136 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.18 2.00e-01 2.50e+01 7.85e-01 chirality pdb=" CA ASP A 81 " pdb=" N ASP A 81 " pdb=" C ASP A 81 " pdb=" CB ASP A 81 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.04e-01 ... (remaining 2513 not shown) Planarity restraints: 1794 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP L 33 " 0.017 2.00e-02 2.50e+03 1.41e-02 4.96e+00 pdb=" CG TRP L 33 " -0.038 2.00e-02 2.50e+03 pdb=" CD1 TRP L 33 " 0.015 2.00e-02 2.50e+03 pdb=" CD2 TRP L 33 " -0.000 2.00e-02 2.50e+03 pdb=" NE1 TRP L 33 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 TRP L 33 " 0.000 2.00e-02 2.50e+03 pdb=" CE3 TRP L 33 " 0.002 2.00e-02 2.50e+03 pdb=" CZ2 TRP L 33 " 0.004 2.00e-02 2.50e+03 pdb=" CZ3 TRP L 33 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP L 33 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LYS K 37 " 0.032 5.00e-02 4.00e+02 4.93e-02 3.89e+00 pdb=" N PRO K 38 " -0.085 5.00e-02 4.00e+02 pdb=" CA PRO K 38 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO K 38 " 0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG A 42 " -0.030 5.00e-02 4.00e+02 4.54e-02 3.30e+00 pdb=" N PRO A 43 " 0.079 5.00e-02 4.00e+02 pdb=" CA PRO A 43 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 43 " -0.025 5.00e-02 4.00e+02 ... (remaining 1791 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1953 2.76 - 3.47: 19799 3.47 - 4.19: 38184 4.19 - 4.90: 59543 Nonbonded interactions: 119481 Sorted by model distance: nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.331 3.350 nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.331 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.136 2.496 nonbonded pdb=" O ASP L 87 " pdb=" OG SER L 91 " model vdw 2.213 3.040 nonbonded pdb=" ND2 ASN A 108 " pdb=" O GLY B 42 " model vdw 2.222 3.120 ... (remaining 119476 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 102) selection = (chain 'F' and (resid 21 through 101 or (resid 102 and (name N or name CA or nam \ e C or name O )))) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 11 through 118) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 115 or resid 117 throu \ gh 123)) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.17 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.750 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: 0.560 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 41.920 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.070 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: 0.010 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8330 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 0.034 15472 Z= 0.176 Angle : 0.552 9.232 22171 Z= 0.321 Chirality : 0.034 0.262 2516 Planarity : 0.004 0.049 1794 Dihedral : 25.751 178.102 6577 Min Nonbonded Distance : 1.331 Molprobity Statistics. All-atom Clashscore : 8.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.28 % Favored : 97.72 % Rotamer: Outliers : 0.00 % Allowed : 0.43 % Favored : 99.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.84 (0.26), residues: 1057 helix: 2.28 (0.21), residues: 643 sheet: 1.82 (0.76), residues: 48 loop : -0.85 (0.30), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.038 0.003 TRP L 33 HIS 0.007 0.001 HIS L 55 PHE 0.009 0.001 PHE D 65 TYR 0.022 0.001 TYR H 40 ARG 0.008 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2114 Ramachandran restraints generated. 1057 Oldfield, 0 Emsley, 1057 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 213 time to evaluate : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8469 (m110) cc_final: 0.8112 (m110) REVERT: C 11 SER cc_start: 0.8505 (t) cc_final: 0.8201 (p) REVERT: D 40 TYR cc_start: 0.9159 (m-80) cc_final: 0.8378 (m-80) REVERT: D 51 ASP cc_start: 0.7966 (p0) cc_final: 0.7740 (p0) REVERT: F 74 GLU cc_start: 0.8136 (tm-30) cc_final: 0.7890 (tm-30) REVERT: L 7 ASN cc_start: 0.9106 (m-40) cc_final: 0.8813 (m110) REVERT: M 1 MET cc_start: 0.8023 (tmm) cc_final: 0.7345 (tmm) outliers start: 0 outliers final: 0 residues processed: 213 average time/residue: 0.3372 time to fit residues: 98.1436 Evaluate side-chains 164 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 164 time to evaluate : 1.191 ------------------------------------------------------------------------------- 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: 4.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 2.9990 chunk 33 optimal weight: 0.6980 chunk 65 optimal weight: 4.9990 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 0.0370 chunk 39 optimal weight: 0.5980 chunk 61 optimal weight: 0.5980 chunk 75 optimal weight: 3.9990 chunk 117 optimal weight: 0.0970 overall best weight: 0.4056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS M 2 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8333 moved from start: 0.0973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 15472 Z= 0.179 Angle : 0.560 8.829 22171 Z= 0.323 Chirality : 0.035 0.176 2516 Planarity : 0.004 0.051 1794 Dihedral : 28.717 178.207 4413 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 1.30 % Allowed : 10.50 % Favored : 88.20 % 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: 2.07 (0.26), residues: 1057 helix: 2.45 (0.21), residues: 648 sheet: 2.17 (0.79), residues: 51 loop : -0.86 (0.30), residues: 358 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.003 TRP L 33 HIS 0.009 0.001 HIS K 83 PHE 0.015 0.001 PHE L 50 TYR 0.018 0.001 TYR H 40 ARG 0.005 0.000 ARG D 86 *********************** 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 184 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 172 time to evaluate : 1.177 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: B 25 ASN cc_start: 0.8438 (m110) cc_final: 0.8196 (m110) REVERT: C 99 ARG cc_start: 0.7734 (mmt180) cc_final: 0.7498 (mmt180) REVERT: D 40 TYR cc_start: 0.9187 (m-80) cc_final: 0.8398 (m-80) REVERT: D 51 ASP cc_start: 0.7910 (p0) cc_final: 0.7696 (p0) REVERT: F 74 GLU cc_start: 0.8140 (tm-30) cc_final: 0.7758 (tm-30) REVERT: F 88 TYR cc_start: 0.8647 (m-10) cc_final: 0.8190 (m-10) REVERT: G 74 LYS cc_start: 0.8933 (mtmt) cc_final: 0.8669 (mttm) REVERT: H 62 MET cc_start: 0.8771 (mmm) cc_final: 0.8516 (mmm) REVERT: L 7 ASN cc_start: 0.9261 (m-40) cc_final: 0.9055 (m110) REVERT: L 32 HIS cc_start: 0.6604 (m90) cc_final: 0.6215 (m90) REVERT: L 81 ASN cc_start: 0.8140 (p0) cc_final: 0.7912 (p0) REVERT: M 1 MET cc_start: 0.7907 (tmm) cc_final: 0.7234 (tmm) outliers start: 12 outliers final: 8 residues processed: 176 average time/residue: 0.2995 time to fit residues: 74.7373 Evaluate side-chains 169 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 161 time to evaluate : 1.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 109 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 3.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 117 optimal weight: 3.9990 chunk 126 optimal weight: 10.0000 chunk 104 optimal weight: 1.9990 chunk 116 optimal weight: 6.9990 chunk 40 optimal weight: 2.9990 chunk 94 optimal weight: 3.9990 overall best weight: 3.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 83 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1863 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.073 15472 Z= 0.592 Angle : 0.728 10.605 22171 Z= 0.411 Chirality : 0.046 0.179 2516 Planarity : 0.006 0.050 1794 Dihedral : 29.306 176.081 4413 Min Nonbonded Distance : 1.998 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.70 % Favored : 96.30 % Rotamer: Outliers : 3.79 % Allowed : 12.55 % Favored : 83.66 % 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: 1.21 (0.25), residues: 1057 helix: 1.78 (0.20), residues: 644 sheet: 1.48 (0.74), residues: 53 loop : -1.14 (0.30), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP L 33 HIS 0.005 0.001 HIS E 113 PHE 0.020 0.003 PHE D 70 TYR 0.047 0.003 TYR H 83 ARG 0.007 0.001 ARG E 131 *********************** 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 214 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 179 time to evaluate : 1.114 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8527 (m110) cc_final: 0.8326 (m110) REVERT: D 51 ASP cc_start: 0.7908 (p0) cc_final: 0.7595 (p0) REVERT: D 116 LYS cc_start: 0.8678 (tppt) cc_final: 0.8437 (ttmm) REVERT: E 59 GLU cc_start: 0.8344 (OUTLIER) cc_final: 0.7862 (pm20) REVERT: E 86 SER cc_start: 0.8775 (m) cc_final: 0.8551 (p) REVERT: F 73 THR cc_start: 0.9468 (t) cc_final: 0.9206 (m) REVERT: F 74 GLU cc_start: 0.8099 (tm-30) cc_final: 0.7601 (tm-30) REVERT: F 88 TYR cc_start: 0.8534 (m-10) cc_final: 0.8041 (m-10) REVERT: K 46 LYS cc_start: 0.9035 (mttp) cc_final: 0.8798 (mttm) REVERT: L 4 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8273 (ptpt) REVERT: L 8 LYS cc_start: 0.8590 (mttp) cc_final: 0.8380 (mttp) REVERT: L 32 HIS cc_start: 0.7743 (m90) cc_final: 0.7503 (m90) REVERT: L 63 LYS cc_start: 0.9040 (mttp) cc_final: 0.8662 (mttp) REVERT: L 79 ASN cc_start: 0.7322 (m-40) cc_final: 0.7013 (m110) REVERT: L 81 ASN cc_start: 0.8057 (p0) cc_final: 0.7822 (p0) REVERT: M 1 MET cc_start: 0.7971 (tmm) cc_final: 0.7162 (tmm) outliers start: 35 outliers final: 24 residues processed: 198 average time/residue: 0.3299 time to fit residues: 90.5158 Evaluate side-chains 193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 50 ILE Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain D residue 119 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 59 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain E residue 119 ILE Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 54 ILE Chi-restraints excluded: chain H residue 118 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 4 LYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain L residue 110 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 10.0000 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 0.7980 chunk 12 optimal weight: 0.0970 chunk 56 optimal weight: 0.8980 chunk 78 optimal weight: 3.9990 chunk 117 optimal weight: 0.8980 chunk 124 optimal weight: 7.9990 chunk 61 optimal weight: 0.5980 chunk 111 optimal weight: 4.9990 chunk 33 optimal weight: 0.6980 overall best weight: 0.6178 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS E 108 ASN K 83 HIS L 55 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8413 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15472 Z= 0.194 Angle : 0.569 9.693 22171 Z= 0.328 Chirality : 0.035 0.171 2516 Planarity : 0.004 0.046 1794 Dihedral : 28.979 179.476 4413 Min Nonbonded Distance : 2.064 Molprobity Statistics. All-atom Clashscore : 6.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.47 % Favored : 97.53 % Rotamer: Outliers : 2.60 % Allowed : 16.34 % Favored : 81.06 % 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: 1.75 (0.26), residues: 1057 helix: 2.30 (0.21), residues: 648 sheet: 1.51 (0.77), residues: 48 loop : -1.09 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP L 141 HIS 0.004 0.001 HIS E 113 PHE 0.019 0.001 PHE L 50 TYR 0.029 0.002 TYR H 40 ARG 0.006 0.000 ARG G 99 *********************** 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 197 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 173 time to evaluate : 1.220 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8476 (m110) cc_final: 0.8182 (m110) REVERT: B 74 GLU cc_start: 0.7953 (tt0) cc_final: 0.7737 (mt-10) REVERT: C 61 GLU cc_start: 0.9167 (tp30) cc_final: 0.8966 (tp30) REVERT: D 40 TYR cc_start: 0.9178 (m-80) cc_final: 0.8466 (m-80) REVERT: D 51 ASP cc_start: 0.8049 (p0) cc_final: 0.7831 (p0) REVERT: F 73 THR cc_start: 0.9476 (t) cc_final: 0.9210 (m) REVERT: F 74 GLU cc_start: 0.8085 (tm-30) cc_final: 0.7584 (tm-30) REVERT: G 13 LYS cc_start: 0.8792 (mmtt) cc_final: 0.8487 (mmtt) REVERT: G 24 GLN cc_start: 0.8579 (mm-40) cc_final: 0.8290 (mm-40) REVERT: H 68 ASP cc_start: 0.9050 (t70) cc_final: 0.8676 (t0) REVERT: K 83 HIS cc_start: 0.7477 (OUTLIER) cc_final: 0.6791 (t-90) REVERT: L 8 LYS cc_start: 0.8663 (mttp) cc_final: 0.8423 (mttp) REVERT: L 79 ASN cc_start: 0.7285 (m-40) cc_final: 0.7005 (m110) REVERT: L 81 ASN cc_start: 0.8313 (p0) cc_final: 0.8111 (p0) REVERT: M 1 MET cc_start: 0.7813 (tmm) cc_final: 0.7019 (tmm) outliers start: 24 outliers final: 14 residues processed: 182 average time/residue: 0.3152 time to fit residues: 80.3275 Evaluate side-chains 181 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 166 time to evaluate : 1.218 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 66 LYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 0.9990 chunk 70 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 51 optimal weight: 0.7980 chunk 106 optimal weight: 0.7980 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 63 optimal weight: 4.9990 chunk 111 optimal weight: 1.9990 chunk 31 optimal weight: 1.9990 overall best weight: 1.1184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8440 moved from start: 0.1826 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 15472 Z= 0.258 Angle : 0.588 9.249 22171 Z= 0.336 Chirality : 0.036 0.169 2516 Planarity : 0.005 0.046 1794 Dihedral : 29.051 178.055 4413 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.04 % Favored : 96.96 % Rotamer: Outliers : 2.71 % Allowed : 17.32 % Favored : 79.98 % 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: 1.76 (0.26), residues: 1057 helix: 2.31 (0.21), residues: 648 sheet: 1.36 (0.77), residues: 48 loop : -1.06 (0.30), residues: 361 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP L 141 HIS 0.005 0.001 HIS K 83 PHE 0.019 0.002 PHE L 50 TYR 0.039 0.002 TYR H 83 ARG 0.006 0.000 ARG D 86 *********************** 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 195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 170 time to evaluate : 1.229 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8522 (m110) cc_final: 0.8242 (m110) REVERT: C 61 GLU cc_start: 0.9138 (tp30) cc_final: 0.8644 (tp30) REVERT: D 40 TYR cc_start: 0.9267 (m-80) cc_final: 0.8550 (m-80) REVERT: D 51 ASP cc_start: 0.7928 (p0) cc_final: 0.7670 (p0) REVERT: F 73 THR cc_start: 0.9499 (t) cc_final: 0.9242 (m) REVERT: F 74 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7579 (tm-30) REVERT: H 68 ASP cc_start: 0.9089 (t70) cc_final: 0.8735 (t0) REVERT: L 63 LYS cc_start: 0.9035 (mttp) cc_final: 0.8698 (mttp) REVERT: L 79 ASN cc_start: 0.7228 (m-40) cc_final: 0.6909 (m110) REVERT: M 1 MET cc_start: 0.7859 (tmm) cc_final: 0.7057 (tmm) outliers start: 25 outliers final: 19 residues processed: 181 average time/residue: 0.2943 time to fit residues: 75.5532 Evaluate side-chains 183 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 164 time to evaluate : 1.142 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 130 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 52 LEU Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Chi-restraints excluded: chain M residue 23 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.8980 chunk 112 optimal weight: 0.0000 chunk 24 optimal weight: 0.6980 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.6980 chunk 124 optimal weight: 7.9990 chunk 103 optimal weight: 2.9990 chunk 57 optimal weight: 0.5980 chunk 10 optimal weight: 0.8980 chunk 65 optimal weight: 0.8980 chunk 120 optimal weight: 10.0000 overall best weight: 0.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8400 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 15472 Z= 0.188 Angle : 0.566 9.597 22171 Z= 0.324 Chirality : 0.035 0.167 2516 Planarity : 0.004 0.044 1794 Dihedral : 28.958 178.626 4413 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.16 % Allowed : 18.83 % 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 (0.26), residues: 1057 helix: 2.46 (0.21), residues: 649 sheet: 1.20 (0.77), residues: 48 loop : -1.01 (0.31), residues: 360 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.044 0.005 TRP L 141 HIS 0.003 0.001 HIS L 75 PHE 0.019 0.001 PHE L 50 TYR 0.026 0.001 TYR H 40 ARG 0.006 0.000 ARG D 86 *********************** 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 193 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 173 time to evaluate : 1.236 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8529 (m110) cc_final: 0.8234 (m110) REVERT: C 61 GLU cc_start: 0.9127 (tp30) cc_final: 0.8897 (tp30) REVERT: D 40 TYR cc_start: 0.9195 (m-80) cc_final: 0.8488 (m-80) REVERT: D 51 ASP cc_start: 0.8033 (p0) cc_final: 0.7808 (p0) REVERT: E 59 GLU cc_start: 0.7934 (pt0) cc_final: 0.7661 (pm20) REVERT: F 73 THR cc_start: 0.9511 (t) cc_final: 0.9257 (m) REVERT: F 74 GLU cc_start: 0.8103 (tm-30) cc_final: 0.7561 (tm-30) REVERT: H 47 GLN cc_start: 0.8557 (tt0) cc_final: 0.8024 (mt0) REVERT: H 68 ASP cc_start: 0.9068 (t70) cc_final: 0.8706 (t0) REVERT: L 30 MET cc_start: 0.7452 (tpp) cc_final: 0.7061 (tpp) REVERT: L 38 MET cc_start: 0.7943 (OUTLIER) cc_final: 0.6792 (mpp) REVERT: L 63 LYS cc_start: 0.9056 (mttp) cc_final: 0.8739 (mttp) REVERT: M 1 MET cc_start: 0.7882 (tmm) cc_final: 0.7075 (tmm) outliers start: 20 outliers final: 17 residues processed: 180 average time/residue: 0.3144 time to fit residues: 80.4331 Evaluate side-chains 189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 171 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.9990 chunk 71 optimal weight: 0.7980 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.7980 chunk 105 optimal weight: 0.2980 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 9.9990 chunk 77 optimal weight: 3.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.5980 chunk 76 optimal weight: 4.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 24 GLN H 47 GLN L 55 HIS L 79 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.1907 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 15472 Z= 0.195 Angle : 0.570 9.825 22171 Z= 0.325 Chirality : 0.035 0.176 2516 Planarity : 0.004 0.044 1794 Dihedral : 28.948 178.459 4413 Min Nonbonded Distance : 2.067 Molprobity Statistics. All-atom Clashscore : 6.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 2.27 % Allowed : 20.02 % Favored : 77.71 % 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: 1.92 (0.26), residues: 1057 helix: 2.46 (0.21), residues: 650 sheet: 0.92 (0.72), residues: 53 loop : -1.02 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.052 0.004 TRP L 33 HIS 0.008 0.001 HIS K 83 PHE 0.020 0.001 PHE L 50 TYR 0.026 0.001 TYR H 40 ARG 0.007 0.000 ARG D 86 *********************** 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 195 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 174 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8539 (m110) cc_final: 0.8242 (m110) REVERT: C 61 GLU cc_start: 0.9123 (tp30) cc_final: 0.8879 (tp30) REVERT: D 40 TYR cc_start: 0.9258 (m-80) cc_final: 0.8519 (m-80) REVERT: D 51 ASP cc_start: 0.8031 (p0) cc_final: 0.7801 (p0) REVERT: E 59 GLU cc_start: 0.7929 (pt0) cc_final: 0.7637 (pm20) REVERT: F 73 THR cc_start: 0.9532 (t) cc_final: 0.9287 (m) REVERT: F 74 GLU cc_start: 0.8112 (tm-30) cc_final: 0.7559 (tm-30) REVERT: H 68 ASP cc_start: 0.9075 (t70) cc_final: 0.8685 (t0) REVERT: L 102 VAL cc_start: 0.9225 (t) cc_final: 0.9006 (t) REVERT: M 1 MET cc_start: 0.7869 (tmm) cc_final: 0.7040 (tmm) outliers start: 21 outliers final: 16 residues processed: 182 average time/residue: 0.3039 time to fit residues: 77.8245 Evaluate side-chains 188 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 172 time to evaluate : 1.101 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9980 chunk 74 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.6980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 2.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 47 GLN K 83 HIS L 55 HIS ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8465 moved from start: 0.2133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 15472 Z= 0.351 Angle : 0.630 9.908 22171 Z= 0.356 Chirality : 0.038 0.172 2516 Planarity : 0.005 0.048 1794 Dihedral : 29.149 177.403 4413 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer: Outliers : 2.71 % Allowed : 20.13 % Favored : 77.16 % 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: 1.63 (0.26), residues: 1057 helix: 2.23 (0.21), residues: 647 sheet: 0.93 (0.72), residues: 53 loop : -1.14 (0.31), residues: 357 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.003 TRP L 33 HIS 0.006 0.001 HIS L 55 PHE 0.021 0.002 PHE L 50 TYR 0.034 0.002 TYR H 40 ARG 0.006 0.001 ARG D 86 *********************** 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 196 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 171 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8523 (m110) cc_final: 0.8288 (m110) REVERT: C 61 GLU cc_start: 0.9152 (tp30) cc_final: 0.8669 (tp30) REVERT: D 51 ASP cc_start: 0.7971 (p0) cc_final: 0.7694 (p0) REVERT: F 73 THR cc_start: 0.9543 (t) cc_final: 0.9307 (m) REVERT: F 74 GLU cc_start: 0.8117 (tm-30) cc_final: 0.7546 (tm-30) REVERT: H 68 ASP cc_start: 0.9099 (t70) cc_final: 0.8778 (t0) REVERT: H 83 TYR cc_start: 0.8311 (m-10) cc_final: 0.8031 (m-10) REVERT: M 1 MET cc_start: 0.7787 (tmm) cc_final: 0.6902 (tmm) outliers start: 25 outliers final: 19 residues processed: 182 average time/residue: 0.3396 time to fit residues: 86.9705 Evaluate side-chains 189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 170 time to evaluate : 1.175 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain K residue 83 HIS Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 6.9990 chunk 115 optimal weight: 5.9990 chunk 119 optimal weight: 0.0270 chunk 69 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 104 optimal weight: 0.1980 chunk 109 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 overall best weight: 0.9040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 HIS L 46 GLN L 79 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8427 moved from start: 0.2123 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 15472 Z= 0.231 Angle : 0.597 9.901 22171 Z= 0.337 Chirality : 0.036 0.161 2516 Planarity : 0.005 0.047 1794 Dihedral : 29.058 178.501 4413 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer: Outliers : 2.38 % Allowed : 20.78 % Favored : 76.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 1.70 (0.26), residues: 1057 helix: 2.29 (0.21), residues: 651 sheet: 0.92 (0.72), residues: 53 loop : -1.14 (0.31), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.004 TRP L 33 HIS 0.004 0.001 HIS L 55 PHE 0.029 0.002 PHE M 45 TYR 0.028 0.002 TYR H 40 ARG 0.007 0.000 ARG D 86 *********************** 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 194 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 172 time to evaluate : 1.173 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8508 (m110) cc_final: 0.8222 (m110) REVERT: C 61 GLU cc_start: 0.9161 (tp30) cc_final: 0.8674 (tp30) REVERT: D 40 TYR cc_start: 0.9247 (m-80) cc_final: 0.8526 (m-80) REVERT: D 51 ASP cc_start: 0.7995 (p0) cc_final: 0.7759 (p0) REVERT: F 73 THR cc_start: 0.9531 (t) cc_final: 0.9280 (m) REVERT: F 74 GLU cc_start: 0.8105 (tm-30) cc_final: 0.7542 (tm-30) REVERT: H 47 GLN cc_start: 0.8547 (tt0) cc_final: 0.8204 (mt0) REVERT: H 68 ASP cc_start: 0.9096 (t70) cc_final: 0.8734 (t0) REVERT: L 60 TYR cc_start: 0.8532 (t80) cc_final: 0.8299 (t80) REVERT: M 1 MET cc_start: 0.7787 (tmm) cc_final: 0.7066 (tmm) outliers start: 22 outliers final: 19 residues processed: 181 average time/residue: 0.3242 time to fit residues: 81.4386 Evaluate side-chains 190 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 171 time to evaluate : 1.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 38 MET Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 103 LEU Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 85 optimal weight: 5.9990 chunk 128 optimal weight: 8.9990 chunk 118 optimal weight: 0.6980 chunk 102 optimal weight: 2.9990 chunk 10 optimal weight: 0.8980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 0.0770 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 overall best weight: 1.3342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 83 HIS L 46 GLN ** M 41 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2216 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 15472 Z= 0.291 Angle : 0.621 9.935 22171 Z= 0.349 Chirality : 0.037 0.292 2516 Planarity : 0.005 0.047 1794 Dihedral : 29.127 177.853 4413 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 6.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.06 % Allowed : 21.21 % Favored : 76.73 % 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: 1.59 (0.26), residues: 1057 helix: 2.22 (0.21), residues: 650 sheet: 0.81 (0.72), residues: 53 loop : -1.21 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.003 TRP L 33 HIS 0.005 0.001 HIS L 55 PHE 0.021 0.002 PHE L 50 TYR 0.032 0.002 TYR H 40 ARG 0.007 0.000 ARG D 86 ********************** 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 192 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 173 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 25 ASN cc_start: 0.8528 (m110) cc_final: 0.8213 (m110) REVERT: C 61 GLU cc_start: 0.9166 (tp30) cc_final: 0.8670 (tp30) REVERT: D 40 TYR cc_start: 0.9269 (m-80) cc_final: 0.8597 (m-80) REVERT: D 51 ASP cc_start: 0.8005 (p0) cc_final: 0.7767 (p0) REVERT: F 73 THR cc_start: 0.9532 (t) cc_final: 0.9281 (m) REVERT: F 74 GLU cc_start: 0.8116 (tm-30) cc_final: 0.7546 (tm-30) REVERT: H 68 ASP cc_start: 0.9088 (t70) cc_final: 0.8768 (t0) REVERT: K 83 HIS cc_start: 0.8181 (t-90) cc_final: 0.7723 (m170) REVERT: L 60 TYR cc_start: 0.8570 (t80) cc_final: 0.8348 (t80) REVERT: M 1 MET cc_start: 0.7749 (tmm) cc_final: 0.7036 (tmm) outliers start: 19 outliers final: 17 residues processed: 182 average time/residue: 0.3208 time to fit residues: 81.6995 Evaluate side-chains 189 residues out of total 918 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 172 time to evaluate : 1.152 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 82 THR Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 118 VAL Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 82 LEU Chi-restraints excluded: chain F residue 82 THR Chi-restraints excluded: chain G residue 18 SER Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain K residue 51 CYS Chi-restraints excluded: chain L residue 51 PHE Chi-restraints excluded: chain L residue 85 CYS Chi-restraints excluded: chain L residue 92 GLN Chi-restraints excluded: chain L residue 109 LEU Chi-restraints excluded: chain M residue 3 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.5980 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.8980 chunk 28 optimal weight: 0.6980 chunk 102 optimal weight: 0.9990 chunk 42 optimal weight: 0.5980 chunk 105 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 18 optimal weight: 0.5980 chunk 89 optimal weight: 3.9990 chunk 5 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 46 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3724 r_free = 0.3724 target = 0.140416 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3050 r_free = 0.3050 target = 0.092219 restraints weight = 37120.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3028 r_free = 0.3028 target = 0.091758 restraints weight = 22528.943| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 25)----------------| | r_work = 0.3041 r_free = 0.3041 target = 0.092786 restraints weight = 18936.902| |-----------------------------------------------------------------------------| r_work (final): 0.3000 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3000 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3000 r_free = 0.3000 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.17 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2997 r_free = 0.2997 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2997 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.2190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 15472 Z= 0.196 Angle : 0.590 10.161 22171 Z= 0.333 Chirality : 0.035 0.176 2516 Planarity : 0.005 0.050 1794 Dihedral : 29.002 178.828 4413 Min Nonbonded Distance : 2.072 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 1.95 % Allowed : 21.10 % Favored : 76.95 % 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: 1.75 (0.27), residues: 1057 helix: 2.37 (0.21), residues: 650 sheet: 0.68 (0.71), residues: 53 loop : -1.16 (0.31), residues: 354 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.004 TRP L 33 HIS 0.006 0.001 HIS K 65 PHE 0.020 0.001 PHE L 50 TYR 0.025 0.002 TYR H 40 ARG 0.007 0.000 ARG D 86 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2499.79 seconds wall clock time: 46 minutes 42.25 seconds (2802.25 seconds total)