Starting phenix.real_space_refine on Mon Apr 8 21:43:17 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/04_2024/8sn3_40611.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/04_2024/8sn3_40611.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/8sn3_40611/04_2024/8sn3_40611.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/04_2024/8sn3_40611.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/04_2024/8sn3_40611.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8sn3_40611/04_2024/8sn3_40611.pdb" } 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= 0.004 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 8276 2.51 5 N 2716 2.21 5 O 3291 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 54": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 77": "OD1" <-> "OD2" Residue "C TYR 39": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 41": "OE1" <-> "OE2" Residue "D TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F TYR 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G GLU 61": "OE1" <-> "OE2" Residue "G GLU 92": "OE1" <-> "OE2" Residue "H TYR 83": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K PHE 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L GLU 9": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14612 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: 704 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 704 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 6, 'TRANS': 80} 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: 601 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 601 Classifications: {'peptide': 76} 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 12313 SG CYS K 31 31.696 74.358 48.206 1.00 55.65 S ATOM 12463 SG CYS K 51 30.684 71.325 47.252 1.00 54.45 S ATOM 12487 SG CYS K 54 31.262 73.831 44.365 1.00 65.71 S ATOM 12204 SG CYS K 16 21.823 68.573 53.938 1.00 64.66 S ATOM 12222 SG CYS K 19 19.688 65.906 55.446 1.00 64.84 S ATOM 12352 SG CYS K 36 22.524 67.475 57.565 1.00 50.00 S ATOM 12374 SG CYS K 39 23.418 65.177 54.865 1.00 54.15 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 ... (2 atoms not shown) pdb=" O GLY M 76 " occ=0.25 Time building chain proxies: 7.67, per 1000 atoms: 0.52 Number of scatterers: 14612 At special positions: 0 Unit cell: (108.896, 134.128, 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 3291 8.00 N 2716 7.00 C 8276 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: 7.15 Conformation dependent library (CDL) restraints added in 1.8 seconds Dynamic metal coordination Zn2+ tetrahedral coordination pdb=" ZN K 301 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 31 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 51 " pdb="ZN ZN K 301 " - pdb=" SG CYS K 54 " pdb=" ZN K 302 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 39 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 36 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 19 " pdb="ZN ZN K 302 " - pdb=" SG CYS K 16 " Number of angles added : 6 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2030 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 11 sheets defined 63.1% alpha, 4.5% beta 135 base pairs and 236 stacking pairs defined. Time for finding SS restraints: 6.61 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 3.659A pdb=" N LYS A 56 " --> pdb=" O ARG A 52 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.773A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) removed outlier: 4.142A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 25 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.748A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.210A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N GLY B 56 " --> pdb=" O GLU B 52 " (cutoff:3.500A) removed outlier: 3.611A 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 22 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 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.523A pdb=" N ASN D 84 " --> pdb=" O LEU D 80 " (cutoff:3.500A) Processing helix chain 'D' and resid 90 through 102 removed outlier: 3.713A pdb=" N ILE D 94 " --> pdb=" O THR D 90 " (cutoff:3.500A) Processing helix chain 'D' and resid 103 through 122 removed outlier: 3.714A pdb=" N HIS D 109 " --> pdb=" O GLU D 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 79 removed outlier: 3.513A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.790A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.649A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 25 through 29 removed outlier: 3.505A pdb=" N ILE F 29 " --> pdb=" O ILE F 26 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.002A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 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 74 Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 90 through 97 removed outlier: 3.534A pdb=" N LYS G 95 " --> pdb=" O GLU G 91 " (cutoff:3.500A) Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.527A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 removed outlier: 3.673A pdb=" N ASN H 84 " --> pdb=" O LEU H 80 " (cutoff:3.500A) Processing helix chain 'H' and resid 90 through 102 removed outlier: 3.837A pdb=" N ILE H 94 " --> pdb=" O THR H 90 " (cutoff:3.500A) Processing helix chain 'H' and resid 103 through 123 removed outlier: 3.774A pdb=" N SER H 123 " --> pdb=" O THR H 119 " (cutoff:3.500A) Processing helix chain 'K' and resid 37 through 47 removed outlier: 4.669A pdb=" N GLU K 45 " --> pdb=" O GLN K 41 " (cutoff:3.500A) Processing helix chain 'K' and resid 58 through 69 removed outlier: 3.861A pdb=" N ARG K 67 " --> pdb=" O ARG K 63 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ARG K 68 " --> pdb=" O TYR K 64 " (cutoff:3.500A) Processing helix chain 'K' and resid 73 through 84 Processing helix chain 'K' and resid 84 through 90 removed outlier: 3.792A pdb=" N CYS K 88 " --> pdb=" O TYR K 84 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N LEU K 90 " --> pdb=" O ARG K 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 1 through 16 Processing helix chain 'L' and resid 86 through 91 removed outlier: 3.710A pdb=" N ARG L 90 " --> pdb=" O LEU L 86 " (cutoff:3.500A) Processing helix chain 'L' and resid 98 through 112 removed outlier: 3.549A pdb=" N ASP L 112 " --> pdb=" O SER L 108 " (cutoff:3.500A) Processing helix chain 'L' and resid 120 through 130 removed outlier: 3.564A pdb=" N ASP L 130 " --> pdb=" O ILE L 126 " (cutoff:3.500A) Processing helix chain 'L' and resid 130 through 146 removed outlier: 3.900A pdb=" N TYR L 134 " --> pdb=" O ASP L 130 " (cutoff:3.500A) Processing helix chain 'M' and resid 22 through 35 Processing helix chain 'M' and resid 37 through 41 Processing helix chain 'M' and resid 55 through 60 removed outlier: 3.863A pdb=" N TYR M 59 " --> pdb=" O THR M 55 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A 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 'C' and resid 42 through 43 removed outlier: 8.120A 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 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.878A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 26 through 28 Processing sheet with id=AB1, first strand: chain 'L' and resid 21 through 24 removed outlier: 4.097A pdb=" N SER L 22 " --> pdb=" O THR L 36 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'M' and resid 12 through 15 removed outlier: 3.627A pdb=" N ILE M 13 " --> pdb=" O VAL M 5 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N LEU M 69 " --> pdb=" O LYS M 6 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N HIS M 68 " --> pdb=" O ILE M 44 " (cutoff:3.500A) 493 hydrogen bonds defined for protein. 1447 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 347 hydrogen bonds 690 hydrogen bond angles 0 basepair planarities 135 basepair parallelities 236 stacking parallelities Total time for adding SS restraints: 5.45 Time building geometry restraints manager: 7.63 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 3244 1.33 - 1.45: 4467 1.45 - 1.57: 7137 1.57 - 1.69: 586 1.69 - 1.81: 49 Bond restraints: 15483 Sorted by residual: bond pdb=" CD LYS D 116 " pdb=" CE LYS D 116 " ideal model delta sigma weight residual 1.520 1.480 0.040 3.00e-02 1.11e+03 1.79e+00 bond pdb=" CG LYS D 116 " pdb=" CD LYS D 116 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.63e+00 bond pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " ideal model delta sigma weight residual 1.422 1.454 -0.032 3.00e-02 1.11e+03 1.14e+00 bond pdb=" CB MET H 59 " pdb=" CG MET H 59 " ideal model delta sigma weight residual 1.520 1.488 0.032 3.00e-02 1.11e+03 1.11e+00 bond pdb=" C3' DA J -68 " pdb=" C2' DA J -68 " ideal model delta sigma weight residual 1.525 1.546 -0.021 2.00e-02 2.50e+03 1.05e+00 ... (remaining 15478 not shown) Histogram of bond angle deviations from ideal: 98.44 - 105.54: 1451 105.54 - 112.64: 8677 112.64 - 119.74: 5020 119.74 - 126.84: 6165 126.84 - 133.94: 869 Bond angle restraints: 22182 Sorted by residual: angle pdb=" N VAL E 117 " pdb=" CA VAL E 117 " pdb=" C VAL E 117 " ideal model delta sigma weight residual 111.90 108.81 3.09 8.10e-01 1.52e+00 1.45e+01 angle pdb=" C GLY G 37 " pdb=" N ASN G 38 " pdb=" CA ASN G 38 " ideal model delta sigma weight residual 121.54 126.95 -5.41 1.91e+00 2.74e-01 8.03e+00 angle pdb=" CA LYS D 116 " pdb=" CB LYS D 116 " pdb=" CG LYS D 116 " ideal model delta sigma weight residual 114.10 108.74 5.36 2.00e+00 2.50e-01 7.17e+00 angle pdb=" C ALA K 47 " pdb=" N SER K 48 " pdb=" CA SER K 48 " ideal model delta sigma weight residual 122.55 117.60 4.95 2.03e+00 2.43e-01 5.94e+00 angle pdb=" CB MET H 59 " pdb=" CG MET H 59 " pdb=" SD MET H 59 " ideal model delta sigma weight residual 112.70 105.57 7.13 3.00e+00 1.11e-01 5.65e+00 ... (remaining 22177 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.74: 7299 35.74 - 71.48: 1293 71.48 - 107.22: 17 107.22 - 142.96: 0 142.96 - 178.70: 2 Dihedral angle restraints: 8611 sinusoidal: 5471 harmonic: 3140 Sorted by residual: dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual -140.00 38.70 -178.70 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" CA GLN M 41 " pdb=" C GLN M 41 " pdb=" N ARG M 42 " pdb=" CA ARG M 42 " ideal model delta harmonic sigma weight residual 180.00 160.70 19.30 0 5.00e+00 4.00e-02 1.49e+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 74.33 145.67 1 3.50e+01 8.16e-04 1.43e+01 ... (remaining 8608 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.029: 1731 0.029 - 0.059: 577 0.059 - 0.088: 134 0.088 - 0.117: 66 0.117 - 0.146: 8 Chirality restraints: 2516 Sorted by residual: chirality pdb=" CA LEU E 65 " pdb=" N LEU E 65 " pdb=" C LEU E 65 " pdb=" CB LEU E 65 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.35e-01 chirality pdb=" CA ASN G 38 " pdb=" N ASN G 38 " pdb=" C ASN G 38 " pdb=" CB ASN G 38 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA ILE M 36 " pdb=" N ILE M 36 " pdb=" C ILE M 36 " pdb=" CB ILE M 36 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.62e-01 ... (remaining 2513 not shown) Planarity restraints: 1795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR F 88 " -0.019 2.00e-02 2.50e+03 1.74e-02 6.06e+00 pdb=" CG TYR F 88 " 0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR F 88 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR F 88 " -0.004 2.00e-02 2.50e+03 pdb=" CE1 TYR F 88 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR F 88 " -0.008 2.00e-02 2.50e+03 pdb=" CZ TYR F 88 " -0.001 2.00e-02 2.50e+03 pdb=" OH TYR F 88 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO M 37 " -0.031 5.00e-02 4.00e+02 4.73e-02 3.58e+00 pdb=" N PRO M 38 " 0.082 5.00e-02 4.00e+02 pdb=" CA PRO M 38 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO M 38 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 88 " 0.010 2.00e-02 2.50e+03 1.33e-02 3.53e+00 pdb=" CG TYR B 88 " -0.031 2.00e-02 2.50e+03 pdb=" CD1 TYR B 88 " 0.016 2.00e-02 2.50e+03 pdb=" CD2 TYR B 88 " 0.005 2.00e-02 2.50e+03 pdb=" CE1 TYR B 88 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR B 88 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 88 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR B 88 " 0.000 2.00e-02 2.50e+03 ... (remaining 1792 not shown) Histogram of nonbonded interaction distances: 1.33 - 2.04: 2 2.04 - 2.76: 1938 2.76 - 3.47: 19786 3.47 - 4.19: 38128 4.19 - 4.90: 59060 Nonbonded interactions: 118914 Sorted by model distance: nonbonded pdb=" N SER C 11 " pdb=" C SER D 123 " model vdw 1.329 3.350 nonbonded pdb=" N SER G 11 " pdb=" C SER H 123 " model vdw 1.330 3.350 nonbonded pdb=" O2 DC I 21 " pdb=" N2 DG J -21 " model vdw 2.164 2.496 nonbonded pdb=" O ARG L 139 " pdb=" NE2 GLN L 143 " model vdw 2.205 2.520 nonbonded pdb=" N SER C 11 " pdb=" O SER D 123 " model vdw 2.251 2.520 ... (remaining 118909 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 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=0.25 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: 1.330 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: 4.220 Check model and map are aligned: 0.210 Set scattering table: 0.130 Process input model: 47.880 Find NCS groups from input model: 0.750 Set up NCS constraints: 0.080 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 57.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 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 0.040 15483 Z= 0.201 Angle : 0.553 7.129 22182 Z= 0.322 Chirality : 0.034 0.146 2516 Planarity : 0.004 0.075 1795 Dihedral : 25.549 178.698 6581 Min Nonbonded Distance : 1.329 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 0.00 % Allowed : 0.65 % Favored : 99.35 % 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: 1.98 (0.26), residues: 1058 helix: 2.28 (0.21), residues: 634 sheet: 1.13 (0.76), residues: 46 loop : -0.36 (0.31), residues: 378 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 33 HIS 0.002 0.000 HIS F 75 PHE 0.008 0.001 PHE K 53 TYR 0.043 0.002 TYR F 88 ARG 0.004 0.000 ARG M 74 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 223 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 1.164 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 95 LYS cc_start: 0.8945 (ttmt) cc_final: 0.8701 (tttm) REVERT: D 68 ASP cc_start: 0.8310 (t70) cc_final: 0.7858 (t0) REVERT: G 36 LYS cc_start: 0.8763 (mptt) cc_final: 0.8418 (mmtm) REVERT: H 120 LYS cc_start: 0.9248 (ttpt) cc_final: 0.9041 (ttmt) REVERT: K 41 GLN cc_start: 0.8920 (tp40) cc_final: 0.8709 (tp40) REVERT: K 68 ARG cc_start: 0.7644 (mmm-85) cc_final: 0.6713 (ptm160) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.3705 time to fit residues: 112.4227 Evaluate side-chains 182 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 182 time to evaluate : 1.538 ------------------------------------------------------------------------------- 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: 9.9990 chunk 97 optimal weight: 3.9990 chunk 54 optimal weight: 0.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 0.0060 chunk 52 optimal weight: 1.9990 chunk 101 optimal weight: 8.9990 chunk 39 optimal weight: 0.6980 chunk 61 optimal weight: 0.9990 chunk 75 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 overall best weight: 0.4798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 34 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8155 moved from start: 0.1014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15483 Z= 0.176 Angle : 0.559 9.964 22182 Z= 0.321 Chirality : 0.034 0.162 2516 Planarity : 0.004 0.037 1795 Dihedral : 28.715 178.993 4412 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.95 % Allowed : 10.92 % Favored : 87.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.10 (0.26), residues: 1058 helix: 2.42 (0.21), residues: 650 sheet: 1.04 (0.84), residues: 41 loop : -0.47 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.004 TRP L 141 HIS 0.004 0.001 HIS L 75 PHE 0.009 0.001 PHE A 67 TYR 0.030 0.002 TYR H 83 ARG 0.010 0.000 ARG L 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 194 time to evaluate : 1.153 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9024 (mttm) cc_final: 0.8504 (mttp) REVERT: B 85 ASP cc_start: 0.8787 (m-30) cc_final: 0.8531 (m-30) REVERT: B 88 TYR cc_start: 0.8488 (m-10) cc_final: 0.8113 (m-10) REVERT: C 95 LYS cc_start: 0.8953 (ttmt) cc_final: 0.8721 (tttm) REVERT: D 59 MET cc_start: 0.8689 (tpp) cc_final: 0.8334 (tpp) REVERT: D 68 ASP cc_start: 0.8120 (t70) cc_final: 0.7807 (t0) REVERT: D 83 TYR cc_start: 0.7641 (m-10) cc_final: 0.7278 (m-10) REVERT: G 36 LYS cc_start: 0.8774 (mptt) cc_final: 0.8479 (mmtm) REVERT: H 42 TYR cc_start: 0.8520 (t80) cc_final: 0.8166 (t80) REVERT: L 5 ARG cc_start: 0.7311 (tpt90) cc_final: 0.6933 (tpt-90) REVERT: L 9 GLU cc_start: 0.6328 (tt0) cc_final: 0.5961 (tt0) REVERT: L 147 MET cc_start: 0.4306 (mpp) cc_final: 0.3960 (mpp) outliers start: 18 outliers final: 12 residues processed: 203 average time/residue: 0.3321 time to fit residues: 92.1652 Evaluate side-chains 192 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 180 time to evaluate : 1.138 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 69 PHE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 65 optimal weight: 0.9990 chunk 36 optimal weight: 4.9990 chunk 97 optimal weight: 3.9990 chunk 79 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 117 optimal weight: 7.9990 chunk 126 optimal weight: 0.4980 chunk 104 optimal weight: 4.9990 chunk 116 optimal weight: 0.9990 chunk 40 optimal weight: 0.6980 chunk 94 optimal weight: 3.9990 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 108 ASN D 84 ASN D 95 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1267 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 15483 Z= 0.214 Angle : 0.564 11.311 22182 Z= 0.322 Chirality : 0.034 0.183 2516 Planarity : 0.004 0.037 1795 Dihedral : 28.853 178.937 4412 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.65 % Favored : 97.35 % Rotamer: Outliers : 2.59 % Allowed : 13.19 % Favored : 84.22 % 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: 1058 helix: 2.43 (0.21), residues: 650 sheet: 1.15 (0.85), residues: 41 loop : -0.58 (0.31), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 33 HIS 0.003 0.001 HIS K 65 PHE 0.018 0.001 PHE L 62 TYR 0.030 0.001 TYR H 83 ARG 0.008 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 215 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 191 time to evaluate : 1.145 Fit side-chains revert: symmetry clash REVERT: C 95 LYS cc_start: 0.8967 (ttmt) cc_final: 0.8715 (tttm) REVERT: D 59 MET cc_start: 0.8900 (tpp) cc_final: 0.8621 (tpp) REVERT: D 68 ASP cc_start: 0.8299 (t70) cc_final: 0.7991 (t0) REVERT: D 83 TYR cc_start: 0.7783 (m-10) cc_final: 0.7317 (m-10) REVERT: F 72 TYR cc_start: 0.8652 (m-80) cc_final: 0.8247 (m-80) REVERT: G 36 LYS cc_start: 0.8801 (mptt) cc_final: 0.8475 (mmtm) REVERT: H 42 TYR cc_start: 0.8569 (t80) cc_final: 0.8227 (t80) REVERT: L 147 MET cc_start: 0.4011 (mpp) cc_final: 0.3708 (mpp) outliers start: 24 outliers final: 21 residues processed: 201 average time/residue: 0.3446 time to fit residues: 93.9927 Evaluate side-chains 196 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 175 time to evaluate : 1.311 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 73 GLU Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain H residue 123 SER Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain K residue 66 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 51 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 115 optimal weight: 0.6980 chunk 88 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 12 optimal weight: 0.0970 chunk 56 optimal weight: 0.9980 chunk 78 optimal weight: 4.9990 chunk 117 optimal weight: 0.5980 chunk 124 optimal weight: 30.0000 chunk 61 optimal weight: 0.0770 chunk 111 optimal weight: 6.9990 chunk 33 optimal weight: 0.9980 overall best weight: 0.4936 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8159 moved from start: 0.1481 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 15483 Z= 0.171 Angle : 0.546 11.440 22182 Z= 0.312 Chirality : 0.033 0.152 2516 Planarity : 0.004 0.036 1795 Dihedral : 28.828 179.391 4412 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.70 % Allowed : 14.27 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.26), residues: 1058 helix: 2.50 (0.21), residues: 649 sheet: 0.91 (0.84), residues: 41 loop : -0.52 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP L 33 HIS 0.003 0.000 HIS K 65 PHE 0.015 0.001 PHE L 62 TYR 0.027 0.001 TYR H 83 ARG 0.008 0.000 ARG H 99 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 191 time to evaluate : 1.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8768 (m-10) cc_final: 0.8201 (m-10) REVERT: D 68 ASP cc_start: 0.8217 (t70) cc_final: 0.7892 (t0) REVERT: D 71 GLU cc_start: 0.7907 (tp30) cc_final: 0.7442 (tp30) REVERT: E 125 GLN cc_start: 0.8062 (OUTLIER) cc_final: 0.7312 (mt0) REVERT: G 36 LYS cc_start: 0.8796 (mptt) cc_final: 0.8461 (mmtm) REVERT: H 42 TYR cc_start: 0.8525 (t80) cc_final: 0.8121 (t80) REVERT: L 69 PHE cc_start: 0.6863 (OUTLIER) cc_final: 0.5877 (m-10) REVERT: L 147 MET cc_start: 0.4035 (mpp) cc_final: 0.3697 (mpp) outliers start: 25 outliers final: 15 residues processed: 206 average time/residue: 0.3354 time to fit residues: 94.8948 Evaluate side-chains 196 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 179 time to evaluate : 1.273 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 46 LYS Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 103 optimal weight: 3.9990 chunk 70 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 92 optimal weight: 4.9990 chunk 51 optimal weight: 0.8980 chunk 106 optimal weight: 9.9990 chunk 86 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 63 optimal weight: 0.9990 chunk 111 optimal weight: 7.9990 chunk 31 optimal weight: 0.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 95 GLN G 73 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8224 moved from start: 0.1632 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 15483 Z= 0.254 Angle : 0.586 12.919 22182 Z= 0.330 Chirality : 0.035 0.207 2516 Planarity : 0.004 0.035 1795 Dihedral : 29.006 178.934 4412 Min Nonbonded Distance : 2.105 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 3.24 % Allowed : 15.24 % Favored : 81.51 % 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: 1.99 (0.26), residues: 1058 helix: 2.37 (0.21), residues: 651 sheet: 1.02 (0.84), residues: 41 loop : -0.62 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP K 61 HIS 0.003 0.001 HIS K 65 PHE 0.015 0.001 PHE L 62 TYR 0.041 0.002 TYR H 83 ARG 0.012 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 211 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 181 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8721 (m-10) cc_final: 0.8288 (m-10) REVERT: D 68 ASP cc_start: 0.8393 (t70) cc_final: 0.8162 (t0) REVERT: D 71 GLU cc_start: 0.8011 (tp30) cc_final: 0.7803 (tp30) REVERT: E 125 GLN cc_start: 0.8100 (OUTLIER) cc_final: 0.7311 (mt0) REVERT: G 36 LYS cc_start: 0.8797 (mptt) cc_final: 0.8466 (mmtm) REVERT: H 33 ARG cc_start: 0.6847 (mtm180) cc_final: 0.6462 (mtm180) REVERT: H 42 TYR cc_start: 0.8608 (t80) cc_final: 0.8244 (t80) REVERT: L 56 PHE cc_start: 0.7878 (m-80) cc_final: 0.7521 (m-10) REVERT: L 69 PHE cc_start: 0.6815 (OUTLIER) cc_final: 0.5913 (m-10) REVERT: L 147 MET cc_start: 0.4199 (mpp) cc_final: 0.3734 (mpp) outliers start: 30 outliers final: 20 residues processed: 196 average time/residue: 0.3282 time to fit residues: 88.4629 Evaluate side-chains 199 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 177 time to evaluate : 1.243 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 41 optimal weight: 0.9990 chunk 112 optimal weight: 0.1980 chunk 24 optimal weight: 0.0770 chunk 73 optimal weight: 6.9990 chunk 30 optimal weight: 0.9990 chunk 124 optimal weight: 6.9990 chunk 103 optimal weight: 0.7980 chunk 57 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 65 optimal weight: 1.9990 chunk 120 optimal weight: 0.8980 overall best weight: 0.5938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8179 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 15483 Z= 0.185 Angle : 0.567 13.361 22182 Z= 0.319 Chirality : 0.035 0.421 2516 Planarity : 0.004 0.034 1795 Dihedral : 28.906 179.855 4412 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.56 % Favored : 97.44 % Rotamer: Outliers : 3.03 % Allowed : 17.19 % Favored : 79.78 % 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: 1.98 (0.26), residues: 1058 helix: 2.39 (0.21), residues: 652 sheet: 0.75 (0.86), residues: 36 loop : -0.62 (0.31), residues: 370 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.003 TRP K 77 HIS 0.003 0.000 HIS F 75 PHE 0.014 0.001 PHE L 56 TYR 0.022 0.001 TYR H 83 ARG 0.008 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 212 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 184 time to evaluate : 1.241 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 88 TYR cc_start: 0.8778 (m-10) cc_final: 0.8428 (m-10) REVERT: D 68 ASP cc_start: 0.8250 (t70) cc_final: 0.7812 (t0) REVERT: D 71 GLU cc_start: 0.8065 (tp30) cc_final: 0.7830 (tp30) REVERT: E 125 GLN cc_start: 0.8026 (OUTLIER) cc_final: 0.7280 (mt0) REVERT: G 36 LYS cc_start: 0.8775 (mptt) cc_final: 0.8429 (mmtm) REVERT: H 33 ARG cc_start: 0.6828 (mtm180) cc_final: 0.6491 (mtm180) REVERT: H 42 TYR cc_start: 0.8533 (t80) cc_final: 0.8098 (t80) REVERT: K 20 MET cc_start: 0.7319 (mmm) cc_final: 0.6406 (mmm) REVERT: K 61 TRP cc_start: 0.7756 (t60) cc_final: 0.7215 (t60) REVERT: L 56 PHE cc_start: 0.7877 (m-80) cc_final: 0.7640 (m-10) REVERT: L 147 MET cc_start: 0.4063 (mpp) cc_final: 0.3574 (mpp) outliers start: 28 outliers final: 22 residues processed: 198 average time/residue: 0.3435 time to fit residues: 94.6402 Evaluate side-chains 202 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 179 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 14 optimal weight: 0.1980 chunk 71 optimal weight: 1.9990 chunk 91 optimal weight: 4.9990 chunk 70 optimal weight: 0.5980 chunk 105 optimal weight: 3.9990 chunk 69 optimal weight: 0.6980 chunk 124 optimal weight: 0.0010 chunk 77 optimal weight: 4.9990 chunk 75 optimal weight: 4.9990 chunk 57 optimal weight: 0.9980 chunk 76 optimal weight: 3.9990 overall best weight: 0.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 25 ASN G 73 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1885 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 15483 Z= 0.174 Angle : 0.563 13.800 22182 Z= 0.315 Chirality : 0.034 0.263 2516 Planarity : 0.004 0.040 1795 Dihedral : 28.890 179.538 4412 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 9.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 3.03 % Allowed : 17.62 % Favored : 79.35 % 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: 2.02 (0.26), residues: 1058 helix: 2.41 (0.21), residues: 654 sheet: 0.69 (0.87), residues: 36 loop : -0.59 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP L 33 HIS 0.003 0.000 HIS K 65 PHE 0.009 0.001 PHE L 56 TYR 0.026 0.001 TYR H 83 ARG 0.012 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 213 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 185 time to evaluate : 1.217 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 77 LYS cc_start: 0.9036 (mttm) cc_final: 0.8507 (mttp) REVERT: B 88 TYR cc_start: 0.8672 (m-10) cc_final: 0.8362 (m-10) REVERT: D 68 ASP cc_start: 0.8138 (t70) cc_final: 0.7864 (t0) REVERT: D 71 GLU cc_start: 0.8112 (tp30) cc_final: 0.7847 (tp30) REVERT: E 125 GLN cc_start: 0.8048 (OUTLIER) cc_final: 0.7328 (mt0) REVERT: G 36 LYS cc_start: 0.8784 (mptt) cc_final: 0.8450 (mmtm) REVERT: H 33 ARG cc_start: 0.6825 (mtm180) cc_final: 0.6462 (mtm180) REVERT: H 42 TYR cc_start: 0.8537 (t80) cc_final: 0.8103 (t80) REVERT: K 20 MET cc_start: 0.7428 (mmm) cc_final: 0.6594 (mmm) REVERT: K 68 ARG cc_start: 0.7498 (mmp80) cc_final: 0.6643 (ptp-170) REVERT: L 7 ASN cc_start: 0.7903 (m-40) cc_final: 0.7663 (p0) REVERT: L 66 LYS cc_start: 0.7317 (mmtt) cc_final: 0.7098 (mmtp) REVERT: L 69 PHE cc_start: 0.6685 (OUTLIER) cc_final: 0.5849 (m-10) REVERT: L 147 MET cc_start: 0.4237 (mpp) cc_final: 0.3701 (mpp) outliers start: 28 outliers final: 19 residues processed: 200 average time/residue: 0.3271 time to fit residues: 90.3605 Evaluate side-chains 199 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 178 time to evaluate : 1.163 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 74 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 39 ILE Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 32 HIS Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 98 THR Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 49 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 79 optimal weight: 4.9990 chunk 84 optimal weight: 5.9990 chunk 61 optimal weight: 1.9990 chunk 11 optimal weight: 1.9990 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 119 optimal weight: 10.0000 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN G 89 ASN ** L 7 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 20 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8263 moved from start: 0.2014 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.054 15483 Z= 0.329 Angle : 0.634 13.578 22182 Z= 0.350 Chirality : 0.038 0.426 2516 Planarity : 0.004 0.042 1795 Dihedral : 29.155 179.285 4412 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 10.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.03 % Allowed : 18.49 % Favored : 78.49 % 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: 1.73 (0.26), residues: 1058 helix: 2.10 (0.20), residues: 654 sheet: 1.25 (0.84), residues: 42 loop : -0.68 (0.32), residues: 362 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP L 33 HIS 0.004 0.001 HIS F 75 PHE 0.011 0.002 PHE L 56 TYR 0.037 0.002 TYR H 83 ARG 0.014 0.001 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 172 time to evaluate : 1.296 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8491 (t70) cc_final: 0.8160 (t0) REVERT: D 71 GLU cc_start: 0.8055 (tp30) cc_final: 0.7788 (tp30) REVERT: E 125 GLN cc_start: 0.8108 (OUTLIER) cc_final: 0.7341 (mt0) REVERT: H 33 ARG cc_start: 0.6836 (mtm180) cc_final: 0.6506 (mtm180) REVERT: H 42 TYR cc_start: 0.8635 (t80) cc_final: 0.8314 (t80) REVERT: K 20 MET cc_start: 0.7230 (mmm) cc_final: 0.6285 (mmm) REVERT: K 46 LYS cc_start: 0.7890 (ptpt) cc_final: 0.7353 (ptpt) REVERT: L 147 MET cc_start: 0.4190 (mpp) cc_final: 0.3677 (mpp) outliers start: 28 outliers final: 23 residues processed: 187 average time/residue: 0.3264 time to fit residues: 83.9916 Evaluate side-chains 192 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 168 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 71 VAL Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain H residue 119 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 3 LEU Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 108 optimal weight: 3.9990 chunk 115 optimal weight: 6.9990 chunk 119 optimal weight: 4.9990 chunk 69 optimal weight: 0.7980 chunk 50 optimal weight: 0.9990 chunk 90 optimal weight: 4.9990 chunk 35 optimal weight: 0.5980 chunk 104 optimal weight: 0.8980 chunk 109 optimal weight: 8.9990 chunk 76 optimal weight: 4.9990 chunk 122 optimal weight: 40.0000 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN G 89 ASN ** L 32 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 15483 Z= 0.303 Angle : 0.630 14.130 22182 Z= 0.348 Chirality : 0.037 0.396 2516 Planarity : 0.004 0.046 1795 Dihedral : 29.133 179.951 4412 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 9.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.92 % Allowed : 19.57 % Favored : 77.51 % 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: 1058 helix: 2.05 (0.21), residues: 654 sheet: 1.00 (0.90), residues: 37 loop : -0.72 (0.32), residues: 367 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP L 33 HIS 0.003 0.001 HIS F 75 PHE 0.022 0.001 PHE L 62 TYR 0.040 0.002 TYR H 83 ARG 0.008 0.000 ARG L 136 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 176 time to evaluate : 1.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8470 (t70) cc_final: 0.8159 (t0) REVERT: D 71 GLU cc_start: 0.8060 (tp30) cc_final: 0.7802 (tp30) REVERT: E 125 GLN cc_start: 0.8105 (OUTLIER) cc_final: 0.7327 (mt0) REVERT: H 33 ARG cc_start: 0.6831 (mtm180) cc_final: 0.6487 (mtm180) REVERT: H 42 TYR cc_start: 0.8608 (t80) cc_final: 0.8281 (t80) REVERT: H 59 MET cc_start: 0.9019 (tpp) cc_final: 0.8806 (mmm) REVERT: K 20 MET cc_start: 0.7370 (mmm) cc_final: 0.6228 (mmm) REVERT: L 147 MET cc_start: 0.4192 (mpp) cc_final: 0.3700 (mpp) outliers start: 27 outliers final: 21 residues processed: 190 average time/residue: 0.3349 time to fit residues: 87.6290 Evaluate side-chains 195 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 173 time to evaluate : 1.128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 74 optimal weight: 3.9990 chunk 58 optimal weight: 0.7980 chunk 85 optimal weight: 6.9990 chunk 128 optimal weight: 6.9990 chunk 118 optimal weight: 7.9990 chunk 102 optimal weight: 6.9990 chunk 10 optimal weight: 0.5980 chunk 79 optimal weight: 4.9990 chunk 62 optimal weight: 2.9990 chunk 81 optimal weight: 4.9990 chunk 109 optimal weight: 0.0370 overall best weight: 1.6862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 89 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2181 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 15483 Z= 0.343 Angle : 0.653 13.828 22182 Z= 0.359 Chirality : 0.038 0.425 2516 Planarity : 0.005 0.040 1795 Dihedral : 29.205 179.647 4412 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 10.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.49 % Allowed : 19.78 % Favored : 77.73 % 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: 1.48 (0.26), residues: 1058 helix: 1.98 (0.21), residues: 647 sheet: 0.97 (0.91), residues: 37 loop : -0.83 (0.31), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP L 33 HIS 0.004 0.001 HIS H 82 PHE 0.026 0.002 PHE L 62 TYR 0.044 0.002 TYR H 83 ARG 0.013 0.001 ARG L 136 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2116 Ramachandran restraints generated. 1058 Oldfield, 0 Emsley, 1058 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 174 time to evaluate : 1.253 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: D 68 ASP cc_start: 0.8489 (t70) cc_final: 0.8101 (t0) REVERT: D 71 GLU cc_start: 0.8065 (tp30) cc_final: 0.7803 (tp30) REVERT: E 125 GLN cc_start: 0.8116 (OUTLIER) cc_final: 0.7369 (mt0) REVERT: H 33 ARG cc_start: 0.6863 (mtm180) cc_final: 0.6497 (mtm180) REVERT: H 42 TYR cc_start: 0.8612 (t80) cc_final: 0.8299 (t80) REVERT: L 147 MET cc_start: 0.4263 (mpp) cc_final: 0.3698 (mpp) outliers start: 23 outliers final: 21 residues processed: 186 average time/residue: 0.3257 time to fit residues: 83.1592 Evaluate side-chains 191 residues out of total 921 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 169 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 80 THR Chi-restraints excluded: chain C residue 23 LEU Chi-restraints excluded: chain C residue 100 VAL Chi-restraints excluded: chain D residue 31 ARG Chi-restraints excluded: chain D residue 36 SER Chi-restraints excluded: chain D residue 80 LEU Chi-restraints excluded: chain D residue 90 THR Chi-restraints excluded: chain E residue 58 THR Chi-restraints excluded: chain E residue 112 ILE Chi-restraints excluded: chain E residue 125 GLN Chi-restraints excluded: chain F residue 73 THR Chi-restraints excluded: chain G residue 15 CYS Chi-restraints excluded: chain G residue 89 ASN Chi-restraints excluded: chain H residue 52 THR Chi-restraints excluded: chain K residue 28 THR Chi-restraints excluded: chain K residue 62 THR Chi-restraints excluded: chain L residue 50 PHE Chi-restraints excluded: chain L residue 69 PHE Chi-restraints excluded: chain L residue 97 LEU Chi-restraints excluded: chain L residue 102 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 129 random chunks: chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 5.9990 chunk 42 optimal weight: 0.9980 chunk 105 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 89 optimal weight: 4.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3788 r_free = 0.3788 target = 0.145480 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 27)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.104508 restraints weight = 26444.516| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 31)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.104657 restraints weight = 51804.396| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 27)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.105567 restraints weight = 37803.573| |-----------------------------------------------------------------------------| r_work (final): 0.3089 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3123 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3123 r_free = 0.3123 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3120 r_free = 0.3120 target_work(ls_wunit_k1) = 0.096 | | occupancies: max = 1.00 min = 0.31 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3120 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8219 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 15483 Z= 0.231 Angle : 0.621 14.160 22182 Z= 0.342 Chirality : 0.036 0.426 2516 Planarity : 0.004 0.033 1795 Dihedral : 29.110 179.581 4412 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 10.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.94 % Favored : 97.06 % Rotamer: Outliers : 2.59 % Allowed : 20.11 % Favored : 77.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.65 (0.26), residues: 1058 helix: 2.13 (0.21), residues: 649 sheet: 0.86 (0.90), residues: 37 loop : -0.79 (0.31), residues: 372 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP L 33 HIS 0.003 0.001 HIS F 75 PHE 0.035 0.001 PHE L 62 TYR 0.023 0.002 TYR H 83 ARG 0.008 0.000 ARG L 136 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2629.63 seconds wall clock time: 48 minutes 58.32 seconds (2938.32 seconds total)