Starting phenix.real_space_refine on Mon Jul 22 06:42:26 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u13_41800/07_2024/8u13_41800_neut.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u13_41800/07_2024/8u13_41800.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u13_41800/07_2024/8u13_41800.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u13_41800/07_2024/8u13_41800.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u13_41800/07_2024/8u13_41800_neut.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u13_41800/07_2024/8u13_41800_neut.cif" } resolution = 3.8 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= 0.002 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 5925 atoms to isotropic. 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 293 5.49 5 S 25 5.16 5 C 7139 2.51 5 N 2408 2.21 5 O 2958 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A TYR 99": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 106": "OD1" <-> "OD2" Residue "B GLU 52": "OE1" <-> "OE2" Residue "D ASP 68": "OD1" <-> "OD2" Residue "D GLU 71": "OE1" <-> "OE2" Residue "D GLU 76": "OE1" <-> "OE2" Residue "D TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 59": "OE1" <-> "OE2" Residue "E PHE 67": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 73": "OE1" <-> "OE2" Residue "E ASP 77": "OD1" <-> "OD2" Residue "E PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 105": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 93": "OE1" <-> "OE2" Residue "K GLU 45": "OE1" <-> "OE2" Residue "K TYR 64": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 50": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 92": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 12825 Number of models: 1 Model: "" Number of chains: 12 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: "D" Number of atoms: 751 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 751 Classifications: {'peptide': 95} Link IDs: {'PTRANS': 2, 'TRANS': 92} 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: "H" Number of atoms: 737 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: 735 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: 3010 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3010 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 706 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} Conformer: "B" Number of residues, atoms: 88, 702 Classifications: {'peptide': 88} Link IDs: {'PTRANS': 6, 'TRANS': 81} bond proxies already assigned to first conformer: 713 Chain: "C" 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: "G" Number of atoms: 843 Number of conformers: 1 Conformer: "" Number of residues, atoms: 110, 843 Classifications: {'peptide': 110} Link IDs: {'PTRANS': 5, 'TRANS': 104} 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 10617 SG CYS K 31 27.021 59.998 74.288 1.00394.38 S ATOM 10767 SG CYS K 51 26.391 63.713 73.415 1.00417.10 S ATOM 10791 SG CYS K 54 27.019 62.691 77.048 1.00421.64 S ATOM 10508 SG CYS K 16 19.411 66.329 66.379 1.00424.33 S ATOM 10526 SG CYS K 19 18.344 69.167 64.157 1.00433.92 S ATOM 10656 SG CYS K 36 20.356 66.435 62.624 1.00418.58 S ATOM 10678 SG CYS K 39 21.999 68.761 65.379 1.00418.47 S Time building chain proxies: 7.56, per 1000 atoms: 0.59 Number of scatterers: 12825 At special positions: 0 Unit cell: (103.788, 117.146, 117.146, 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 25 16.00 P 293 15.00 O 2958 8.00 N 2408 7.00 C 7139 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.43 Conformation dependent library (CDL) restraints added in 1.7 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 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " Number of angles added : 9 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1612 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 11 sheets defined 68.9% alpha, 2.6% beta 141 base pairs and 245 stacking pairs defined. Time for finding SS restraints: 6.01 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 Processing helix chain 'A' and resid 85 through 114 removed outlier: 3.756A pdb=" N ALA A 114 " --> pdb=" O CYS A 110 " (cutoff:3.500A) Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.685A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.498A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N ALA B 76 " --> pdb=" O TYR B 72 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.528A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 103 through 123 Processing helix chain 'E' and resid 44 through 56 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 132 removed outlier: 3.657A pdb=" N GLY E 132 " --> pdb=" O ARG E 128 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 Processing helix chain 'F' and resid 30 through 41 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.933A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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: 3.654A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 Processing helix chain 'K' and resid 36 through 45 Processing helix chain 'K' and resid 58 through 68 removed outlier: 4.417A 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: 4.140A pdb=" N ARG K 91 " --> pdb=" O GLU K 87 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 27 through 37 Processing helix chain 'C' and resid 46 through 73 Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 91 through 98 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: 3.543A 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 'G' and resid 112 through 116 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.449A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA4, first strand: chain 'D' and resid 53 through 54 removed outlier: 7.391A pdb=" N GLY D 53 " --> pdb=" O ILE C 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'D' and resid 88 through 89 Processing sheet with id=AA6, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.545A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA8, first strand: chain 'F' and resid 97 through 98 removed outlier: 3.565A pdb=" N TYR F 98 " --> pdb=" O THR C 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'H' and resid 53 through 54 removed outlier: 7.296A pdb=" N GLY H 53 " --> pdb=" O ILE G 78 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'H' and resid 88 through 89 Processing sheet with id=AB2, first strand: chain 'K' and resid 27 through 28 removed outlier: 3.579A pdb=" N VAL K 27 " --> pdb=" O LEU K 35 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N LEU K 35 " --> pdb=" O VAL K 27 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 432 hydrogen bonds defined for protein. 1273 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 359 hydrogen bonds 714 hydrogen bond angles 0 basepair planarities 141 basepair parallelities 245 stacking parallelities Total time for adding SS restraints: 4.53 Time building geometry restraints manager: 6.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 2525 1.33 - 1.45: 4369 1.45 - 1.57: 6137 1.57 - 1.69: 584 1.69 - 1.81: 36 Bond restraints: 13651 Sorted by residual: bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.467 -0.045 3.00e-02 1.11e+03 2.24e+00 bond pdb=" CG GLU B 63 " pdb=" CD GLU B 63 " ideal model delta sigma weight residual 1.516 1.480 0.036 2.50e-02 1.60e+03 2.05e+00 bond pdb=" N ASP B 24 " pdb=" CA ASP B 24 " ideal model delta sigma weight residual 1.457 1.475 -0.017 1.29e-02 6.01e+03 1.80e+00 bond pdb=" CB ARG F 39 " pdb=" CG ARG F 39 " ideal model delta sigma weight residual 1.520 1.486 0.034 3.00e-02 1.11e+03 1.32e+00 bond pdb=" CG1 ILE G 62 " pdb=" CD1 ILE G 62 " ideal model delta sigma weight residual 1.513 1.471 0.042 3.90e-02 6.57e+02 1.17e+00 ... (remaining 13646 not shown) Histogram of bond angle deviations from ideal: 98.52 - 105.61: 1439 105.61 - 112.71: 7618 112.71 - 119.80: 4591 119.80 - 126.89: 5251 126.89 - 133.98: 793 Bond angle restraints: 19692 Sorted by residual: angle pdb=" N GLU B 63 " pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " ideal model delta sigma weight residual 110.28 116.80 -6.52 1.55e+00 4.16e-01 1.77e+01 angle pdb=" C LEU B 62 " pdb=" N GLU B 63 " pdb=" CA GLU B 63 " ideal model delta sigma weight residual 120.31 114.63 5.68 1.52e+00 4.33e-01 1.40e+01 angle pdb=" CA GLU B 63 " pdb=" CB GLU B 63 " pdb=" CG GLU B 63 " ideal model delta sigma weight residual 114.10 120.77 -6.67 2.00e+00 2.50e-01 1.11e+01 angle pdb=" C SER H 112 " pdb=" N GLU H 113 " pdb=" CA GLU H 113 " ideal model delta sigma weight residual 121.14 115.58 5.56 1.75e+00 3.27e-01 1.01e+01 angle pdb=" C GLU E 50 " pdb=" CA GLU E 50 " pdb=" CB GLU E 50 " ideal model delta sigma weight residual 109.72 115.15 -5.43 1.92e+00 2.71e-01 8.00e+00 ... (remaining 19687 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.48: 6090 34.48 - 68.96: 1363 68.96 - 103.44: 28 103.44 - 137.92: 0 137.92 - 172.40: 2 Dihedral angle restraints: 7483 sinusoidal: 4986 harmonic: 2497 Sorted by residual: dihedral pdb=" CA GLU E 50 " pdb=" C GLU E 50 " pdb=" N ILE E 51 " pdb=" CA ILE E 51 " ideal model delta harmonic sigma weight residual 180.00 151.88 28.12 0 5.00e+00 4.00e-02 3.16e+01 dihedral pdb=" CA ARG E 63 " pdb=" C ARG E 63 " pdb=" N LYS E 64 " pdb=" CA LYS E 64 " ideal model delta harmonic sigma weight residual -180.00 -158.92 -21.08 0 5.00e+00 4.00e-02 1.78e+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 220.00 47.60 172.40 1 3.50e+01 8.16e-04 1.56e+01 ... (remaining 7480 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1866 0.045 - 0.091: 309 0.091 - 0.136: 61 0.136 - 0.181: 4 0.181 - 0.226: 1 Chirality restraints: 2241 Sorted by residual: chirality pdb=" CA GLU E 50 " pdb=" N GLU E 50 " pdb=" C GLU E 50 " pdb=" CB GLU E 50 " both_signs ideal model delta sigma weight residual False 2.51 2.28 0.23 2.00e-01 2.50e+01 1.28e+00 chirality pdb=" CB ILE E 51 " pdb=" CA ILE E 51 " pdb=" CG1 ILE E 51 " pdb=" CG2 ILE E 51 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.18 2.00e-01 2.50e+01 7.97e-01 chirality pdb=" CA TYR E 54 " pdb=" N TYR E 54 " pdb=" C TYR E 54 " pdb=" CB TYR E 54 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.95e-01 ... (remaining 2238 not shown) Planarity restraints: 1475 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG E 129 " 0.169 9.50e-02 1.11e+02 7.58e-02 3.72e+00 pdb=" NE ARG E 129 " -0.007 2.00e-02 2.50e+03 pdb=" CZ ARG E 129 " -0.010 2.00e-02 2.50e+03 pdb=" NH1 ARG E 129 " 0.001 2.00e-02 2.50e+03 pdb=" NH2 ARG E 129 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLU H 113 " 0.008 2.00e-02 2.50e+03 1.67e-02 2.80e+00 pdb=" CD GLU H 113 " -0.029 2.00e-02 2.50e+03 pdb=" OE1 GLU H 113 " 0.010 2.00e-02 2.50e+03 pdb=" OE2 GLU H 113 " 0.010 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 48 " 0.022 2.00e-02 2.50e+03 9.15e-03 2.51e+00 pdb=" N9 DG I 48 " -0.019 2.00e-02 2.50e+03 pdb=" C8 DG I 48 " -0.008 2.00e-02 2.50e+03 pdb=" N7 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C5 DG I 48 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 48 " 0.006 2.00e-02 2.50e+03 pdb=" N1 DG I 48 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 48 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" N3 DG I 48 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 48 " -0.002 2.00e-02 2.50e+03 ... (remaining 1472 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1763 2.76 - 3.47: 18828 3.47 - 4.19: 36553 4.19 - 4.90: 53847 Nonbonded interactions: 110993 Sorted by model distance: nonbonded pdb=" C SER D 123 " pdb=" N SER C 11 " model vdw 1.330 3.350 nonbonded pdb=" C SER H 123 " pdb=" N SER G 11 " model vdw 1.332 3.350 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.145 2.520 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.153 2.496 nonbonded pdb=" OE1 GLU D 71 " pdb=" OH TYR C 39 " model vdw 2.180 2.440 ... (remaining 110988 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' 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 119) } ncs_group { reference = (chain 'D' and (resid 31 through 107 or resid 109 through 123)) selection = (chain 'H' and (resid 31 through 107 or resid 109 through 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=0.00 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: 1.240 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.510 Check model and map are aligned: 0.090 Set scattering table: 0.130 Process input model: 44.800 Find NCS groups from input model: 0.340 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.840 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8410 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 : 0.004 0.045 13651 Z= 0.193 Angle : 0.638 7.991 19692 Z= 0.368 Chirality : 0.036 0.226 2241 Planarity : 0.005 0.076 1475 Dihedral : 27.097 172.397 5871 Min Nonbonded Distance : 1.330 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.50 % Favored : 97.50 % Rotamer: Outliers : 0.00 % Allowed : 0.41 % Favored : 99.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.79 (0.28), residues: 842 helix: 1.16 (0.21), residues: 580 sheet: None (None), residues: 0 loop : -0.84 (0.37), residues: 262 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.004 0.001 HIS K 65 PHE 0.009 0.001 PHE G 25 TYR 0.021 0.002 TYR B 88 ARG 0.015 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 347 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 347 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7812 (mt-10) cc_final: 0.7092 (mt-10) REVERT: A 125 GLN cc_start: 0.9259 (mp10) cc_final: 0.8940 (mp10) REVERT: B 23 ARG cc_start: 0.8496 (mmp80) cc_final: 0.8126 (mmp80) REVERT: B 25 ASN cc_start: 0.8800 (m110) cc_final: 0.8440 (m110) REVERT: B 49 LEU cc_start: 0.9349 (pt) cc_final: 0.8356 (pt) REVERT: B 50 ILE cc_start: 0.9347 (tp) cc_final: 0.9047 (tp) REVERT: B 88 TYR cc_start: 0.8364 (m-80) cc_final: 0.8101 (m-80) REVERT: D 34 LYS cc_start: 0.8971 (mptt) cc_final: 0.8688 (mmtm) REVERT: D 57 LYS cc_start: 0.8926 (mmtt) cc_final: 0.8600 (mmmm) REVERT: D 105 GLU cc_start: 0.8261 (tp30) cc_final: 0.7678 (tp30) REVERT: D 109 HIS cc_start: 0.8834 (m170) cc_final: 0.8628 (m170) REVERT: D 120 LYS cc_start: 0.9231 (tttp) cc_final: 0.8842 (ttmm) REVERT: E 53 ARG cc_start: 0.8788 (tmt-80) cc_final: 0.8330 (tmt-80) REVERT: E 54 TYR cc_start: 0.7863 (m-80) cc_final: 0.7639 (m-80) REVERT: E 57 SER cc_start: 0.7526 (p) cc_final: 0.6916 (p) REVERT: E 59 GLU cc_start: 0.8178 (pm20) cc_final: 0.7882 (pm20) REVERT: E 60 LEU cc_start: 0.8664 (mm) cc_final: 0.8015 (mm) REVERT: E 68 GLN cc_start: 0.8675 (pp30) cc_final: 0.8321 (pp30) REVERT: E 81 ASP cc_start: 0.8075 (m-30) cc_final: 0.7859 (m-30) REVERT: E 92 LEU cc_start: 0.9668 (mt) cc_final: 0.9462 (mt) REVERT: E 120 MET cc_start: 0.7832 (mtt) cc_final: 0.7405 (mtp) REVERT: E 125 GLN cc_start: 0.8554 (mp10) cc_final: 0.8001 (mp10) REVERT: F 49 LEU cc_start: 0.8913 (mm) cc_final: 0.8215 (mm) REVERT: H 68 ASP cc_start: 0.8399 (t70) cc_final: 0.8061 (t0) REVERT: H 83 TYR cc_start: 0.8409 (m-10) cc_final: 0.7681 (m-10) REVERT: C 84 GLN cc_start: 0.9172 (tm-30) cc_final: 0.8811 (tp-100) REVERT: G 61 GLU cc_start: 0.8032 (mm-30) cc_final: 0.7763 (mm-30) REVERT: G 68 ASN cc_start: 0.8959 (m-40) cc_final: 0.8649 (m-40) REVERT: G 104 GLN cc_start: 0.8967 (mp10) cc_final: 0.8679 (mp10) outliers start: 0 outliers final: 0 residues processed: 347 average time/residue: 0.2862 time to fit residues: 133.7599 Evaluate side-chains 289 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 289 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 1.9990 chunk 82 optimal weight: 4.9990 chunk 45 optimal weight: 3.9990 chunk 28 optimal weight: 9.9990 chunk 55 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 85 optimal weight: 5.9990 chunk 33 optimal weight: 0.1980 chunk 51 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 chunk 98 optimal weight: 20.0000 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN B 93 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 67 ASN H 82 HIS H 84 ASN C 89 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13651 Z= 0.286 Angle : 0.648 7.832 19692 Z= 0.373 Chirality : 0.037 0.158 2241 Planarity : 0.005 0.035 1475 Dihedral : 30.184 173.084 4161 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.44 % Allowed : 17.06 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.90 (0.29), residues: 842 helix: 1.34 (0.21), residues: 581 sheet: None (None), residues: 0 loop : -1.05 (0.37), residues: 261 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 77 HIS 0.004 0.001 HIS B 75 PHE 0.018 0.002 PHE H 65 TYR 0.020 0.002 TYR H 40 ARG 0.010 0.001 ARG G 29 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 295 time to evaluate : 0.977 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7894 (mt-10) cc_final: 0.6978 (mt-10) REVERT: A 125 GLN cc_start: 0.9246 (mp10) cc_final: 0.8919 (mp10) REVERT: B 23 ARG cc_start: 0.8566 (mmp80) cc_final: 0.8172 (mmp80) REVERT: B 25 ASN cc_start: 0.8749 (m110) cc_final: 0.8095 (m110) REVERT: B 88 TYR cc_start: 0.8633 (m-10) cc_final: 0.8340 (m-80) REVERT: D 31 ARG cc_start: 0.8109 (mmp80) cc_final: 0.7854 (mmp80) REVERT: D 34 LYS cc_start: 0.9096 (mptt) cc_final: 0.8812 (mmtm) REVERT: D 57 LYS cc_start: 0.8981 (mmtt) cc_final: 0.8735 (mmmm) REVERT: D 79 ARG cc_start: 0.7974 (mtm110) cc_final: 0.7585 (mtm110) REVERT: D 105 GLU cc_start: 0.8411 (tp30) cc_final: 0.7851 (tp30) REVERT: D 120 LYS cc_start: 0.9270 (tttp) cc_final: 0.8857 (ttmm) REVERT: E 60 LEU cc_start: 0.8802 (mm) cc_final: 0.8383 (mm) REVERT: E 68 GLN cc_start: 0.8846 (pp30) cc_final: 0.8519 (pp30) REVERT: E 97 GLU cc_start: 0.8180 (mt-10) cc_final: 0.7750 (mt-10) REVERT: F 88 TYR cc_start: 0.8517 (m-10) cc_final: 0.7451 (m-10) REVERT: H 68 ASP cc_start: 0.8545 (t70) cc_final: 0.8241 (t0) REVERT: H 83 TYR cc_start: 0.8299 (m-10) cc_final: 0.7484 (m-10) REVERT: H 86 ARG cc_start: 0.9043 (tpp80) cc_final: 0.8843 (tpp80) REVERT: H 120 LYS cc_start: 0.9432 (ttmt) cc_final: 0.9053 (tptt) REVERT: C 78 ILE cc_start: 0.9002 (mm) cc_final: 0.8757 (mm) REVERT: G 104 GLN cc_start: 0.9039 (mp10) cc_final: 0.8688 (mp10) outliers start: 25 outliers final: 17 residues processed: 304 average time/residue: 0.3086 time to fit residues: 128.3133 Evaluate side-chains 291 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 274 time to evaluate : 1.036 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 6.9990 chunk 30 optimal weight: 4.9990 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 8.9990 chunk 27 optimal weight: 10.0000 chunk 99 optimal weight: 6.9990 chunk 107 optimal weight: 4.9990 chunk 88 optimal weight: 10.0000 chunk 98 optimal weight: 0.9990 chunk 33 optimal weight: 4.9990 chunk 79 optimal weight: 10.0000 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN C 73 ASN C 89 ASN ** G 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8558 moved from start: 0.2419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.059 13651 Z= 0.437 Angle : 0.714 7.774 19692 Z= 0.408 Chirality : 0.041 0.162 2241 Planarity : 0.005 0.035 1475 Dihedral : 30.537 173.918 4161 Min Nonbonded Distance : 2.053 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 6.46 % Allowed : 19.94 % Favored : 73.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.60 (0.28), residues: 842 helix: 1.15 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -1.29 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 61 HIS 0.007 0.001 HIS B 75 PHE 0.031 0.002 PHE E 67 TYR 0.023 0.003 TYR H 40 ARG 0.010 0.001 ARG C 99 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 272 time to evaluate : 1.023 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 93 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8394 (tp40) REVERT: A 125 GLN cc_start: 0.9201 (mp10) cc_final: 0.8840 (mp10) REVERT: B 23 ARG cc_start: 0.8553 (mmp80) cc_final: 0.8208 (mmp80) REVERT: B 25 ASN cc_start: 0.8738 (m110) cc_final: 0.8319 (m-40) REVERT: D 31 ARG cc_start: 0.8222 (mmp80) cc_final: 0.7852 (mmp80) REVERT: D 34 LYS cc_start: 0.9204 (mptt) cc_final: 0.8880 (mmtm) REVERT: D 57 LYS cc_start: 0.9031 (mmtt) cc_final: 0.8817 (mmmm) REVERT: D 76 GLU cc_start: 0.9065 (tp30) cc_final: 0.8831 (tp30) REVERT: D 79 ARG cc_start: 0.8164 (OUTLIER) cc_final: 0.7698 (mtm110) REVERT: D 105 GLU cc_start: 0.8487 (tp30) cc_final: 0.7563 (tp30) REVERT: D 120 LYS cc_start: 0.9256 (tttp) cc_final: 0.8904 (ttmm) REVERT: E 60 LEU cc_start: 0.8864 (mm) cc_final: 0.8482 (mm) REVERT: E 68 GLN cc_start: 0.8945 (pp30) cc_final: 0.8588 (pp30) REVERT: E 97 GLU cc_start: 0.8227 (mt-10) cc_final: 0.7854 (mt-10) REVERT: E 120 MET cc_start: 0.7923 (mtt) cc_final: 0.7209 (mtp) REVERT: F 88 TYR cc_start: 0.8601 (m-10) cc_final: 0.7483 (m-10) REVERT: H 68 ASP cc_start: 0.8697 (t70) cc_final: 0.8397 (t0) REVERT: H 83 TYR cc_start: 0.8291 (m-10) cc_final: 0.7510 (m-10) REVERT: H 85 LYS cc_start: 0.9382 (mptt) cc_final: 0.9175 (mmmm) REVERT: H 120 LYS cc_start: 0.9470 (ttmt) cc_final: 0.9077 (tptt) REVERT: C 78 ILE cc_start: 0.9115 (mm) cc_final: 0.8827 (mm) REVERT: C 91 GLU cc_start: 0.9299 (tp30) cc_final: 0.8875 (tp30) REVERT: C 92 GLU cc_start: 0.8770 (mt-10) cc_final: 0.8055 (mp0) REVERT: G 57 TYR cc_start: 0.9282 (t80) cc_final: 0.8989 (t80) REVERT: G 104 GLN cc_start: 0.9144 (mp10) cc_final: 0.8863 (mp10) outliers start: 47 outliers final: 29 residues processed: 292 average time/residue: 0.2856 time to fit residues: 113.4597 Evaluate side-chains 293 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 262 time to evaluate : 1.003 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 60 LEU Chi-restraints excluded: chain A residue 93 GLN Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 52 THR Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 102 LEU Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 69 ILE Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 8.9990 chunk 74 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 47 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 99 optimal weight: 5.9990 chunk 105 optimal weight: 2.9990 chunk 94 optimal weight: 2.9990 chunk 28 optimal weight: 5.9990 chunk 87 optimal weight: 4.9990 overall best weight: 1.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN C 73 ASN C 89 ASN G 112 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8498 moved from start: 0.2355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 13651 Z= 0.250 Angle : 0.641 7.929 19692 Z= 0.369 Chirality : 0.037 0.165 2241 Planarity : 0.004 0.034 1475 Dihedral : 30.200 173.466 4161 Min Nonbonded Distance : 2.150 Molprobity Statistics. All-atom Clashscore : 15.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.95 % Allowed : 24.35 % Favored : 70.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.29), residues: 842 helix: 1.27 (0.21), residues: 585 sheet: None (None), residues: 0 loop : -1.27 (0.37), residues: 257 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP K 61 HIS 0.004 0.001 HIS F 75 PHE 0.013 0.002 PHE E 67 TYR 0.029 0.002 TYR F 98 ARG 0.007 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 324 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 36 poor density : 288 time to evaluate : 0.869 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 125 GLN cc_start: 0.9101 (mp10) cc_final: 0.8794 (mp10) REVERT: B 23 ARG cc_start: 0.8592 (mmp80) cc_final: 0.8122 (mmp80) REVERT: D 34 LYS cc_start: 0.9206 (mptt) cc_final: 0.8861 (mmtm) REVERT: D 35 GLU cc_start: 0.8925 (tp30) cc_final: 0.8699 (tp30) REVERT: D 57 LYS cc_start: 0.8962 (mmtt) cc_final: 0.8617 (mmmm) REVERT: D 59 MET cc_start: 0.9289 (tpp) cc_final: 0.9009 (tpp) REVERT: D 96 THR cc_start: 0.9551 (m) cc_final: 0.9331 (p) REVERT: D 105 GLU cc_start: 0.8402 (tp30) cc_final: 0.7428 (tp30) REVERT: D 120 LYS cc_start: 0.9257 (tttp) cc_final: 0.8862 (ttmm) REVERT: E 60 LEU cc_start: 0.8935 (mm) cc_final: 0.8514 (mm) REVERT: E 68 GLN cc_start: 0.8843 (pp30) cc_final: 0.8493 (pp30) REVERT: E 97 GLU cc_start: 0.8174 (mt-10) cc_final: 0.7800 (mt-10) REVERT: E 120 MET cc_start: 0.7921 (mtt) cc_final: 0.7209 (mtp) REVERT: F 88 TYR cc_start: 0.8502 (m-10) cc_final: 0.7300 (m-10) REVERT: H 68 ASP cc_start: 0.8583 (t70) cc_final: 0.8349 (t0) REVERT: H 83 TYR cc_start: 0.8218 (m-10) cc_final: 0.7247 (m-10) REVERT: H 120 LYS cc_start: 0.9460 (ttmt) cc_final: 0.9048 (tptt) REVERT: C 78 ILE cc_start: 0.9022 (mm) cc_final: 0.8749 (mm) REVERT: C 91 GLU cc_start: 0.9290 (tp30) cc_final: 0.8923 (tp30) REVERT: C 92 GLU cc_start: 0.8829 (mt-10) cc_final: 0.8003 (mp0) REVERT: G 104 GLN cc_start: 0.9014 (mp10) cc_final: 0.8693 (mp10) outliers start: 36 outliers final: 25 residues processed: 302 average time/residue: 0.2868 time to fit residues: 118.5997 Evaluate side-chains 302 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 277 time to evaluate : 1.014 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain K residue 41 GLN Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 7.9990 chunk 43 optimal weight: 8.9990 chunk 89 optimal weight: 0.6980 chunk 72 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 35 optimal weight: 2.9990 overall best weight: 3.5388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** K 41 GLN C 89 ASN G 112 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8539 moved from start: 0.2649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.055 13651 Z= 0.372 Angle : 0.681 7.700 19692 Z= 0.390 Chirality : 0.039 0.171 2241 Planarity : 0.005 0.039 1475 Dihedral : 30.296 172.680 4161 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 18.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.12 % Favored : 94.88 % Rotamer: Outliers : 5.64 % Allowed : 25.58 % Favored : 68.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.68 (0.28), residues: 842 helix: 1.23 (0.21), residues: 583 sheet: None (None), residues: 0 loop : -1.33 (0.37), residues: 259 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP K 61 HIS 0.006 0.001 HIS B 75 PHE 0.017 0.002 PHE H 65 TYR 0.035 0.002 TYR F 98 ARG 0.009 0.001 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 318 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 277 time to evaluate : 0.992 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9086 (mp10) cc_final: 0.8778 (mp10) REVERT: B 23 ARG cc_start: 0.8585 (mmp80) cc_final: 0.8264 (mmp80) REVERT: B 25 ASN cc_start: 0.8709 (m110) cc_final: 0.8277 (m-40) REVERT: B 77 LYS cc_start: 0.9066 (mmtt) cc_final: 0.8328 (mmtt) REVERT: D 31 ARG cc_start: 0.8303 (mmp80) cc_final: 0.7728 (mmp80) REVERT: D 34 LYS cc_start: 0.9235 (mptt) cc_final: 0.8902 (mmtm) REVERT: D 57 LYS cc_start: 0.9023 (mmtt) cc_final: 0.8786 (mmmm) REVERT: D 92 ARG cc_start: 0.8745 (ttp80) cc_final: 0.8064 (ttp80) REVERT: D 105 GLU cc_start: 0.8545 (tp30) cc_final: 0.7649 (tp30) REVERT: D 120 LYS cc_start: 0.9262 (tttp) cc_final: 0.8869 (ttmm) REVERT: E 52 ARG cc_start: 0.8622 (mtm-85) cc_final: 0.7970 (mtm-85) REVERT: E 60 LEU cc_start: 0.8941 (mm) cc_final: 0.8610 (mm) REVERT: E 68 GLN cc_start: 0.8962 (pp30) cc_final: 0.8625 (pp30) REVERT: E 97 GLU cc_start: 0.8231 (mt-10) cc_final: 0.7867 (mt-10) REVERT: E 120 MET cc_start: 0.7990 (mtt) cc_final: 0.7260 (mtp) REVERT: F 88 TYR cc_start: 0.8577 (m-10) cc_final: 0.7465 (m-10) REVERT: H 68 ASP cc_start: 0.8648 (t70) cc_final: 0.8380 (t0) REVERT: H 83 TYR cc_start: 0.8223 (m-10) cc_final: 0.7384 (m-10) REVERT: H 120 LYS cc_start: 0.9476 (ttmt) cc_final: 0.9039 (tptt) REVERT: C 91 GLU cc_start: 0.9314 (tp30) cc_final: 0.9047 (tp30) REVERT: C 92 GLU cc_start: 0.8856 (mt-10) cc_final: 0.8068 (mp0) REVERT: G 104 GLN cc_start: 0.9073 (mp10) cc_final: 0.8704 (mp10) outliers start: 41 outliers final: 30 residues processed: 292 average time/residue: 0.2895 time to fit residues: 115.0583 Evaluate side-chains 296 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 266 time to evaluate : 0.958 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 79 ARG Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 81 ASP Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 48 VAL Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 92 GLU Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 107 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 4.9990 chunk 20 optimal weight: 0.9980 chunk 61 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 105 optimal weight: 0.8980 chunk 87 optimal weight: 10.0000 chunk 48 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 34 optimal weight: 5.9990 chunk 55 optimal weight: 6.9990 chunk 101 optimal weight: 0.9980 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS C 89 ASN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 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 : 0.004 0.051 13651 Z= 0.211 Angle : 0.647 9.917 19692 Z= 0.370 Chirality : 0.036 0.152 2241 Planarity : 0.004 0.045 1475 Dihedral : 30.011 171.770 4161 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 15.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 4.26 % Allowed : 28.61 % Favored : 67.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.74 (0.28), residues: 842 helix: 1.27 (0.21), residues: 582 sheet: None (None), residues: 0 loop : -1.28 (0.37), residues: 260 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP K 61 HIS 0.005 0.001 HIS F 75 PHE 0.014 0.002 PHE H 65 TYR 0.027 0.002 TYR F 98 ARG 0.006 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 334 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 303 time to evaluate : 0.880 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8495 (OUTLIER) cc_final: 0.8217 (mm-30) REVERT: A 125 GLN cc_start: 0.9038 (mp10) cc_final: 0.8738 (mp10) REVERT: B 23 ARG cc_start: 0.8613 (mmp80) cc_final: 0.8246 (mmp80) REVERT: B 84 MET cc_start: 0.8213 (mmm) cc_final: 0.7928 (tpp) REVERT: D 31 ARG cc_start: 0.8309 (mmp80) cc_final: 0.7747 (mmp80) REVERT: D 34 LYS cc_start: 0.9244 (mptt) cc_final: 0.8888 (mmtm) REVERT: D 35 GLU cc_start: 0.8883 (tp30) cc_final: 0.8640 (tp30) REVERT: D 57 LYS cc_start: 0.8943 (mmtt) cc_final: 0.8703 (mmmm) REVERT: D 59 MET cc_start: 0.9262 (tpp) cc_final: 0.8989 (tpp) REVERT: D 92 ARG cc_start: 0.8572 (ttp80) cc_final: 0.7682 (ttp80) REVERT: D 105 GLU cc_start: 0.8453 (tp30) cc_final: 0.7535 (tp30) REVERT: D 120 LYS cc_start: 0.9232 (tttp) cc_final: 0.8870 (ttmm) REVERT: E 52 ARG cc_start: 0.8652 (mtm-85) cc_final: 0.7993 (mtm-85) REVERT: E 68 GLN cc_start: 0.8825 (pp30) cc_final: 0.8467 (pp30) REVERT: E 120 MET cc_start: 0.8044 (mtt) cc_final: 0.7426 (mtp) REVERT: F 88 TYR cc_start: 0.8448 (m-10) cc_final: 0.7182 (m-10) REVERT: H 83 TYR cc_start: 0.8249 (m-10) cc_final: 0.7083 (m-10) REVERT: H 120 LYS cc_start: 0.9470 (ttmt) cc_final: 0.9058 (tptt) REVERT: C 91 GLU cc_start: 0.9280 (tp30) cc_final: 0.8951 (tp30) REVERT: C 92 GLU cc_start: 0.8837 (mt-10) cc_final: 0.7967 (mp0) REVERT: G 104 GLN cc_start: 0.8900 (mp10) cc_final: 0.8518 (mp10) outliers start: 31 outliers final: 23 residues processed: 313 average time/residue: 0.2707 time to fit residues: 116.4270 Evaluate side-chains 307 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 283 time to evaluate : 0.955 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 100 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 56 GLU Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 6.9990 chunk 60 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 59 optimal weight: 5.9990 chunk 88 optimal weight: 4.9990 chunk 58 optimal weight: 6.9990 chunk 105 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 64 optimal weight: 7.9990 chunk 48 optimal weight: 3.9990 chunk 41 optimal weight: 3.9990 overall best weight: 3.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 68 GLN ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8545 moved from start: 0.2915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.058 13651 Z= 0.405 Angle : 0.705 7.980 19692 Z= 0.403 Chirality : 0.041 0.207 2241 Planarity : 0.005 0.048 1475 Dihedral : 30.294 171.506 4161 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 19.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 5.78 % Allowed : 27.51 % Favored : 66.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.28), residues: 842 helix: 1.17 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -1.32 (0.37), residues: 258 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP K 61 HIS 0.007 0.001 HIS B 75 PHE 0.017 0.002 PHE H 65 TYR 0.032 0.003 TYR F 98 ARG 0.008 0.001 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 277 time to evaluate : 0.978 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8550 (OUTLIER) cc_final: 0.8332 (mm-30) REVERT: A 125 GLN cc_start: 0.9074 (mp10) cc_final: 0.8691 (mp10) REVERT: B 25 ASN cc_start: 0.8725 (m110) cc_final: 0.8286 (m-40) REVERT: B 93 GLN cc_start: 0.8451 (tt0) cc_final: 0.8241 (tm-30) REVERT: D 31 ARG cc_start: 0.8301 (mmp80) cc_final: 0.7657 (mmp80) REVERT: D 34 LYS cc_start: 0.9258 (mptt) cc_final: 0.8907 (mmtm) REVERT: D 35 GLU cc_start: 0.8848 (tp30) cc_final: 0.8577 (tp30) REVERT: D 57 LYS cc_start: 0.9052 (mmtt) cc_final: 0.8808 (mmmm) REVERT: D 92 ARG cc_start: 0.8700 (ttp80) cc_final: 0.7966 (ttp80) REVERT: D 105 GLU cc_start: 0.8567 (tp30) cc_final: 0.7645 (tp30) REVERT: D 120 LYS cc_start: 0.9259 (tttp) cc_final: 0.8878 (ttmm) REVERT: E 68 GLN cc_start: 0.8966 (pp30) cc_final: 0.8552 (pp30) REVERT: E 93 GLN cc_start: 0.9307 (tt0) cc_final: 0.9023 (tt0) REVERT: F 88 TYR cc_start: 0.8565 (m-10) cc_final: 0.7435 (m-10) REVERT: H 83 TYR cc_start: 0.8272 (m-10) cc_final: 0.7290 (m-10) REVERT: H 105 GLU cc_start: 0.7502 (pm20) cc_final: 0.7224 (pm20) REVERT: H 120 LYS cc_start: 0.9472 (ttmt) cc_final: 0.9020 (tptt) REVERT: C 91 GLU cc_start: 0.9313 (tp30) cc_final: 0.9082 (tp30) REVERT: C 92 GLU cc_start: 0.8891 (mt-10) cc_final: 0.8102 (mp0) REVERT: G 104 GLN cc_start: 0.9076 (mp10) cc_final: 0.8690 (mp10) outliers start: 42 outliers final: 28 residues processed: 292 average time/residue: 0.2827 time to fit residues: 112.2956 Evaluate side-chains 300 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 271 time to evaluate : 0.939 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 100 LEU Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 66 VAL Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain F residue 97 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain H residue 90 THR Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 87 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 59 THR Chi-restraints excluded: chain G residue 76 THR Chi-restraints excluded: chain G residue 87 ILE Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 5.9990 chunk 31 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 66 optimal weight: 10.0000 chunk 71 optimal weight: 5.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 82 optimal weight: 6.9990 chunk 95 optimal weight: 0.8980 chunk 100 optimal weight: 0.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.9182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 55 GLN A 68 GLN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8451 moved from start: 0.2799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 13651 Z= 0.208 Angle : 0.669 10.348 19692 Z= 0.378 Chirality : 0.037 0.170 2241 Planarity : 0.004 0.044 1475 Dihedral : 29.938 171.038 4161 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.40 % Allowed : 30.12 % Favored : 65.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.53 (0.28), residues: 842 helix: 1.11 (0.21), residues: 589 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 253 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 61 HIS 0.005 0.001 HIS F 75 PHE 0.016 0.002 PHE H 65 TYR 0.030 0.002 TYR F 98 ARG 0.005 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 329 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 297 time to evaluate : 1.072 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 GLU cc_start: 0.8497 (OUTLIER) cc_final: 0.8261 (mm-30) REVERT: A 125 GLN cc_start: 0.9004 (OUTLIER) cc_final: 0.8678 (mp10) REVERT: B 23 ARG cc_start: 0.8637 (mmp80) cc_final: 0.8365 (mmp80) REVERT: B 44 LYS cc_start: 0.9015 (mtpp) cc_final: 0.8498 (mtmm) REVERT: D 31 ARG cc_start: 0.8314 (mmp80) cc_final: 0.7715 (mmp80) REVERT: D 34 LYS cc_start: 0.9262 (mptt) cc_final: 0.8877 (mmtm) REVERT: D 57 LYS cc_start: 0.8964 (mmtt) cc_final: 0.8722 (mmmm) REVERT: D 59 MET cc_start: 0.9242 (tpp) cc_final: 0.9006 (tpp) REVERT: D 105 GLU cc_start: 0.8397 (tp30) cc_final: 0.7421 (tp30) REVERT: D 120 LYS cc_start: 0.9219 (tttp) cc_final: 0.8855 (ttmm) REVERT: E 52 ARG cc_start: 0.8650 (mtm-85) cc_final: 0.7968 (mtm-85) REVERT: E 68 GLN cc_start: 0.8760 (pp30) cc_final: 0.8429 (pp30) REVERT: E 93 GLN cc_start: 0.9267 (tt0) cc_final: 0.8901 (tt0) REVERT: E 120 MET cc_start: 0.8320 (mtp) cc_final: 0.7942 (mtt) REVERT: F 88 TYR cc_start: 0.8432 (m-10) cc_final: 0.7159 (m-10) REVERT: H 83 TYR cc_start: 0.8159 (m-10) cc_final: 0.6977 (m-10) REVERT: H 105 GLU cc_start: 0.7462 (pm20) cc_final: 0.7226 (pm20) REVERT: H 120 LYS cc_start: 0.9451 (ttmt) cc_final: 0.9045 (tptt) REVERT: C 84 GLN cc_start: 0.9199 (tm-30) cc_final: 0.8576 (tp-100) REVERT: C 92 GLU cc_start: 0.8874 (mt-10) cc_final: 0.7929 (mp0) REVERT: G 104 GLN cc_start: 0.8896 (mp10) cc_final: 0.8501 (mp10) outliers start: 32 outliers final: 22 residues processed: 306 average time/residue: 0.2659 time to fit residues: 111.1223 Evaluate side-chains 308 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 284 time to evaluate : 0.977 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 100 LEU Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain H residue 39 ILE Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 61 GLU Chi-restraints excluded: chain C residue 79 ILE Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 3.9990 chunk 100 optimal weight: 1.9990 chunk 58 optimal weight: 6.9990 chunk 42 optimal weight: 0.6980 chunk 76 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 88 optimal weight: 5.9990 chunk 92 optimal weight: 1.9990 chunk 64 optimal weight: 8.9990 chunk 103 optimal weight: 0.8980 chunk 63 optimal weight: 6.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 47 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 82 HIS ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 24 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 73 ASN G 112 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8462 moved from start: 0.2891 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 13651 Z= 0.231 Angle : 0.679 12.249 19692 Z= 0.385 Chirality : 0.038 0.186 2241 Planarity : 0.004 0.044 1475 Dihedral : 29.945 170.612 4161 Min Nonbonded Distance : 2.124 Molprobity Statistics. All-atom Clashscore : 15.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 3.71 % Allowed : 31.22 % Favored : 65.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.28), residues: 842 helix: 1.03 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -1.44 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 61 HIS 0.005 0.001 HIS D 82 PHE 0.028 0.002 PHE H 65 TYR 0.028 0.002 TYR F 98 ARG 0.010 0.000 ARG D 92 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 310 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 283 time to evaluate : 0.946 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 LEU cc_start: 0.9606 (tp) cc_final: 0.9397 (tt) REVERT: A 73 GLU cc_start: 0.7805 (mt-10) cc_final: 0.6916 (mt-10) REVERT: A 105 GLU cc_start: 0.8524 (OUTLIER) cc_final: 0.8260 (mm-30) REVERT: A 125 GLN cc_start: 0.9014 (OUTLIER) cc_final: 0.8668 (mp10) REVERT: B 23 ARG cc_start: 0.8553 (mmp80) cc_final: 0.8242 (mmp80) REVERT: B 25 ASN cc_start: 0.8885 (m110) cc_final: 0.8572 (m110) REVERT: B 79 LYS cc_start: 0.9190 (OUTLIER) cc_final: 0.8639 (mtmm) REVERT: D 31 ARG cc_start: 0.8313 (mmp80) cc_final: 0.7701 (mmp80) REVERT: D 34 LYS cc_start: 0.9257 (mptt) cc_final: 0.8866 (mmtm) REVERT: D 35 GLU cc_start: 0.8811 (tp30) cc_final: 0.8590 (tp30) REVERT: D 57 LYS cc_start: 0.8955 (mmtt) cc_final: 0.8704 (mmmm) REVERT: D 59 MET cc_start: 0.9253 (tpp) cc_final: 0.9002 (tpp) REVERT: D 105 GLU cc_start: 0.8362 (tp30) cc_final: 0.7430 (tp30) REVERT: D 120 LYS cc_start: 0.9173 (tttp) cc_final: 0.8839 (ttmm) REVERT: E 68 GLN cc_start: 0.8862 (pp30) cc_final: 0.8452 (pp30) REVERT: E 120 MET cc_start: 0.8367 (mtp) cc_final: 0.7774 (mtt) REVERT: F 88 TYR cc_start: 0.8470 (m-10) cc_final: 0.7253 (m-10) REVERT: H 83 TYR cc_start: 0.8230 (m-10) cc_final: 0.7013 (m-10) REVERT: H 120 LYS cc_start: 0.9413 (ttmt) cc_final: 0.9021 (tptt) REVERT: C 92 GLU cc_start: 0.8850 (mt-10) cc_final: 0.7986 (mp0) REVERT: G 104 GLN cc_start: 0.8876 (mp10) cc_final: 0.8473 (mp10) outliers start: 27 outliers final: 19 residues processed: 292 average time/residue: 0.2884 time to fit residues: 114.2349 Evaluate side-chains 298 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 276 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.0570 chunk 71 optimal weight: 6.9990 chunk 108 optimal weight: 6.9990 chunk 99 optimal weight: 3.9990 chunk 86 optimal weight: 20.0000 chunk 8 optimal weight: 0.9980 chunk 66 optimal weight: 10.0000 chunk 53 optimal weight: 10.0000 chunk 68 optimal weight: 7.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 20.0000 overall best weight: 2.5302 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2977 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.044 13651 Z= 0.306 Angle : 0.719 12.376 19692 Z= 0.401 Chirality : 0.040 0.264 2241 Planarity : 0.005 0.043 1475 Dihedral : 30.042 171.271 4161 Min Nonbonded Distance : 2.083 Molprobity Statistics. All-atom Clashscore : 16.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % Rotamer: Outliers : 3.44 % Allowed : 32.05 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.28), residues: 842 helix: 0.99 (0.21), residues: 590 sheet: None (None), residues: 0 loop : -1.47 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 61 HIS 0.004 0.001 HIS B 75 PHE 0.027 0.002 PHE E 67 TYR 0.031 0.003 TYR F 98 ARG 0.009 0.000 ARG D 92 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 304 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 279 time to evaluate : 0.985 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 73 GLU cc_start: 0.7830 (mt-10) cc_final: 0.6905 (mt-10) REVERT: A 105 GLU cc_start: 0.8533 (OUTLIER) cc_final: 0.8278 (mm-30) REVERT: A 125 GLN cc_start: 0.9046 (mp10) cc_final: 0.8697 (mp10) REVERT: B 23 ARG cc_start: 0.8512 (mmp80) cc_final: 0.8192 (mmp80) REVERT: B 25 ASN cc_start: 0.8915 (m110) cc_final: 0.8586 (m110) REVERT: B 79 LYS cc_start: 0.9222 (OUTLIER) cc_final: 0.8676 (mtmm) REVERT: D 34 LYS cc_start: 0.9274 (mptt) cc_final: 0.8887 (mmtm) REVERT: D 35 GLU cc_start: 0.8818 (tp30) cc_final: 0.8597 (tp30) REVERT: D 57 LYS cc_start: 0.8997 (mmtt) cc_final: 0.8746 (mmmm) REVERT: D 59 MET cc_start: 0.9299 (tpp) cc_final: 0.9014 (tpp) REVERT: D 105 GLU cc_start: 0.8428 (tp30) cc_final: 0.7527 (tp30) REVERT: D 120 LYS cc_start: 0.9236 (tttp) cc_final: 0.8883 (ttmm) REVERT: E 68 GLN cc_start: 0.8869 (pp30) cc_final: 0.8455 (pp30) REVERT: E 120 MET cc_start: 0.8428 (mtp) cc_final: 0.7833 (mtt) REVERT: F 88 TYR cc_start: 0.8535 (m-10) cc_final: 0.7394 (m-10) REVERT: H 83 TYR cc_start: 0.8219 (m-10) cc_final: 0.7231 (m-10) REVERT: H 120 LYS cc_start: 0.9429 (ttmt) cc_final: 0.9062 (tptt) REVERT: C 92 GLU cc_start: 0.8895 (mt-10) cc_final: 0.8046 (mp0) REVERT: G 104 GLN cc_start: 0.8937 (mp10) cc_final: 0.8588 (mp10) outliers start: 25 outliers final: 21 residues processed: 289 average time/residue: 0.2849 time to fit residues: 111.7626 Evaluate side-chains 294 residues out of total 723 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 271 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 45 THR Chi-restraints excluded: chain A residue 105 GLU Chi-restraints excluded: chain A residue 110 CYS Chi-restraints excluded: chain A residue 126 LEU Chi-restraints excluded: chain B residue 62 LEU Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain B residue 85 ASP Chi-restraints excluded: chain D residue 122 THR Chi-restraints excluded: chain E residue 51 ILE Chi-restraints excluded: chain E residue 55 GLN Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 133 GLU Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain F residue 60 VAL Chi-restraints excluded: chain F residue 62 LEU Chi-restraints excluded: chain H residue 51 ASP Chi-restraints excluded: chain C residue 16 THR Chi-restraints excluded: chain C residue 33 LEU Chi-restraints excluded: chain C residue 43 VAL Chi-restraints excluded: chain C residue 49 VAL Chi-restraints excluded: chain C residue 107 VAL Chi-restraints excluded: chain G residue 49 VAL Chi-restraints excluded: chain G residue 100 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 10.0000 chunk 12 optimal weight: 0.6980 chunk 24 optimal weight: 0.0670 chunk 86 optimal weight: 0.0970 chunk 36 optimal weight: 0.9990 chunk 88 optimal weight: 6.9990 chunk 10 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 4.9990 chunk 62 optimal weight: 5.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 64 ASN ** F 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 38 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** G 112 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3541 r_free = 0.3541 target = 0.077506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2973 r_free = 0.2973 target = 0.053744 restraints weight = 69147.414| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 51)----------------| | r_work = 0.3005 r_free = 0.3005 target = 0.055167 restraints weight = 31101.162| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.3031 r_free = 0.3031 target = 0.056163 restraints weight = 20153.881| |-----------------------------------------------------------------------------| r_work (final): 0.3002 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3002 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3002 r_free = 0.3002 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3001 r_free = 0.3001 target_work(ls_wunit_k1) = 0.054 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 11 | |-----------------------------------------------------------------------------| r_final: 0.3001 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8459 moved from start: 0.3025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 13651 Z= 0.211 Angle : 0.710 12.522 19692 Z= 0.393 Chirality : 0.038 0.267 2241 Planarity : 0.004 0.044 1475 Dihedral : 29.890 170.318 4161 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 14.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.93 % Favored : 96.07 % Rotamer: Outliers : 3.58 % Allowed : 31.91 % Favored : 64.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.28), residues: 842 helix: 0.95 (0.20), residues: 590 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 252 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP K 61 HIS 0.005 0.001 HIS F 75 PHE 0.028 0.002 PHE H 65 TYR 0.030 0.002 TYR F 98 ARG 0.009 0.001 ARG D 92 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2743.97 seconds wall clock time: 49 minutes 20.87 seconds (2960.87 seconds total)