Starting phenix.real_space_refine on Sun Jul 21 02:28:11 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/07_2024/8t9f_41109.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/07_2024/8t9f_41109.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.6 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/07_2024/8t9f_41109.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/07_2024/8t9f_41109.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/07_2024/8t9f_41109.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8t9f_41109/07_2024/8t9f_41109.cif" } resolution = 2.6 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= 0.005 sd= 0.041 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: 5 Type Number sf(0) Gaussians P 244 5.49 5 S 30 5.16 5 C 7475 2.51 5 N 2445 2.21 5 O 2938 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "K PHE 270": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 123": "OD1" <-> "OD2" Residue "D TYR 42": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 13132 Number of models: 1 Model: "" Number of chains: 12 Chain: "K" Number of atoms: 2060 Number of conformers: 1 Conformer: "" Number of residues, atoms: 264, 2060 Classifications: {'peptide': 264} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 5, 'TRANS': 258} Chain breaks: 2 Unresolved non-hydrogen bonds: 81 Unresolved non-hydrogen angles: 98 Unresolved non-hydrogen dihedrals: 73 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'HIS:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 4, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 50 Chain: "I" Number of atoms: 2484 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2484 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "J" Number of atoms: 2518 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 2518 Classifications: {'DNA': 122} Link IDs: {'rna3p': 121} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 698 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: "A" Number of atoms: 785 Number of conformers: 1 Conformer: "" Number of residues, atoms: 96, 785 Classifications: {'peptide': 96} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 92} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" 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: "G" Number of atoms: 781 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 781 Classifications: {'peptide': 103} Link IDs: {'PTRANS': 3, 'TRANS': 99} Chain: "H" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "E" Number of atoms: 835 Number of conformers: 1 Conformer: "" Number of residues, atoms: 103, 835 Classifications: {'peptide': 103} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 4, 'TRANS': 98} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "C" Number of atoms: 816 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 816 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 3, 'TRANS': 104} Chain: "D" Number of atoms: 745 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 745 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "K" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Classifications: {'peptide': 1} Time building chain proxies: 7.82, per 1000 atoms: 0.60 Number of scatterers: 13132 At special positions: 0 Unit cell: (97.11, 117.611, 118.69, 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 30 16.00 P 244 15.00 O 2938 8.00 N 2445 7.00 C 7475 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: 5.95 Conformation dependent library (CDL) restraints added in 1.6 seconds 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1928 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 14 sheets defined 64.7% alpha, 5.0% beta 122 base pairs and 211 stacking pairs defined. Time for finding SS restraints: 5.80 Creating SS restraints... Processing helix chain 'K' and resid 73 through 88 Processing helix chain 'K' and resid 88 through 94 Processing helix chain 'K' and resid 134 through 148 Processing helix chain 'K' and resid 149 through 159 removed outlier: 3.995A pdb=" N ALA K 153 " --> pdb=" O HIS K 149 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N SER K 159 " --> pdb=" O LYS K 155 " (cutoff:3.500A) Processing helix chain 'K' and resid 160 through 169 Processing helix chain 'K' and resid 171 through 187 removed outlier: 3.779A pdb=" N TYR K 185 " --> pdb=" O HIS K 181 " (cutoff:3.500A) Processing helix chain 'K' and resid 188 through 190 No H-bonds generated for 'chain 'K' and resid 188 through 190' Processing helix chain 'K' and resid 235 through 242 Processing helix chain 'K' and resid 266 through 271 removed outlier: 3.679A pdb=" N PHE K 270 " --> pdb=" O PRO K 267 " (cutoff:3.500A) removed outlier: 3.672A pdb=" N ILE K 271 " --> pdb=" O ALA K 268 " (cutoff:3.500A) Processing helix chain 'K' and resid 321 through 328 Processing helix chain 'K' and resid 329 through 333 Processing helix chain 'K' and resid 354 through 362 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 41 Processing helix chain 'B' and resid 49 through 76 removed outlier: 3.824A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) removed outlier: 4.635A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.546A pdb=" N VAL B 86 " --> pdb=" O THR B 82 " (cutoff:3.500A) Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 76 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 removed outlier: 3.550A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 24 through 29 removed outlier: 3.947A pdb=" N GLN F 27 " --> pdb=" O ASP F 24 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.964A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) removed outlier: 3.758A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.610A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 18 through 23 Processing helix chain 'G' and resid 28 through 39 Processing helix chain 'G' and resid 47 through 76 removed outlier: 3.552A pdb=" N ALA G 51 " --> pdb=" O GLY G 47 " (cutoff:3.500A) Processing helix chain 'G' and resid 82 through 93 Processing helix chain 'G' and resid 93 through 100 Processing helix chain 'H' and resid 38 through 50 Processing helix chain 'H' and resid 56 through 85 Processing helix chain 'H' and resid 91 through 103 Processing helix chain 'H' and resid 105 through 124 removed outlier: 3.870A pdb=" N LYS H 109 " --> pdb=" O GLY H 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.532A pdb=" N PHE E 67 " --> pdb=" O ARG E 63 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 131 removed outlier: 3.555A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'C' and resid 18 through 23 Processing helix chain 'C' and resid 28 through 39 Processing helix chain 'C' and resid 47 through 76 removed outlier: 3.570A pdb=" N ALA C 51 " --> pdb=" O GLY C 47 " (cutoff:3.500A) Processing helix chain 'C' and resid 82 through 93 removed outlier: 3.609A pdb=" N ASP C 93 " --> pdb=" O ALA C 89 " (cutoff:3.500A) Processing helix chain 'C' and resid 93 through 100 Processing helix chain 'C' and resid 114 through 119 removed outlier: 3.934A pdb=" N ILE C 118 " --> pdb=" O HIS C 114 " (cutoff:3.500A) Processing helix chain 'D' and resid 37 through 49 Processing helix chain 'D' and resid 55 through 84 Processing helix chain 'D' and resid 90 through 102 Processing helix chain 'D' and resid 104 through 123 removed outlier: 3.702A pdb=" N LYS D 108 " --> pdb=" O GLY D 104 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'K' and resid 195 through 199 Processing sheet with id=AA2, first strand: chain 'K' and resid 230 through 234 removed outlier: 4.344A pdb=" N ALA K 261 " --> pdb=" O LEU K 234 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'K' and resid 272 through 273 removed outlier: 6.436A pdb=" N ASN K 272 " --> pdb=" O CYS K 305 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'K' and resid 279 through 283 Processing sheet with id=AA5, first strand: chain 'B' and resid 45 through 46 removed outlier: 7.437A pdb=" N ARG B 45 " --> pdb=" O ILE E 119 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 80 through 81 Processing sheet with id=AA7, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA8, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.873A pdb=" N ARG A 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AB1, first strand: chain 'F' and resid 97 through 98 Processing sheet with id=AB2, first strand: chain 'G' and resid 45 through 46 removed outlier: 6.597A pdb=" N ARG G 45 " --> pdb=" O ILE H 90 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB2 Processing sheet with id=AB3, first strand: chain 'G' and resid 80 through 81 Processing sheet with id=AB4, first strand: chain 'C' and resid 45 through 46 removed outlier: 6.529A pdb=" N ARG C 45 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AB4 Processing sheet with id=AB5, first strand: chain 'C' and resid 80 through 81 489 hydrogen bonds defined for protein. 1434 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 315 hydrogen bonds 630 hydrogen bond angles 0 basepair planarities 122 basepair parallelities 211 stacking parallelities Total time for adding SS restraints: 5.44 Time building geometry restraints manager: 6.33 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: 2736 1.33 - 1.45: 4080 1.45 - 1.57: 6509 1.57 - 1.69: 486 1.69 - 1.81: 47 Bond restraints: 13858 Sorted by residual: bond pdb=" N GLN K 374 " pdb=" CA GLN K 374 " ideal model delta sigma weight residual 1.457 1.488 -0.031 1.06e-02 8.90e+03 8.38e+00 bond pdb=" C2 SAM K 401 " pdb=" N3 SAM K 401 " ideal model delta sigma weight residual 1.322 1.379 -0.057 2.00e-02 2.50e+03 8.22e+00 bond pdb=" N ASP K 372 " pdb=" CA ASP K 372 " ideal model delta sigma weight residual 1.457 1.487 -0.030 1.10e-02 8.26e+03 7.42e+00 bond pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " ideal model delta sigma weight residual 1.422 1.503 -0.081 3.00e-02 1.11e+03 7.33e+00 bond pdb=" C8 SAM K 401 " pdb=" N7 SAM K 401 " ideal model delta sigma weight residual 1.298 1.351 -0.053 2.00e-02 2.50e+03 7.05e+00 ... (remaining 13853 not shown) Histogram of bond angle deviations from ideal: 97.85 - 105.06: 1074 105.06 - 112.27: 7633 112.27 - 119.49: 4257 119.49 - 126.70: 6030 126.70 - 133.91: 744 Bond angle restraints: 19738 Sorted by residual: angle pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sigma weight residual 120.20 125.95 -5.75 1.50e+00 4.44e-01 1.47e+01 angle pdb=" N ASP K 372 " pdb=" CA ASP K 372 " pdb=" C ASP K 372 " ideal model delta sigma weight residual 112.57 108.70 3.87 1.13e+00 7.83e-01 1.17e+01 angle pdb=" CA ASN K 370 " pdb=" C ASN K 370 " pdb=" O ASN K 370 " ideal model delta sigma weight residual 121.99 118.36 3.63 1.14e+00 7.69e-01 1.01e+01 angle pdb=" O4' DT J 28 " pdb=" C1' DT J 28 " pdb=" N1 DT J 28 " ideal model delta sigma weight residual 108.40 113.13 -4.73 1.50e+00 4.44e-01 9.96e+00 angle pdb=" CA SER K 371 " pdb=" C SER K 371 " pdb=" O SER K 371 " ideal model delta sigma weight residual 121.56 118.19 3.37 1.09e+00 8.42e-01 9.55e+00 ... (remaining 19733 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.14: 6504 35.14 - 70.28: 1200 70.28 - 105.42: 18 105.42 - 140.57: 1 140.57 - 175.71: 3 Dihedral angle restraints: 7726 sinusoidal: 4741 harmonic: 2985 Sorted by residual: dihedral pdb=" C4' DA J 110 " pdb=" C3' DA J 110 " pdb=" O3' DA J 110 " pdb=" P DC J 111 " ideal model delta sinusoidal sigma weight residual -140.00 35.71 -175.71 1 3.50e+01 8.16e-04 1.57e+01 dihedral pdb=" C4' DG J 106 " pdb=" C3' DG J 106 " pdb=" O3' DG J 106 " pdb=" P DT J 107 " ideal model delta sinusoidal sigma weight residual 220.00 47.47 172.53 1 3.50e+01 8.16e-04 1.56e+01 dihedral pdb=" C4' DC J 27 " pdb=" C3' DC J 27 " pdb=" O3' DC J 27 " pdb=" P DT J 28 " ideal model delta sinusoidal sigma weight residual -140.00 15.85 -155.85 1 3.50e+01 8.16e-04 1.50e+01 ... (remaining 7723 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 1742 0.042 - 0.084: 398 0.084 - 0.126: 90 0.126 - 0.167: 4 0.167 - 0.209: 2 Chirality restraints: 2236 Sorted by residual: chirality pdb=" P DT J 28 " pdb=" OP1 DT J 28 " pdb=" OP2 DT J 28 " pdb=" O5' DT J 28 " both_signs ideal model delta sigma weight residual True 2.35 -2.55 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" C2' SAM K 401 " pdb=" C1' SAM K 401 " pdb=" C3' SAM K 401 " pdb=" O2' SAM K 401 " both_signs ideal model delta sigma weight residual False -2.76 -2.56 -0.20 2.00e-01 2.50e+01 9.95e-01 chirality pdb=" C1' SAM K 401 " pdb=" C2' SAM K 401 " pdb=" N9 SAM K 401 " pdb=" O4' SAM K 401 " both_signs ideal model delta sigma weight residual False 2.30 2.46 -0.16 2.00e-01 2.50e+01 6.70e-01 ... (remaining 2233 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DC J 27 " 0.050 2.00e-02 2.50e+03 2.91e-02 1.91e+01 pdb=" N1 DC J 27 " -0.039 2.00e-02 2.50e+03 pdb=" C2 DC J 27 " -0.034 2.00e-02 2.50e+03 pdb=" O2 DC J 27 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DC J 27 " 0.031 2.00e-02 2.50e+03 pdb=" C4 DC J 27 " -0.024 2.00e-02 2.50e+03 pdb=" N4 DC J 27 " 0.030 2.00e-02 2.50e+03 pdb=" C5 DC J 27 " -0.010 2.00e-02 2.50e+03 pdb=" C6 DC J 27 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU B 63 " 0.013 2.00e-02 2.50e+03 2.51e-02 6.28e+00 pdb=" C GLU B 63 " -0.043 2.00e-02 2.50e+03 pdb=" O GLU B 63 " 0.016 2.00e-02 2.50e+03 pdb=" N ASN B 64 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LYS B 59 " 0.011 2.00e-02 2.50e+03 2.15e-02 4.62e+00 pdb=" C LYS B 59 " -0.037 2.00e-02 2.50e+03 pdb=" O LYS B 59 " 0.014 2.00e-02 2.50e+03 pdb=" N VAL B 60 " 0.012 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 1.47 - 2.16: 5 2.16 - 2.84: 3786 2.84 - 3.53: 17560 3.53 - 4.21: 34723 4.21 - 4.90: 53586 Nonbonded interactions: 109660 Sorted by model distance: nonbonded pdb=" OH TYR K 306 " pdb=" OD1 ASP K 309 " model vdw 1.469 2.440 nonbonded pdb=" CD2 LEU K 150 " pdb=" CE1 PHE K 183 " model vdw 1.636 3.760 nonbonded pdb=" O GLU K 325 " pdb=" CE2 PHE K 332 " model vdw 2.081 3.340 nonbonded pdb=" CD2 LEU K 150 " pdb=" CD1 PHE K 183 " model vdw 2.084 3.760 nonbonded pdb=" CD2 LEU K 150 " pdb=" CZ PHE K 183 " model vdw 2.106 3.760 ... (remaining 109655 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 40 through 135) } ncs_group { reference = (chain 'B' and resid 23 through 102) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 16 through 118) selection = chain 'G' } ncs_group { reference = chain 'D' 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: 1.780 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.490 Check model and map are aligned: 0.100 Set scattering table: 0.120 Process input model: 41.800 Find NCS groups from input model: 0.410 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.280 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 58.050 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.081 13858 Z= 0.221 Angle : 0.589 8.743 19738 Z= 0.351 Chirality : 0.037 0.209 2236 Planarity : 0.004 0.049 1658 Dihedral : 25.251 175.707 5798 Min Nonbonded Distance : 1.469 Molprobity Statistics. All-atom Clashscore : 4.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 0.00 % Allowed : 6.16 % Favored : 93.84 % 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: 1.11 (0.25), residues: 1009 helix: 1.75 (0.20), residues: 635 sheet: 0.01 (0.71), residues: 44 loop : -1.20 (0.31), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP K 264 HIS 0.003 0.001 HIS F 75 PHE 0.008 0.001 PHE H 66 TYR 0.009 0.001 TYR E 54 ARG 0.002 0.000 ARG K 257 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 225 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: K 180 GLU cc_start: 0.8933 (mt-10) cc_final: 0.8728 (mm-30) REVERT: K 225 GLU cc_start: 0.7675 (pt0) cc_final: 0.7339 (tp30) REVERT: A 81 ASP cc_start: 0.8311 (m-30) cc_final: 0.8081 (m-30) REVERT: F 44 LYS cc_start: 0.8674 (mtpt) cc_final: 0.8473 (mtpp) REVERT: D 42 TYR cc_start: 0.8146 (t80) cc_final: 0.7929 (t80) outliers start: 0 outliers final: 1 residues processed: 225 average time/residue: 1.5861 time to fit residues: 380.5890 Evaluate side-chains 166 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 165 time to evaluate : 1.112 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 271 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.6980 chunk 93 optimal weight: 0.8980 chunk 51 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 96 optimal weight: 3.9990 chunk 37 optimal weight: 3.9990 chunk 58 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 134 GLN K 207 GLN K 273 HIS ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS B 25 ASN A 85 GLN F 25 ASN F 93 GLN G 26 GLN H 110 HIS E 68 GLN Total number of N/Q/H flips: 11 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.1522 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.046 13858 Z= 0.279 Angle : 0.552 8.582 19738 Z= 0.328 Chirality : 0.037 0.226 2236 Planarity : 0.004 0.037 1658 Dihedral : 29.631 178.711 3830 Min Nonbonded Distance : 2.088 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.55 % Allowed : 13.98 % Favored : 82.46 % 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: 1.70 (0.26), residues: 1009 helix: 2.28 (0.21), residues: 638 sheet: -0.05 (0.71), residues: 44 loop : -1.12 (0.31), residues: 327 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.007 0.001 HIS H 83 PHE 0.010 0.001 PHE E 84 TYR 0.013 0.001 TYR E 54 ARG 0.007 0.001 ARG D 79 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 198 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 168 time to evaluate : 1.104 Fit side-chains revert: symmetry clash REVERT: K 143 ARG cc_start: 0.6255 (ttp80) cc_final: 0.5978 (ptm-80) REVERT: K 187 ARG cc_start: 0.9021 (OUTLIER) cc_final: 0.8699 (tpp80) REVERT: K 225 GLU cc_start: 0.7807 (pt0) cc_final: 0.7399 (tp30) REVERT: F 44 LYS cc_start: 0.8653 (mtpt) cc_final: 0.8427 (mtpp) REVERT: G 21 GLN cc_start: 0.8529 (tt0) cc_final: 0.8172 (tm-30) REVERT: G 25 LEU cc_start: 0.9172 (OUTLIER) cc_final: 0.8932 (pp) REVERT: G 67 GLU cc_start: 0.8519 (OUTLIER) cc_final: 0.7971 (tp30) REVERT: G 74 LYS cc_start: 0.8191 (tptt) cc_final: 0.7961 (mmmt) outliers start: 30 outliers final: 16 residues processed: 189 average time/residue: 1.6323 time to fit residues: 329.1868 Evaluate side-chains 180 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 161 time to evaluate : 1.034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 67 GLU Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 62 optimal weight: 0.8980 chunk 34 optimal weight: 1.9990 chunk 92 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 120 optimal weight: 0.9990 chunk 99 optimal weight: 0.7980 chunk 110 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 89 optimal weight: 1.9990 overall best weight: 1.3386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** K 278 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** F 93 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1922 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 13858 Z= 0.278 Angle : 0.541 5.014 19738 Z= 0.325 Chirality : 0.036 0.131 2236 Planarity : 0.004 0.035 1658 Dihedral : 29.642 176.559 3828 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 3.91 % Allowed : 14.81 % Favored : 81.28 % 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: 1.79 (0.27), residues: 1009 helix: 2.36 (0.21), residues: 646 sheet: -0.17 (0.70), residues: 44 loop : -1.17 (0.31), residues: 319 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.010 0.001 PHE K 281 TYR 0.011 0.001 TYR E 54 ARG 0.008 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 166 time to evaluate : 1.215 Fit side-chains revert: symmetry clash REVERT: K 187 ARG cc_start: 0.9001 (OUTLIER) cc_final: 0.8730 (tpp80) REVERT: K 225 GLU cc_start: 0.7956 (pt0) cc_final: 0.7453 (tp30) REVERT: F 44 LYS cc_start: 0.8669 (mtpt) cc_final: 0.8466 (mtpp) REVERT: G 21 GLN cc_start: 0.8497 (tt0) cc_final: 0.8238 (tm-30) REVERT: G 74 LYS cc_start: 0.8171 (tptt) cc_final: 0.7948 (mmmt) REVERT: E 120 MET cc_start: 0.9079 (OUTLIER) cc_final: 0.8514 (mmm) REVERT: C 67 GLU cc_start: 0.8594 (OUTLIER) cc_final: 0.7931 (tp30) REVERT: C 74 LYS cc_start: 0.7511 (tppt) cc_final: 0.7280 (tppt) outliers start: 33 outliers final: 18 residues processed: 186 average time/residue: 1.5657 time to fit residues: 311.7597 Evaluate side-chains 183 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 162 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 120 MET Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 110 optimal weight: 0.0870 chunk 84 optimal weight: 0.6980 chunk 58 optimal weight: 0.8980 chunk 12 optimal weight: 0.0020 chunk 53 optimal weight: 0.9980 chunk 75 optimal weight: 2.9990 chunk 112 optimal weight: 0.1980 chunk 118 optimal weight: 0.8980 chunk 106 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 99 optimal weight: 0.6980 overall best weight: 0.3366 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8482 moved from start: 0.1949 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 13858 Z= 0.160 Angle : 0.523 5.781 19738 Z= 0.316 Chirality : 0.034 0.135 2236 Planarity : 0.005 0.116 1658 Dihedral : 29.650 176.849 3828 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.49 % Favored : 98.51 % Rotamer: Outliers : 2.96 % Allowed : 15.76 % Favored : 81.28 % 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: 2.01 (0.27), residues: 1009 helix: 2.54 (0.21), residues: 642 sheet: -0.13 (0.75), residues: 38 loop : -1.02 (0.31), residues: 329 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 264 HIS 0.006 0.001 HIS H 83 PHE 0.007 0.001 PHE K 95 TYR 0.017 0.001 TYR H 84 ARG 0.013 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 169 time to evaluate : 1.135 Fit side-chains REVERT: K 143 ARG cc_start: 0.5838 (ptm-80) cc_final: 0.5588 (tmm160) REVERT: K 187 ARG cc_start: 0.8971 (OUTLIER) cc_final: 0.8709 (tpp80) REVERT: K 225 GLU cc_start: 0.7916 (pt0) cc_final: 0.7405 (tp30) REVERT: A 133 GLU cc_start: 0.8201 (OUTLIER) cc_final: 0.7581 (mt-10) REVERT: G 25 LEU cc_start: 0.9160 (OUTLIER) cc_final: 0.8955 (pp) REVERT: G 74 LYS cc_start: 0.8136 (tptt) cc_final: 0.7901 (mmmt) REVERT: C 67 GLU cc_start: 0.8556 (OUTLIER) cc_final: 0.7910 (tp30) REVERT: C 74 LYS cc_start: 0.7384 (tppt) cc_final: 0.7100 (tppt) REVERT: C 79 LYS cc_start: 0.8412 (mmtm) cc_final: 0.8139 (mmtm) outliers start: 25 outliers final: 19 residues processed: 186 average time/residue: 1.5841 time to fit residues: 315.0309 Evaluate side-chains 188 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain C residue 118 ILE Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 67 optimal weight: 0.0870 chunk 1 optimal weight: 3.9990 chunk 88 optimal weight: 2.9990 chunk 49 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 chunk 82 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 60 optimal weight: 0.0970 chunk 106 optimal weight: 2.9990 chunk 30 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 overall best weight: 1.6362 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 272 ASN K 278 ASN E 68 GLN D 67 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.044 13858 Z= 0.320 Angle : 0.557 7.977 19738 Z= 0.332 Chirality : 0.038 0.151 2236 Planarity : 0.004 0.046 1658 Dihedral : 29.659 175.456 3828 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 6.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 3.91 % Allowed : 15.28 % Favored : 80.81 % 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: 1.82 (0.27), residues: 1009 helix: 2.41 (0.21), residues: 645 sheet: -0.16 (0.75), residues: 38 loop : -1.20 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 264 HIS 0.003 0.001 HIS G 43 PHE 0.009 0.001 PHE K 281 TYR 0.022 0.002 TYR K 92 ARG 0.010 0.001 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 164 time to evaluate : 1.001 Fit side-chains REVERT: K 143 ARG cc_start: 0.5941 (ptm-80) cc_final: 0.5379 (tmm160) REVERT: K 187 ARG cc_start: 0.8959 (OUTLIER) cc_final: 0.8719 (tpp80) REVERT: K 225 GLU cc_start: 0.8016 (pt0) cc_final: 0.7557 (tp30) REVERT: A 133 GLU cc_start: 0.8330 (OUTLIER) cc_final: 0.7815 (mt-10) REVERT: G 25 LEU cc_start: 0.9253 (OUTLIER) cc_final: 0.9036 (pp) REVERT: G 74 LYS cc_start: 0.8231 (tptt) cc_final: 0.7974 (mmmt) REVERT: G 84 ARG cc_start: 0.9033 (OUTLIER) cc_final: 0.8523 (tpt-90) REVERT: C 67 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.7969 (tp30) REVERT: C 74 LYS cc_start: 0.7429 (tppt) cc_final: 0.7197 (tppt) outliers start: 33 outliers final: 21 residues processed: 185 average time/residue: 1.6515 time to fit residues: 325.7255 Evaluate side-chains 189 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 163 time to evaluate : 1.096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 41 THR Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 107 optimal weight: 0.8980 chunk 23 optimal weight: 5.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 119 optimal weight: 2.9990 chunk 98 optimal weight: 0.0070 chunk 55 optimal weight: 0.8980 chunk 9 optimal weight: 1.9990 chunk 39 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 114 optimal weight: 0.8980 overall best weight: 0.6598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: K 262 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.2218 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 13858 Z= 0.187 Angle : 0.511 7.020 19738 Z= 0.307 Chirality : 0.034 0.150 2236 Planarity : 0.004 0.048 1658 Dihedral : 29.432 177.670 3828 Min Nonbonded Distance : 2.096 Molprobity Statistics. All-atom Clashscore : 7.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.96 % Allowed : 16.71 % Favored : 80.33 % 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: 2.06 (0.27), residues: 1009 helix: 2.62 (0.21), residues: 645 sheet: -0.11 (0.75), residues: 38 loop : -1.13 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.011 0.001 TYR H 84 ARG 0.010 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 195 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 170 time to evaluate : 1.177 Fit side-chains REVERT: K 143 ARG cc_start: 0.6009 (ptm-80) cc_final: 0.5319 (tmm160) REVERT: K 174 GLN cc_start: 0.8747 (OUTLIER) cc_final: 0.8524 (pm20) REVERT: K 187 ARG cc_start: 0.8995 (OUTLIER) cc_final: 0.8721 (tpp80) REVERT: K 225 GLU cc_start: 0.7986 (pt0) cc_final: 0.7402 (tp30) REVERT: A 133 GLU cc_start: 0.8091 (OUTLIER) cc_final: 0.7533 (mt-10) REVERT: G 25 LEU cc_start: 0.9208 (OUTLIER) cc_final: 0.8986 (pp) REVERT: G 74 LYS cc_start: 0.8121 (tptt) cc_final: 0.7868 (mmmt) REVERT: E 115 LYS cc_start: 0.8407 (OUTLIER) cc_final: 0.8081 (mptt) outliers start: 25 outliers final: 18 residues processed: 185 average time/residue: 1.6354 time to fit residues: 322.4875 Evaluate side-chains 188 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 165 time to evaluate : 1.078 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 174 GLN Chi-restraints excluded: chain K residue 187 ARG Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 98 SER Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 13 optimal weight: 0.9990 chunk 67 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 100 optimal weight: 0.6980 chunk 66 optimal weight: 0.6980 chunk 118 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 54 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 47 optimal weight: 5.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8484 moved from start: 0.2276 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.203 Angle : 0.517 6.367 19738 Z= 0.310 Chirality : 0.034 0.145 2236 Planarity : 0.004 0.052 1658 Dihedral : 29.402 177.439 3828 Min Nonbonded Distance : 2.090 Molprobity Statistics. All-atom Clashscore : 7.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.84 % Allowed : 17.77 % Favored : 79.38 % 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: 2.11 (0.27), residues: 1009 helix: 2.62 (0.21), residues: 648 sheet: 0.02 (0.76), residues: 38 loop : -1.06 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.012 0.001 TYR D 83 ARG 0.011 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 166 time to evaluate : 1.077 Fit side-chains REVERT: K 143 ARG cc_start: 0.6000 (ptm-80) cc_final: 0.5202 (tmm160) REVERT: K 225 GLU cc_start: 0.8005 (pt0) cc_final: 0.7425 (tp30) REVERT: K 226 LEU cc_start: 0.9087 (OUTLIER) cc_final: 0.8887 (mm) REVERT: A 133 GLU cc_start: 0.8128 (OUTLIER) cc_final: 0.7566 (mt-10) REVERT: G 25 LEU cc_start: 0.9202 (OUTLIER) cc_final: 0.8968 (pp) REVERT: G 74 LYS cc_start: 0.8126 (tptt) cc_final: 0.7891 (mmmt) REVERT: G 84 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8454 (tpt-90) REVERT: E 115 LYS cc_start: 0.8424 (OUTLIER) cc_final: 0.8110 (mptt) outliers start: 24 outliers final: 17 residues processed: 182 average time/residue: 1.6679 time to fit residues: 323.4656 Evaluate side-chains 185 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 163 time to evaluate : 1.082 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain A residue 80 THR Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 68 LEU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 70 optimal weight: 0.7980 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 75 optimal weight: 0.0870 chunk 80 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 107 optimal weight: 0.9990 chunk 113 optimal weight: 0.9980 overall best weight: 0.7558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8477 moved from start: 0.2314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.197 Angle : 0.515 8.411 19738 Z= 0.309 Chirality : 0.034 0.154 2236 Planarity : 0.004 0.050 1658 Dihedral : 29.334 177.628 3828 Min Nonbonded Distance : 2.099 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.96 % Allowed : 17.65 % Favored : 79.38 % 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: 2.14 (0.27), residues: 1009 helix: 2.62 (0.21), residues: 648 sheet: 0.01 (0.76), residues: 38 loop : -0.99 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.022 0.001 TYR K 92 ARG 0.012 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 166 time to evaluate : 1.204 Fit side-chains REVERT: K 143 ARG cc_start: 0.5992 (ptm-80) cc_final: 0.5190 (tmm160) REVERT: K 225 GLU cc_start: 0.7984 (pt0) cc_final: 0.7393 (tp30) REVERT: K 226 LEU cc_start: 0.9082 (OUTLIER) cc_final: 0.8881 (mm) REVERT: A 133 GLU cc_start: 0.8102 (OUTLIER) cc_final: 0.7623 (mt-10) REVERT: F 23 ARG cc_start: 0.5528 (ppt170) cc_final: 0.5253 (ppp-140) REVERT: G 25 LEU cc_start: 0.9188 (OUTLIER) cc_final: 0.8973 (pp) REVERT: G 74 LYS cc_start: 0.8084 (tptt) cc_final: 0.7851 (mmmt) REVERT: G 84 ARG cc_start: 0.8986 (OUTLIER) cc_final: 0.8451 (tpt-90) REVERT: E 56 LYS cc_start: 0.8429 (OUTLIER) cc_final: 0.8116 (ttpt) REVERT: E 115 LYS cc_start: 0.8421 (OUTLIER) cc_final: 0.8103 (mptt) REVERT: C 67 GLU cc_start: 0.8588 (OUTLIER) cc_final: 0.7919 (tp30) REVERT: C 94 GLU cc_start: 0.7382 (tp30) cc_final: 0.6991 (tp30) outliers start: 25 outliers final: 18 residues processed: 180 average time/residue: 1.6532 time to fit residues: 317.4194 Evaluate side-chains 188 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 163 time to evaluate : 1.093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 197 ILE Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 103 optimal weight: 0.9990 chunk 110 optimal weight: 0.9980 chunk 113 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 8.9990 chunk 86 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 2.9990 chunk 104 optimal weight: 5.9990 chunk 72 optimal weight: 0.9990 chunk 116 optimal weight: 0.7980 overall best weight: 0.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 68 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8494 moved from start: 0.2420 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.226 Angle : 0.528 7.543 19738 Z= 0.316 Chirality : 0.035 0.153 2236 Planarity : 0.004 0.056 1658 Dihedral : 29.336 177.398 3828 Min Nonbonded Distance : 2.119 Molprobity Statistics. All-atom Clashscore : 6.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 3.20 % Allowed : 17.54 % Favored : 79.27 % 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: 2.08 (0.27), residues: 1009 helix: 2.59 (0.21), residues: 645 sheet: -0.04 (0.76), residues: 38 loop : -1.02 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.005 0.001 HIS H 83 PHE 0.007 0.001 PHE H 66 TYR 0.051 0.002 TYR D 83 ARG 0.013 0.000 ARG C 39 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 163 time to evaluate : 1.104 Fit side-chains REVERT: K 143 ARG cc_start: 0.5921 (ptm-80) cc_final: 0.5138 (tmm160) REVERT: K 225 GLU cc_start: 0.8035 (pt0) cc_final: 0.7423 (tp30) REVERT: K 226 LEU cc_start: 0.9097 (OUTLIER) cc_final: 0.8893 (mm) REVERT: A 133 GLU cc_start: 0.8172 (OUTLIER) cc_final: 0.7654 (mt-10) REVERT: G 25 LEU cc_start: 0.9206 (OUTLIER) cc_final: 0.8974 (pp) REVERT: G 74 LYS cc_start: 0.8124 (tptt) cc_final: 0.7893 (mmmt) REVERT: G 84 ARG cc_start: 0.9000 (OUTLIER) cc_final: 0.8461 (tpt-90) REVERT: E 56 LYS cc_start: 0.8477 (OUTLIER) cc_final: 0.8164 (ttpt) REVERT: E 115 LYS cc_start: 0.8457 (OUTLIER) cc_final: 0.8148 (mptt) REVERT: C 67 GLU cc_start: 0.8597 (OUTLIER) cc_final: 0.7921 (tp30) REVERT: C 94 GLU cc_start: 0.7407 (tp30) cc_final: 0.6999 (tp30) outliers start: 27 outliers final: 18 residues processed: 179 average time/residue: 1.6914 time to fit residues: 322.7651 Evaluate side-chains 187 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 162 time to evaluate : 1.001 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 71 optimal weight: 0.6980 chunk 55 optimal weight: 0.7980 chunk 81 optimal weight: 4.9990 chunk 122 optimal weight: 2.9990 chunk 112 optimal weight: 2.9990 chunk 97 optimal weight: 0.6980 chunk 10 optimal weight: 0.9980 chunk 75 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 103 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.2418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.210 Angle : 0.535 7.574 19738 Z= 0.318 Chirality : 0.035 0.153 2236 Planarity : 0.004 0.060 1658 Dihedral : 29.331 177.532 3828 Min Nonbonded Distance : 2.085 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.88 % Favored : 98.12 % Rotamer: Outliers : 2.96 % Allowed : 18.01 % Favored : 79.03 % 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: 2.09 (0.27), residues: 1009 helix: 2.59 (0.21), residues: 645 sheet: -0.04 (0.76), residues: 38 loop : -1.00 (0.31), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.023 0.002 TYR D 83 ARG 0.013 0.000 ARG C 39 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2018 Ramachandran restraints generated. 1009 Oldfield, 0 Emsley, 1009 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 189 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.105 Fit side-chains REVERT: K 143 ARG cc_start: 0.5915 (ptm-80) cc_final: 0.5134 (tmm160) REVERT: K 225 GLU cc_start: 0.8022 (pt0) cc_final: 0.7412 (tp30) REVERT: K 226 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8887 (mm) REVERT: A 133 GLU cc_start: 0.8155 (OUTLIER) cc_final: 0.7658 (mt-10) REVERT: G 25 LEU cc_start: 0.9205 (OUTLIER) cc_final: 0.8980 (pp) REVERT: G 74 LYS cc_start: 0.8112 (tptt) cc_final: 0.7877 (mmmt) REVERT: G 84 ARG cc_start: 0.8994 (OUTLIER) cc_final: 0.8452 (tpt-90) REVERT: E 56 LYS cc_start: 0.8455 (OUTLIER) cc_final: 0.8142 (ttpt) REVERT: E 115 LYS cc_start: 0.8448 (OUTLIER) cc_final: 0.8138 (mptt) REVERT: C 67 GLU cc_start: 0.8601 (OUTLIER) cc_final: 0.7911 (tp30) REVERT: C 94 GLU cc_start: 0.7410 (tp30) cc_final: 0.6990 (tp30) outliers start: 25 outliers final: 18 residues processed: 179 average time/residue: 1.6603 time to fit residues: 316.6243 Evaluate side-chains 189 residues out of total 869 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.108 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 226 LEU Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 96 SER Chi-restraints excluded: chain A residue 133 GLU Chi-restraints excluded: chain G residue 25 LEU Chi-restraints excluded: chain G residue 38 SER Chi-restraints excluded: chain G residue 54 SER Chi-restraints excluded: chain G residue 84 ARG Chi-restraints excluded: chain G residue 103 THR Chi-restraints excluded: chain G residue 116 SER Chi-restraints excluded: chain H residue 40 ILE Chi-restraints excluded: chain H residue 81 LEU Chi-restraints excluded: chain E residue 56 LYS Chi-restraints excluded: chain E residue 57 SER Chi-restraints excluded: chain E residue 86 SER Chi-restraints excluded: chain E residue 115 LYS Chi-restraints excluded: chain C residue 41 THR Chi-restraints excluded: chain C residue 54 SER Chi-restraints excluded: chain C residue 67 GLU Chi-restraints excluded: chain C residue 75 ASP Chi-restraints excluded: chain C residue 78 VAL Chi-restraints excluded: chain C residue 80 ARG Chi-restraints excluded: chain C residue 109 VAL Chi-restraints excluded: chain D residue 42 TYR Chi-restraints excluded: chain D residue 47 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 123 random chunks: chunk 29 optimal weight: 2.9990 chunk 89 optimal weight: 2.9990 chunk 14 optimal weight: 0.4980 chunk 27 optimal weight: 10.0000 chunk 97 optimal weight: 0.6980 chunk 40 optimal weight: 2.9990 chunk 100 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 18 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 5 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- 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 = 0.4012 r_free = 0.4012 target = 0.116411 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.082192 restraints weight = 24241.265| |-----------------------------------------------------------------------------| r_work (start): 0.3424 rms_B_bonded: 1.63 r_work: 0.3226 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.3087 rms_B_bonded: 4.06 restraints_weight: 0.2500 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8513 moved from start: 0.2432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 13858 Z= 0.202 Angle : 0.528 7.530 19738 Z= 0.314 Chirality : 0.034 0.150 2236 Planarity : 0.004 0.060 1658 Dihedral : 29.317 177.659 3828 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 6.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 2.96 % Allowed : 17.77 % Favored : 79.27 % 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: 2.12 (0.27), residues: 1009 helix: 2.58 (0.21), residues: 648 sheet: -0.03 (0.76), residues: 38 loop : -0.95 (0.32), residues: 323 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP K 264 HIS 0.004 0.001 HIS H 83 PHE 0.007 0.001 PHE F 61 TYR 0.020 0.001 TYR H 84 ARG 0.013 0.000 ARG C 39 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5524.33 seconds wall clock time: 96 minutes 26.95 seconds (5786.95 seconds total)