Starting phenix.real_space_refine on Fri Feb 16 02:54:33 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d20_30552/02_2024/7d20_30552.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d20_30552/02_2024/7d20_30552.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d20_30552/02_2024/7d20_30552.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d20_30552/02_2024/7d20_30552.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d20_30552/02_2024/7d20_30552.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d20_30552/02_2024/7d20_30552.pdb" } resolution = 3.0 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= 1.000 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 1358 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: 5 Type Number sf(0) Gaussians P 272 5.49 5 S 14 5.16 5 C 7237 2.51 5 N 2397 2.21 5 O 2916 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 73": "OE1" <-> "OE2" Residue "A ARG 80": "NH1" <-> "NH2" Residue "E GLU 96": "OE1" <-> "OE2" Residue "E GLU 107": "OE1" <-> "OE2" Residue "C GLU 91": "OE1" <-> "OE2" Residue "F GLU 52": "OE1" <-> "OE2" Residue "F GLU 74": "OE1" <-> "OE2" Residue "G ARG 11": "NH1" <-> "NH2" Residue "K ARG 188": "NH1" <-> "NH2" Residue "K ARG 189": "NH1" <-> "NH2" Residue "K ARG 192": "NH1" <-> "NH2" Residue "K GLU 197": "OE1" <-> "OE2" Residue "K GLU 215": "OE1" <-> "OE2" Residue "K GLU 216": "OE1" <-> "OE2" Residue "K GLU 251": "OE1" <-> "OE2" Residue "K GLU 259": "OE1" <-> "OE2" Residue "K GLU 331": "OE1" <-> "OE2" Residue "H GLU 35": "OE1" <-> "OE2" Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H GLU 76": "OE1" <-> "OE2" Residue "H GLU 105": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 12836 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 732 Number of conformers: 1 Conformer: "" Number of residues, atoms: 89, 732 Classifications: {'peptide': 89} Link IDs: {'PTRANS': 2, 'TRANS': 86} Chain: "E" Number of atoms: 749 Number of conformers: 1 Conformer: "" Number of residues, atoms: 91, 749 Classifications: {'peptide': 91} Link IDs: {'PTRANS': 2, 'TRANS': 88} Chain: "B" Number of atoms: 638 Number of conformers: 1 Conformer: "" Number of residues, atoms: 80, 638 Classifications: {'peptide': 80} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 78} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 699 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "I" Number of atoms: 2768 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2768 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "J" Number of atoms: 2808 Number of conformers: 1 Conformer: "" Number of residues, atoms: 136, 2808 Classifications: {'DNA': 136} Link IDs: {'rna3p': 135} Chain: "K" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Time building chain proxies: 7.19, per 1000 atoms: 0.56 Number of scatterers: 12836 At special positions: 0 Unit cell: (118.65, 99.75, 116.55, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 14 16.00 P 272 15.00 O 2916 8.00 N 2397 7.00 C 7237 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: 7.35 Conformation dependent library (CDL) restraints added in 1.4 seconds 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1694 Finding SS restraints... Secondary structure from input PDB file: 37 helices and 12 sheets defined 61.9% alpha, 6.0% beta 132 base pairs and 237 stacking pairs defined. Time for finding SS restraints: 6.29 Creating SS restraints... Processing helix chain 'A' and resid 47 through 56 removed outlier: 3.758A pdb=" N LYS A 53 " --> pdb=" O LYS A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 75 Processing helix chain 'A' and resid 87 through 114 removed outlier: 4.010A pdb=" N LEU A 92 " --> pdb=" O ALA A 88 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 127 removed outlier: 3.854A pdb=" N VAL A 126 " --> pdb=" O PHE A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 127 through 132 removed outlier: 3.592A pdb=" N ARG A 131 " --> pdb=" O GLN A 127 " (cutoff:3.500A) Processing helix chain 'E' and resid 46 through 55 Processing helix chain 'E' and resid 63 through 78 removed outlier: 3.575A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) removed outlier: 3.736A pdb=" N VAL E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N LYS E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) removed outlier: 3.589A pdb=" N PHE E 78 " --> pdb=" O ILE E 74 " (cutoff:3.500A) Processing helix chain 'E' and resid 87 through 110 removed outlier: 3.833A pdb=" N LEU E 92 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'E' and resid 122 through 134 removed outlier: 3.620A pdb=" N ARG E 133 " --> pdb=" O ALA E 129 " (cutoff:3.500A) 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: 3.581A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 removed outlier: 3.606A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.397A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N ASN C 73 " --> pdb=" O ALA C 69 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.569A pdb=" N ASP C 90 " --> pdb=" O ALA C 86 " (cutoff:3.500A) Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 removed outlier: 3.616A 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 124 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.618A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N ALA F 76 " --> pdb=" O TYR F 72 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.524A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.568A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'K' and resid 194 through 213 Processing helix chain 'K' and resid 254 through 264 removed outlier: 3.885A pdb=" N GLU K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N ALA K 260 " --> pdb=" O LYS K 256 " (cutoff:3.500A) removed outlier: 3.506A pdb=" N GLN K 264 " --> pdb=" O ALA K 260 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 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 Processing helix chain 'H' and resid 103 through 124 Processing sheet with id=AA1, first strand: chain 'A' and resid 120 through 121 Processing sheet with id=AA2, first strand: chain 'E' and resid 85 through 86 removed outlier: 7.260A pdb=" N ASN E 85 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'E' and resid 120 through 121 Processing sheet with id=AA4, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA5, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.401A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA7, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.913A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.034A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB1, first strand: chain 'K' and resid 218 through 223 removed outlier: 3.931A pdb=" N GLY K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'K' and resid 241 through 244 removed outlier: 7.160A pdb=" N LEU K 320 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 5.030A pdb=" N GLU K 244 " --> pdb=" O LEU K 318 " (cutoff:3.500A) removed outlier: 7.166A pdb=" N LEU K 318 " --> pdb=" O GLU K 244 " (cutoff:3.500A) removed outlier: 3.829A pdb=" N VAL K 315 " --> pdb=" O ILE K 312 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 248 through 250 removed outlier: 3.685A pdb=" N CYS K 283 " --> pdb=" O ILE K 250 " (cutoff:3.500A) removed outlier: 3.791A pdb=" N PHE K 275 " --> pdb=" O TYR K 282 " (cutoff:3.500A) 423 hydrogen bonds defined for protein. 1248 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 341 hydrogen bonds 682 hydrogen bond angles 0 basepair planarities 132 basepair parallelities 237 stacking parallelities Total time for adding SS restraints: 6.30 Time building geometry restraints manager: 7.71 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: 2145 1.33 - 1.45: 4532 1.45 - 1.57: 6382 1.57 - 1.69: 542 1.69 - 1.81: 22 Bond restraints: 13623 Sorted by residual: bond pdb=" CA ALA B 76 " pdb=" C ALA B 76 " ideal model delta sigma weight residual 1.523 1.468 0.055 1.80e-02 3.09e+03 9.40e+00 bond pdb=" CB ILE F 46 " pdb=" CG2 ILE F 46 " ideal model delta sigma weight residual 1.521 1.450 0.071 3.30e-02 9.18e+02 4.68e+00 bond pdb=" CB THR E 113 " pdb=" CG2 THR E 113 " ideal model delta sigma weight residual 1.521 1.454 0.067 3.30e-02 9.18e+02 4.09e+00 bond pdb=" CB VAL B 70 " pdb=" CG1 VAL B 70 " ideal model delta sigma weight residual 1.521 1.458 0.063 3.30e-02 9.18e+02 3.66e+00 bond pdb=" CB ILE B 50 " pdb=" CG2 ILE B 50 " ideal model delta sigma weight residual 1.521 1.460 0.061 3.30e-02 9.18e+02 3.43e+00 ... (remaining 13618 not shown) Histogram of bond angle deviations from ideal: 80.57 - 91.25: 2 91.25 - 101.94: 287 101.94 - 112.63: 8667 112.63 - 123.32: 9279 123.32 - 134.00: 1319 Bond angle restraints: 19554 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP1 DG J 21 " ideal model delta sigma weight residual 108.00 80.57 27.43 3.00e+00 1.11e-01 8.36e+01 angle pdb=" N VAL E 119 " pdb=" CA VAL E 119 " pdb=" C VAL E 119 " ideal model delta sigma weight residual 113.71 106.10 7.61 9.50e-01 1.11e+00 6.41e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 87.00 21.00 3.00e+00 1.11e-01 4.90e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 98.12 5.88 1.50e+00 4.44e-01 1.54e+01 angle pdb=" OP1 DG J 21 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 120.00 130.43 -10.43 3.00e+00 1.11e-01 1.21e+01 ... (remaining 19549 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.94: 5845 32.94 - 65.88: 1564 65.88 - 98.82: 53 98.82 - 131.76: 1 131.76 - 164.71: 1 Dihedral angle restraints: 7464 sinusoidal: 4830 harmonic: 2634 Sorted by residual: dihedral pdb=" CA THR E 113 " pdb=" C THR E 113 " pdb=" N LEU E 114 " pdb=" CA LEU E 114 " ideal model delta harmonic sigma weight residual 180.00 150.65 29.35 0 5.00e+00 4.00e-02 3.45e+01 dihedral pdb=" CA ILE F 29 " pdb=" C ILE F 29 " pdb=" N THR F 30 " pdb=" CA THR F 30 " ideal model delta harmonic sigma weight residual -180.00 -160.25 -19.75 0 5.00e+00 4.00e-02 1.56e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual 180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 ... (remaining 7461 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.405: 2211 0.405 - 0.809: 0 0.809 - 1.214: 0 1.214 - 1.619: 0 1.619 - 2.023: 1 Chirality restraints: 2212 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 0.32 2.02 2.00e-01 2.50e+01 1.02e+02 chirality pdb=" CB ILE D 54 " pdb=" CA ILE D 54 " pdb=" CG1 ILE D 54 " pdb=" CG2 ILE D 54 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.27e-01 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.60 -0.16 2.00e-01 2.50e+01 6.74e-01 ... (remaining 2209 not shown) Planarity restraints: 1531 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.029 2.00e-02 2.50e+03 1.24e-02 4.61e+00 pdb=" N9 DG I 26 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.006 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.007 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.030 2.00e-02 2.50e+03 1.29e-02 4.55e+00 pdb=" N9 DA I -35 " -0.027 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.003 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.011 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.001 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.007 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DC J 24 " -0.002 2.00e-02 2.50e+03 1.32e-02 3.91e+00 pdb=" N1 DC J 24 " 0.004 2.00e-02 2.50e+03 pdb=" C2 DC J 24 " -0.031 2.00e-02 2.50e+03 pdb=" O2 DC J 24 " 0.018 2.00e-02 2.50e+03 pdb=" N3 DC J 24 " 0.008 2.00e-02 2.50e+03 pdb=" C4 DC J 24 " -0.012 2.00e-02 2.50e+03 pdb=" N4 DC J 24 " 0.005 2.00e-02 2.50e+03 pdb=" C5 DC J 24 " 0.005 2.00e-02 2.50e+03 pdb=" C6 DC J 24 " 0.005 2.00e-02 2.50e+03 ... (remaining 1528 not shown) Histogram of nonbonded interaction distances: 1.75 - 2.38: 38 2.38 - 3.01: 6761 3.01 - 3.64: 21719 3.64 - 4.27: 34416 4.27 - 4.90: 50373 Nonbonded interactions: 113307 Sorted by model distance: nonbonded pdb=" OXT GLY B 102 " pdb=" ND2 ASN H 67 " model vdw 1.752 2.520 nonbonded pdb=" OG1 THR A 79 " pdb=" O VAL A 82 " model vdw 2.039 2.440 nonbonded pdb=" O ALA K 255 " pdb=" OH TYR K 274 " model vdw 2.088 2.440 nonbonded pdb=" OD2 ASP D 68 " pdb=" OH TYR F 98 " model vdw 2.121 2.440 nonbonded pdb=" OH TYR B 98 " pdb=" OD2 ASP H 68 " model vdw 2.132 2.440 ... (remaining 113302 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' and resid 46 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 23 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.260 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.010 Extract box with map and model: 1.930 Check model and map are aligned: 0.180 Set scattering table: 0.120 Process input model: 45.290 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.050 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:10.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.350 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7622 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 : 0.009 0.071 13623 Z= 0.562 Angle : 0.811 27.433 19554 Z= 0.464 Chirality : 0.061 2.023 2212 Planarity : 0.004 0.039 1531 Dihedral : 28.627 164.706 5770 Min Nonbonded Distance : 1.752 Molprobity Statistics. All-atom Clashscore : 12.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 7.28 % Favored : 92.72 % 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: -3.29 (0.23), residues: 896 helix: -1.58 (0.18), residues: 561 sheet: -3.38 (0.76), residues: 26 loop : -3.03 (0.29), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.002 TRP K 349 HIS 0.006 0.001 HIS F 75 PHE 0.027 0.002 PHE G 25 TYR 0.015 0.002 TYR K 274 ARG 0.007 0.001 ARG A 118 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 161 time to evaluate : 0.921 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8397 (tttt) cc_final: 0.7808 (tttp) REVERT: E 53 LYS cc_start: 0.8337 (ttmt) cc_final: 0.7983 (ttmm) REVERT: E 59 HIS cc_start: 0.7451 (m-70) cc_final: 0.6808 (m170) REVERT: E 131 ARG cc_start: 0.8275 (tmt-80) cc_final: 0.8042 (ttp80) REVERT: B 44 LYS cc_start: 0.8510 (tttt) cc_final: 0.8292 (tttt) REVERT: C 15 LYS cc_start: 0.8510 (pttm) cc_final: 0.8252 (pttt) REVERT: C 36 LYS cc_start: 0.8870 (ptmm) cc_final: 0.8542 (ptpt) REVERT: C 50 TYR cc_start: 0.8890 (t80) cc_final: 0.8543 (t80) REVERT: C 75 LYS cc_start: 0.8255 (mttp) cc_final: 0.8021 (mtpp) REVERT: C 90 ASP cc_start: 0.7868 (t0) cc_final: 0.7547 (t0) REVERT: C 95 LYS cc_start: 0.8820 (ttmt) cc_final: 0.8407 (mtpp) REVERT: C 104 GLN cc_start: 0.8798 (mm-40) cc_final: 0.8291 (mm110) REVERT: D 51 ASP cc_start: 0.7960 (p0) cc_final: 0.7621 (p0) REVERT: D 76 GLU cc_start: 0.8022 (tp30) cc_final: 0.7530 (tp30) REVERT: D 85 LYS cc_start: 0.9043 (mtpt) cc_final: 0.8761 (mtmm) REVERT: G 19 SER cc_start: 0.9475 (t) cc_final: 0.9121 (p) REVERT: K 218 MET cc_start: 0.5989 (mpp) cc_final: 0.5753 (mpp) REVERT: K 310 HIS cc_start: 0.7529 (t70) cc_final: 0.6996 (t70) outliers start: 0 outliers final: 0 residues processed: 161 average time/residue: 1.8343 time to fit residues: 312.9429 Evaluate side-chains 119 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 119 time to evaluate : 1.047 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 95 optimal weight: 0.5980 chunk 85 optimal weight: 8.9990 chunk 47 optimal weight: 1.9990 chunk 29 optimal weight: 0.8980 chunk 57 optimal weight: 0.9990 chunk 45 optimal weight: 1.9990 chunk 88 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 53 optimal weight: 0.9980 chunk 65 optimal weight: 8.9990 chunk 102 optimal weight: 9.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 59 HIS E 115 HIS B 27 GLN C 24 GLN D 49 HIS D 84 ASN D 95 GLN F 18 HIS ** F 75 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7570 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 13623 Z= 0.185 Angle : 0.655 26.808 19554 Z= 0.362 Chirality : 0.056 2.031 2212 Planarity : 0.004 0.036 1531 Dihedral : 30.959 164.486 3983 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 10.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.79 % Favored : 97.21 % Rotamer: Outliers : 2.12 % Allowed : 16.01 % Favored : 81.88 % 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: -0.80 (0.27), residues: 896 helix: 0.37 (0.21), residues: 573 sheet: -2.67 (0.65), residues: 44 loop : -1.95 (0.34), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.005 0.001 HIS C 82 PHE 0.011 0.001 PHE K 275 TYR 0.014 0.001 TYR D 40 ARG 0.006 0.001 ARG D 86 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 1.126 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8243 (tttt) cc_final: 0.7697 (tttm) REVERT: E 53 LYS cc_start: 0.8277 (ttmt) cc_final: 0.7964 (ttmm) REVERT: E 59 HIS cc_start: 0.7081 (m90) cc_final: 0.6512 (m90) REVERT: C 15 LYS cc_start: 0.8521 (pttm) cc_final: 0.8284 (pttt) REVERT: C 19 SER cc_start: 0.9379 (t) cc_final: 0.8859 (p) REVERT: C 36 LYS cc_start: 0.8724 (ptmm) cc_final: 0.8433 (ptpt) REVERT: C 61 GLU cc_start: 0.7235 (tp30) cc_final: 0.6983 (tp30) REVERT: C 92 GLU cc_start: 0.8536 (mm-30) cc_final: 0.7493 (mt-10) REVERT: C 95 LYS cc_start: 0.8759 (ttmt) cc_final: 0.8368 (mtpp) REVERT: D 85 LYS cc_start: 0.8988 (mtpt) cc_final: 0.8736 (mtmm) REVERT: G 19 SER cc_start: 0.9450 (t) cc_final: 0.9205 (p) REVERT: G 36 LYS cc_start: 0.8980 (pptt) cc_final: 0.8419 (pttt) REVERT: G 72 ASP cc_start: 0.8317 (m-30) cc_final: 0.8011 (m-30) REVERT: K 310 HIS cc_start: 0.7424 (t70) cc_final: 0.6662 (t-90) outliers start: 16 outliers final: 4 residues processed: 144 average time/residue: 1.6302 time to fit residues: 251.0957 Evaluate side-chains 122 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 118 time to evaluate : 1.000 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain D residue 113 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 57 optimal weight: 0.7980 chunk 31 optimal weight: 8.9990 chunk 85 optimal weight: 8.9990 chunk 69 optimal weight: 7.9990 chunk 28 optimal weight: 0.9990 chunk 102 optimal weight: 40.0000 chunk 111 optimal weight: 3.9990 chunk 91 optimal weight: 9.9990 chunk 101 optimal weight: 6.9990 chunk 35 optimal weight: 0.3980 chunk 82 optimal weight: 5.9990 overall best weight: 2.4386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 95 GLN E 127 GLN B 27 GLN C 38 ASN C 104 GLN D 49 HIS F 25 ASN F 27 GLN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 110 ASN ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7621 moved from start: 0.1919 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13623 Z= 0.283 Angle : 0.664 27.072 19554 Z= 0.364 Chirality : 0.056 1.992 2212 Planarity : 0.004 0.035 1531 Dihedral : 31.105 166.868 3983 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 10.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.35 % Favored : 96.65 % Rotamer: Outliers : 3.31 % Allowed : 18.39 % Favored : 78.31 % 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: 0.01 (0.27), residues: 896 helix: 0.94 (0.21), residues: 577 sheet: -2.29 (0.70), residues: 44 loop : -1.53 (0.35), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 86 HIS 0.005 0.001 HIS B 75 PHE 0.017 0.001 PHE G 25 TYR 0.015 0.001 TYR D 40 ARG 0.012 0.001 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 126 time to evaluate : 0.994 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8283 (tttt) cc_final: 0.7735 (tttm) REVERT: E 53 LYS cc_start: 0.8310 (ttmt) cc_final: 0.8011 (ttmm) REVERT: E 59 HIS cc_start: 0.7053 (m90) cc_final: 0.6664 (m90) REVERT: E 83 ASP cc_start: 0.8476 (OUTLIER) cc_final: 0.7621 (p0) REVERT: B 74 GLU cc_start: 0.8449 (mt-10) cc_final: 0.8244 (mt-10) REVERT: C 15 LYS cc_start: 0.8451 (pttm) cc_final: 0.8186 (pttt) REVERT: C 19 SER cc_start: 0.9383 (t) cc_final: 0.8804 (p) REVERT: C 29 ARG cc_start: 0.8202 (OUTLIER) cc_final: 0.6581 (ttp-170) REVERT: C 36 LYS cc_start: 0.8724 (ptmm) cc_final: 0.8419 (ptpt) REVERT: C 61 GLU cc_start: 0.7191 (tp30) cc_final: 0.6965 (tp30) REVERT: C 72 ASP cc_start: 0.8462 (m-30) cc_final: 0.8257 (m-30) REVERT: C 90 ASP cc_start: 0.7617 (t0) cc_final: 0.7208 (t0) REVERT: C 92 GLU cc_start: 0.8593 (mm-30) cc_final: 0.7571 (mt-10) REVERT: C 95 LYS cc_start: 0.8740 (ttmt) cc_final: 0.8329 (mtpp) REVERT: D 85 LYS cc_start: 0.8964 (mtpt) cc_final: 0.8725 (mtmm) REVERT: F 21 VAL cc_start: 0.5348 (OUTLIER) cc_final: 0.4803 (p) REVERT: F 84 MET cc_start: 0.7713 (mmm) cc_final: 0.7484 (mmt) REVERT: G 19 SER cc_start: 0.9446 (t) cc_final: 0.9215 (p) REVERT: G 36 LYS cc_start: 0.8897 (pptt) cc_final: 0.8393 (pttt) REVERT: G 72 ASP cc_start: 0.8238 (m-30) cc_final: 0.7932 (m-30) REVERT: G 92 GLU cc_start: 0.8631 (mt-10) cc_final: 0.8297 (mt-10) REVERT: K 310 HIS cc_start: 0.7343 (t70) cc_final: 0.6534 (t-90) outliers start: 25 outliers final: 12 residues processed: 143 average time/residue: 1.5526 time to fit residues: 237.9287 Evaluate side-chains 128 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 113 time to evaluate : 1.016 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 29 ARG Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 59 MET Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain G residue 108 LEU Chi-restraints excluded: chain K residue 307 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 77 optimal weight: 10.0000 chunk 53 optimal weight: 0.7980 chunk 11 optimal weight: 0.0570 chunk 49 optimal weight: 1.9990 chunk 69 optimal weight: 6.9990 chunk 103 optimal weight: 50.0000 chunk 109 optimal weight: 3.9990 chunk 97 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 chunk 90 optimal weight: 30.0000 overall best weight: 0.9702 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 115 HIS E 95 GLN E 127 GLN B 27 GLN C 104 GLN D 49 HIS F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 109 HIS Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7568 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 13623 Z= 0.180 Angle : 0.621 26.662 19554 Z= 0.343 Chirality : 0.055 2.003 2212 Planarity : 0.003 0.044 1531 Dihedral : 30.593 167.712 3983 Min Nonbonded Distance : 2.034 Molprobity Statistics. All-atom Clashscore : 8.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 2.38 % Allowed : 20.37 % Favored : 77.25 % 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: 0.77 (0.28), residues: 896 helix: 1.49 (0.21), residues: 584 sheet: -2.14 (0.74), residues: 44 loop : -1.15 (0.36), residues: 268 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP E 86 HIS 0.003 0.001 HIS F 75 PHE 0.006 0.001 PHE A 67 TYR 0.019 0.002 TYR B 88 ARG 0.008 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 124 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8151 (tttt) cc_final: 0.7661 (tttp) REVERT: A 92 LEU cc_start: 0.7870 (OUTLIER) cc_final: 0.7538 (tp) REVERT: E 59 HIS cc_start: 0.6896 (m90) cc_final: 0.6473 (m90) REVERT: E 63 ARG cc_start: 0.7938 (mmp-170) cc_final: 0.7652 (mmp80) REVERT: E 83 ASP cc_start: 0.8369 (m-30) cc_final: 0.7642 (p0) REVERT: B 74 GLU cc_start: 0.8370 (mt-10) cc_final: 0.8144 (mt-10) REVERT: C 19 SER cc_start: 0.9453 (t) cc_final: 0.8939 (p) REVERT: C 36 LYS cc_start: 0.8545 (ptmm) cc_final: 0.8290 (ptpt) REVERT: C 90 ASP cc_start: 0.7703 (t0) cc_final: 0.7232 (t0) REVERT: C 92 GLU cc_start: 0.8620 (mm-30) cc_final: 0.7762 (mt-10) REVERT: C 95 LYS cc_start: 0.8785 (ttmt) cc_final: 0.8355 (mtpp) REVERT: D 85 LYS cc_start: 0.8912 (mtpt) cc_final: 0.8689 (mtmm) REVERT: F 21 VAL cc_start: 0.5275 (OUTLIER) cc_final: 0.4769 (p) REVERT: G 19 SER cc_start: 0.9426 (t) cc_final: 0.9210 (p) REVERT: G 36 LYS cc_start: 0.8655 (pptt) cc_final: 0.8317 (pttt) REVERT: G 72 ASP cc_start: 0.8324 (m-30) cc_final: 0.7968 (m-30) REVERT: G 92 GLU cc_start: 0.8511 (mt-10) cc_final: 0.8061 (mt-10) REVERT: K 310 HIS cc_start: 0.7285 (t70) cc_final: 0.6512 (t-90) outliers start: 18 outliers final: 8 residues processed: 136 average time/residue: 1.4582 time to fit residues: 213.1770 Evaluate side-chains 117 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 107 time to evaluate : 0.969 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 62 optimal weight: 50.0000 chunk 1 optimal weight: 3.9990 chunk 81 optimal weight: 6.9990 chunk 45 optimal weight: 0.8980 chunk 93 optimal weight: 9.9990 chunk 75 optimal weight: 30.0000 chunk 0 optimal weight: 3.9990 chunk 55 optimal weight: 5.9990 chunk 98 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 overall best weight: 2.3586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 89 GLN E 95 GLN E 127 GLN B 27 GLN B 93 GLN C 104 GLN D 47 GLN D 49 HIS F 25 ASN F 27 GLN F 93 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 49 HIS Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.2607 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.041 13623 Z= 0.272 Angle : 0.648 26.901 19554 Z= 0.352 Chirality : 0.055 1.977 2212 Planarity : 0.004 0.050 1531 Dihedral : 30.938 169.887 3983 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.12 % Favored : 96.88 % Rotamer: Outliers : 3.57 % Allowed : 21.03 % Favored : 75.40 % 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: 0.98 (0.28), residues: 896 helix: 1.66 (0.21), residues: 577 sheet: -1.96 (0.75), residues: 44 loop : -1.04 (0.36), residues: 275 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 47 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.001 PHE C 25 TYR 0.026 0.002 TYR B 88 ARG 0.011 0.000 ARG C 71 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 148 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 121 time to evaluate : 1.039 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8173 (tttt) cc_final: 0.7712 (tttp) REVERT: A 92 LEU cc_start: 0.7939 (OUTLIER) cc_final: 0.7602 (tp) REVERT: E 59 HIS cc_start: 0.7087 (m90) cc_final: 0.6707 (m90) REVERT: E 63 ARG cc_start: 0.7955 (mmp-170) cc_final: 0.7673 (mmp80) REVERT: E 83 ASP cc_start: 0.8449 (OUTLIER) cc_final: 0.7798 (p0) REVERT: B 44 LYS cc_start: 0.8577 (tttt) cc_final: 0.8266 (tttp) REVERT: C 15 LYS cc_start: 0.8262 (pttt) cc_final: 0.7950 (pmtt) REVERT: C 19 SER cc_start: 0.9405 (t) cc_final: 0.8911 (p) REVERT: C 36 LYS cc_start: 0.8694 (ptmm) cc_final: 0.8435 (ptpt) REVERT: C 90 ASP cc_start: 0.7741 (t0) cc_final: 0.7200 (t0) REVERT: C 92 GLU cc_start: 0.8634 (mm-30) cc_final: 0.7762 (mt-10) REVERT: C 95 LYS cc_start: 0.8788 (ttmt) cc_final: 0.8377 (mtpp) REVERT: D 85 LYS cc_start: 0.8972 (mtpt) cc_final: 0.8723 (mtmm) REVERT: F 21 VAL cc_start: 0.5400 (OUTLIER) cc_final: 0.4924 (p) REVERT: G 19 SER cc_start: 0.9450 (t) cc_final: 0.9206 (p) REVERT: G 36 LYS cc_start: 0.8681 (pptt) cc_final: 0.8306 (pttt) REVERT: G 92 GLU cc_start: 0.8587 (mt-10) cc_final: 0.8053 (mt-10) REVERT: K 310 HIS cc_start: 0.7279 (t70) cc_final: 0.6494 (t-90) outliers start: 27 outliers final: 13 residues processed: 137 average time/residue: 1.5868 time to fit residues: 232.8511 Evaluate side-chains 126 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 110 time to evaluate : 1.004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 VAL Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 98 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 64 optimal weight: 10.0000 chunk 26 optimal weight: 0.9980 chunk 109 optimal weight: 1.9990 chunk 90 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 0.9990 chunk 105 optimal weight: 3.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN B 27 GLN B 93 GLN C 38 ASN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7595 moved from start: 0.2867 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13623 Z= 0.229 Angle : 0.631 27.027 19554 Z= 0.343 Chirality : 0.055 1.987 2212 Planarity : 0.004 0.045 1531 Dihedral : 30.825 170.745 3983 Min Nonbonded Distance : 2.134 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.57 % Favored : 97.43 % Rotamer: Outliers : 3.04 % Allowed : 22.09 % Favored : 74.87 % 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: 1.17 (0.28), residues: 896 helix: 1.76 (0.21), residues: 582 sheet: -1.76 (0.76), residues: 44 loop : -0.92 (0.37), residues: 270 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 47 HIS 0.005 0.001 HIS F 75 PHE 0.008 0.001 PHE G 25 TYR 0.021 0.001 TYR B 88 ARG 0.010 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 143 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 120 time to evaluate : 1.029 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8103 (tttt) cc_final: 0.7652 (tttp) REVERT: A 92 LEU cc_start: 0.7904 (OUTLIER) cc_final: 0.7560 (tp) REVERT: E 59 HIS cc_start: 0.6988 (m90) cc_final: 0.6595 (m90) REVERT: E 63 ARG cc_start: 0.7913 (mmp-170) cc_final: 0.7651 (mmp80) REVERT: E 83 ASP cc_start: 0.8401 (OUTLIER) cc_final: 0.7974 (p0) REVERT: C 19 SER cc_start: 0.9398 (t) cc_final: 0.8932 (p) REVERT: C 36 LYS cc_start: 0.8678 (ptmm) cc_final: 0.8476 (ptpt) REVERT: C 90 ASP cc_start: 0.7733 (t0) cc_final: 0.7179 (t0) REVERT: C 92 GLU cc_start: 0.8619 (mm-30) cc_final: 0.7772 (mt-10) REVERT: C 95 LYS cc_start: 0.8842 (ttmt) cc_final: 0.8428 (mtpp) REVERT: D 85 LYS cc_start: 0.8942 (mtpt) cc_final: 0.8714 (mtmm) REVERT: F 21 VAL cc_start: 0.5585 (OUTLIER) cc_final: 0.5132 (p) REVERT: G 19 SER cc_start: 0.9449 (t) cc_final: 0.9207 (p) REVERT: G 36 LYS cc_start: 0.8592 (pptt) cc_final: 0.8263 (pttt) REVERT: G 72 ASP cc_start: 0.8296 (m-30) cc_final: 0.8057 (m-30) REVERT: G 92 GLU cc_start: 0.8575 (mt-10) cc_final: 0.8004 (mt-10) REVERT: K 310 HIS cc_start: 0.7251 (t70) cc_final: 0.6462 (t-90) outliers start: 23 outliers final: 12 residues processed: 131 average time/residue: 1.5391 time to fit residues: 216.3513 Evaluate side-chains 124 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 109 time to evaluate : 1.060 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 12 optimal weight: 0.7980 chunk 62 optimal weight: 50.0000 chunk 79 optimal weight: 7.9990 chunk 61 optimal weight: 0.4980 chunk 92 optimal weight: 50.0000 chunk 108 optimal weight: 0.6980 chunk 68 optimal weight: 7.9990 chunk 66 optimal weight: 8.9990 chunk 50 optimal weight: 5.9990 chunk 67 optimal weight: 7.9990 chunk 43 optimal weight: 1.9990 overall best weight: 1.9984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 89 GLN E 127 GLN B 27 GLN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7602 moved from start: 0.2939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 13623 Z= 0.244 Angle : 0.646 27.165 19554 Z= 0.347 Chirality : 0.055 1.992 2212 Planarity : 0.004 0.052 1531 Dihedral : 30.861 172.094 3983 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 9.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 3.04 % Allowed : 23.54 % Favored : 73.41 % 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: 1.28 (0.28), residues: 896 helix: 1.88 (0.21), residues: 576 sheet: -1.72 (0.76), residues: 44 loop : -0.93 (0.36), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 349 HIS 0.005 0.001 HIS F 75 PHE 0.009 0.001 PHE C 25 TYR 0.019 0.001 TYR B 88 ARG 0.011 0.000 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 141 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 118 time to evaluate : 1.067 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8090 (tttt) cc_final: 0.7660 (tttp) REVERT: A 92 LEU cc_start: 0.7926 (OUTLIER) cc_final: 0.7581 (tp) REVERT: E 59 HIS cc_start: 0.7095 (m90) cc_final: 0.6721 (m90) REVERT: E 60 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8310 (mt) REVERT: E 63 ARG cc_start: 0.7904 (mmp-170) cc_final: 0.7638 (mmp80) REVERT: E 83 ASP cc_start: 0.8405 (OUTLIER) cc_final: 0.7999 (p0) REVERT: B 44 LYS cc_start: 0.8529 (tttt) cc_final: 0.8187 (tttp) REVERT: C 19 SER cc_start: 0.9402 (t) cc_final: 0.8928 (p) REVERT: C 36 LYS cc_start: 0.8570 (ptmm) cc_final: 0.8364 (ptpt) REVERT: C 90 ASP cc_start: 0.7737 (t0) cc_final: 0.7179 (t0) REVERT: C 92 GLU cc_start: 0.8592 (mm-30) cc_final: 0.7716 (mt-10) REVERT: C 95 LYS cc_start: 0.8850 (ttmt) cc_final: 0.8439 (mtpp) REVERT: D 85 LYS cc_start: 0.8948 (mtpt) cc_final: 0.8728 (mtmm) REVERT: D 108 LYS cc_start: 0.7591 (mmtt) cc_final: 0.7069 (mmtt) REVERT: F 21 VAL cc_start: 0.5604 (OUTLIER) cc_final: 0.5182 (p) REVERT: G 19 SER cc_start: 0.9443 (t) cc_final: 0.9200 (p) REVERT: G 36 LYS cc_start: 0.8577 (pptt) cc_final: 0.8258 (pttt) REVERT: G 72 ASP cc_start: 0.8276 (m-30) cc_final: 0.7971 (m-30) REVERT: G 92 GLU cc_start: 0.8589 (mt-10) cc_final: 0.8018 (mt-10) REVERT: K 310 HIS cc_start: 0.7297 (t70) cc_final: 0.6517 (t-90) REVERT: H 59 MET cc_start: 0.8437 (tpp) cc_final: 0.8176 (mmm) outliers start: 23 outliers final: 13 residues processed: 131 average time/residue: 1.5690 time to fit residues: 220.6851 Evaluate side-chains 129 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 112 time to evaluate : 0.987 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 LYS Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 60 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 65 optimal weight: 10.0000 chunk 32 optimal weight: 5.9990 chunk 21 optimal weight: 2.9990 chunk 69 optimal weight: 7.9990 chunk 74 optimal weight: 20.0000 chunk 53 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 85 optimal weight: 7.9990 chunk 99 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 9.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN B 27 GLN D 49 HIS F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 84 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7630 moved from start: 0.2908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 13623 Z= 0.321 Angle : 0.675 27.328 19554 Z= 0.361 Chirality : 0.057 1.995 2212 Planarity : 0.004 0.045 1531 Dihedral : 31.058 173.207 3983 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 3.44 % Allowed : 23.28 % Favored : 73.28 % 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: 1.16 (0.28), residues: 896 helix: 1.75 (0.21), residues: 576 sheet: -1.66 (0.75), residues: 44 loop : -0.89 (0.37), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP K 349 HIS 0.006 0.001 HIS F 75 PHE 0.011 0.001 PHE G 25 TYR 0.021 0.002 TYR B 88 ARG 0.013 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 119 time to evaluate : 0.949 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8144 (tttt) cc_final: 0.7697 (tttp) REVERT: E 59 HIS cc_start: 0.7109 (m90) cc_final: 0.6741 (m90) REVERT: E 63 ARG cc_start: 0.7972 (mmp-170) cc_final: 0.7709 (mmp80) REVERT: E 83 ASP cc_start: 0.8434 (OUTLIER) cc_final: 0.8064 (p0) REVERT: C 19 SER cc_start: 0.9413 (t) cc_final: 0.8843 (p) REVERT: C 36 LYS cc_start: 0.8715 (ptmm) cc_final: 0.8515 (ptpt) REVERT: C 90 ASP cc_start: 0.7731 (t0) cc_final: 0.7198 (t0) REVERT: C 92 GLU cc_start: 0.8621 (mm-30) cc_final: 0.7729 (mt-10) REVERT: C 95 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8457 (mtpp) REVERT: D 59 MET cc_start: 0.8382 (tpp) cc_final: 0.8098 (tpt) REVERT: D 85 LYS cc_start: 0.8980 (mtpt) cc_final: 0.8737 (mtmm) REVERT: D 108 LYS cc_start: 0.7639 (mmtt) cc_final: 0.7107 (mmtt) REVERT: F 21 VAL cc_start: 0.5615 (OUTLIER) cc_final: 0.5186 (p) REVERT: G 19 SER cc_start: 0.9449 (t) cc_final: 0.9206 (p) REVERT: G 36 LYS cc_start: 0.8666 (OUTLIER) cc_final: 0.8312 (pttt) REVERT: G 72 ASP cc_start: 0.8192 (m-30) cc_final: 0.7905 (m-30) REVERT: G 92 GLU cc_start: 0.8570 (mt-10) cc_final: 0.8109 (mt-10) REVERT: K 310 HIS cc_start: 0.7302 (t70) cc_final: 0.6530 (t-90) outliers start: 26 outliers final: 14 residues processed: 135 average time/residue: 1.7147 time to fit residues: 246.4838 Evaluate side-chains 130 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 113 time to evaluate : 1.067 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 83 ASP Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain C residue 114 VAL Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 101 optimal weight: 10.0000 chunk 104 optimal weight: 0.9990 chunk 61 optimal weight: 0.8980 chunk 44 optimal weight: 20.0000 chunk 79 optimal weight: 7.9990 chunk 31 optimal weight: 1.9990 chunk 91 optimal weight: 30.0000 chunk 95 optimal weight: 5.9990 chunk 66 optimal weight: 10.0000 chunk 107 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN B 93 GLN C 38 ASN D 49 HIS F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7620 moved from start: 0.3031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13623 Z= 0.287 Angle : 0.667 27.263 19554 Z= 0.356 Chirality : 0.056 1.998 2212 Planarity : 0.004 0.052 1531 Dihedral : 30.903 173.401 3983 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 10.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.91 % Favored : 96.09 % Rotamer: Outliers : 2.25 % Allowed : 24.87 % Favored : 72.88 % 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: 1.25 (0.28), residues: 896 helix: 1.80 (0.21), residues: 575 sheet: -1.70 (0.72), residues: 44 loop : -0.79 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP K 349 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.001 PHE G 25 TYR 0.018 0.002 TYR B 88 ARG 0.014 0.001 ARG C 35 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 117 time to evaluate : 1.095 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8085 (tttt) cc_final: 0.7614 (tttp) REVERT: A 92 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7613 (tp) REVERT: E 59 HIS cc_start: 0.7088 (m90) cc_final: 0.6721 (m90) REVERT: E 63 ARG cc_start: 0.7931 (mmp-170) cc_final: 0.7683 (mmp80) REVERT: C 19 SER cc_start: 0.9401 (t) cc_final: 0.8922 (p) REVERT: C 36 LYS cc_start: 0.8692 (ptmm) cc_final: 0.8469 (ptpt) REVERT: C 90 ASP cc_start: 0.7721 (t0) cc_final: 0.7192 (t0) REVERT: C 92 GLU cc_start: 0.8585 (mm-30) cc_final: 0.7679 (mt-10) REVERT: C 95 LYS cc_start: 0.8837 (ttmt) cc_final: 0.8458 (mtpp) REVERT: D 59 MET cc_start: 0.8352 (tpp) cc_final: 0.8099 (tpt) REVERT: D 85 LYS cc_start: 0.8993 (mtpt) cc_final: 0.8765 (mtmm) REVERT: D 108 LYS cc_start: 0.7613 (mmtt) cc_final: 0.7078 (mmtt) REVERT: F 21 VAL cc_start: 0.5624 (OUTLIER) cc_final: 0.5194 (p) REVERT: G 19 SER cc_start: 0.9451 (t) cc_final: 0.9206 (p) REVERT: G 36 LYS cc_start: 0.8631 (OUTLIER) cc_final: 0.8280 (pttt) REVERT: G 72 ASP cc_start: 0.8272 (m-30) cc_final: 0.7957 (m-30) REVERT: G 92 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8062 (mt-10) REVERT: K 218 MET cc_start: 0.5438 (mpp) cc_final: 0.5219 (pmm) REVERT: K 310 HIS cc_start: 0.7299 (t70) cc_final: 0.6551 (t-90) REVERT: H 59 MET cc_start: 0.8418 (tpp) cc_final: 0.8162 (mmm) outliers start: 17 outliers final: 11 residues processed: 127 average time/residue: 1.5732 time to fit residues: 213.6396 Evaluate side-chains 124 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 110 time to evaluate : 1.065 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 50 optimal weight: 5.9990 chunk 74 optimal weight: 20.0000 chunk 112 optimal weight: 0.9980 chunk 103 optimal weight: 50.0000 chunk 89 optimal weight: 9.9990 chunk 9 optimal weight: 3.9990 chunk 69 optimal weight: 7.9990 chunk 54 optimal weight: 3.9990 chunk 71 optimal weight: 8.9990 chunk 95 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 127 GLN B 27 GLN B 93 GLN C 38 ASN D 49 HIS F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.3096 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 13623 Z= 0.291 Angle : 0.673 27.294 19554 Z= 0.358 Chirality : 0.056 1.997 2212 Planarity : 0.004 0.054 1531 Dihedral : 30.918 174.151 3983 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 2.38 % Allowed : 25.00 % Favored : 72.62 % 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: 1.27 (0.28), residues: 896 helix: 1.80 (0.21), residues: 575 sheet: -1.54 (0.73), residues: 44 loop : -0.76 (0.37), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 47 HIS 0.006 0.001 HIS F 75 PHE 0.010 0.001 PHE G 25 TYR 0.018 0.002 TYR B 88 ARG 0.015 0.001 ARG C 35 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1792 Ramachandran restraints generated. 896 Oldfield, 0 Emsley, 896 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 113 time to evaluate : 1.135 Fit side-chains revert: symmetry clash REVERT: A 53 LYS cc_start: 0.8086 (tttt) cc_final: 0.7618 (tttp) REVERT: A 92 LEU cc_start: 0.7933 (OUTLIER) cc_final: 0.7610 (tp) REVERT: E 59 HIS cc_start: 0.7085 (m90) cc_final: 0.6724 (m90) REVERT: E 63 ARG cc_start: 0.7933 (mmp-170) cc_final: 0.7683 (mmp80) REVERT: B 44 LYS cc_start: 0.8602 (pttt) cc_final: 0.8363 (pttp) REVERT: C 19 SER cc_start: 0.9402 (t) cc_final: 0.8917 (p) REVERT: C 36 LYS cc_start: 0.8649 (ptmm) cc_final: 0.8386 (ptpt) REVERT: C 90 ASP cc_start: 0.7725 (t0) cc_final: 0.7188 (t0) REVERT: C 92 GLU cc_start: 0.8587 (mm-30) cc_final: 0.7679 (mt-10) REVERT: C 95 LYS cc_start: 0.8838 (ttmt) cc_final: 0.8458 (mtpp) REVERT: D 59 MET cc_start: 0.8358 (tpp) cc_final: 0.8114 (tpt) REVERT: D 85 LYS cc_start: 0.9023 (mtpt) cc_final: 0.8792 (mtmm) REVERT: D 108 LYS cc_start: 0.7626 (mmtt) cc_final: 0.7084 (mmtt) REVERT: F 21 VAL cc_start: 0.5567 (OUTLIER) cc_final: 0.5153 (p) REVERT: G 19 SER cc_start: 0.9450 (t) cc_final: 0.9205 (p) REVERT: G 36 LYS cc_start: 0.8618 (OUTLIER) cc_final: 0.8271 (pttt) REVERT: G 72 ASP cc_start: 0.8268 (m-30) cc_final: 0.7977 (m-30) REVERT: G 92 GLU cc_start: 0.8596 (mt-10) cc_final: 0.8110 (mt-10) REVERT: K 310 HIS cc_start: 0.7313 (t70) cc_final: 0.6551 (t-90) REVERT: H 59 MET cc_start: 0.8458 (tpp) cc_final: 0.8242 (mmm) outliers start: 18 outliers final: 14 residues processed: 124 average time/residue: 1.5844 time to fit residues: 210.1682 Evaluate side-chains 127 residues out of total 757 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 92 LEU Chi-restraints excluded: chain E residue 53 LYS Chi-restraints excluded: chain E residue 82 VAL Chi-restraints excluded: chain E residue 92 LEU Chi-restraints excluded: chain E residue 113 THR Chi-restraints excluded: chain B residue 30 THR Chi-restraints excluded: chain B residue 73 THR Chi-restraints excluded: chain B residue 79 LYS Chi-restraints excluded: chain C residue 38 ASN Chi-restraints excluded: chain C residue 101 THR Chi-restraints excluded: chain C residue 108 LEU Chi-restraints excluded: chain D residue 113 GLU Chi-restraints excluded: chain F residue 21 VAL Chi-restraints excluded: chain G residue 36 LYS Chi-restraints excluded: chain G residue 100 VAL Chi-restraints excluded: chain K residue 307 THR Chi-restraints excluded: chain H residue 112 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 113 random chunks: chunk 82 optimal weight: 6.9990 chunk 13 optimal weight: 3.9990 chunk 24 optimal weight: 0.7980 chunk 89 optimal weight: 10.0000 chunk 37 optimal weight: 0.9980 chunk 92 optimal weight: 50.0000 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 0.9980 chunk 78 optimal weight: 10.0000 chunk 5 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 27 GLN C 38 ASN F 25 ASN F 27 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** K 299 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4286 r_free = 0.4286 target = 0.163244 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3421 r_free = 0.3421 target = 0.098173 restraints weight = 20307.665| |-----------------------------------------------------------------------------| r_work (start): 0.3240 rms_B_bonded: 2.38 r_work: 0.3003 rms_B_bonded: 3.95 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6932 moved from start: 0.3328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 13623 Z= 0.200 Angle : 0.647 27.220 19554 Z= 0.346 Chirality : 0.055 2.003 2212 Planarity : 0.004 0.050 1531 Dihedral : 30.640 174.285 3983 Min Nonbonded Distance : 2.152 Molprobity Statistics. All-atom Clashscore : 10.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.90 % Favored : 97.10 % Rotamer: Outliers : 2.25 % Allowed : 24.87 % Favored : 72.88 % 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: 1.57 (0.28), residues: 896 helix: 1.95 (0.21), residues: 583 sheet: -1.20 (0.75), residues: 44 loop : -0.56 (0.38), residues: 269 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP E 86 HIS 0.005 0.001 HIS F 75 PHE 0.007 0.001 PHE F 100 TYR 0.015 0.001 TYR H 40 ARG 0.016 0.000 ARG C 35 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4294.22 seconds wall clock time: 77 minutes 3.25 seconds (4623.25 seconds total)