Starting phenix.real_space_refine on Tue Nov 19 18:08:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/11_2024/6j99_9783.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/11_2024/6j99_9783.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/11_2024/6j99_9783.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/11_2024/6j99_9783.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/11_2024/6j99_9783.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6j99_9783/11_2024/6j99_9783.cif" } resolution = 4.1 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.010 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 5830 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 289 5.49 5 S 29 5.16 5 C 8711 2.51 5 N 2824 2.21 5 O 3413 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 15266 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 698 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 698 Classifications: {'peptide': 86} Link IDs: {'CIS': 1, 'PTRANS': 1, 'TRANS': 83} Chain: "C" Number of atoms: 834 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 834 Classifications: {'peptide': 108} Link IDs: {'PTRANS': 5, 'TRANS': 102} Chain: "D" Number of atoms: 738 Number of conformers: 1 Conformer: "" Number of residues, atoms: 94, 738 Classifications: {'peptide': 94} Link IDs: {'PTRANS': 2, 'TRANS': 91} Chain: "E" Number of atoms: 802 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 802 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "F" Number of atoms: 648 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 648 Classifications: {'peptide': 81} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "G" Number of atoms: 809 Number of conformers: 1 Conformer: "" Number of residues, atoms: 105, 809 Classifications: {'peptide': 105} Link IDs: {'PTRANS': 5, 'TRANS': 99} Chain: "H" Number of atoms: 742 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 742 Classifications: {'peptide': 95} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 92} Chain: "I" Number of atoms: 2935 Number of conformers: 1 Conformer: "" Number of residues, atoms: 144, 2935 Classifications: {'DNA': 144} Link IDs: {'rna3p': 143} Chain: "J" Number of atoms: 2990 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2990 Classifications: {'DNA': 145} Link IDs: {'rna3p': 144} Chain: "L" Number of atoms: 603 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 603 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "K" Number of atoms: 2665 Number of conformers: 1 Conformer: "" Number of residues, atoms: 325, 2665 Classifications: {'peptide': 325} Link IDs: {'CIS': 1, 'PCIS': 1, 'PTRANS': 16, 'TRANS': 306} Chain breaks: 1 Time building chain proxies: 8.29, per 1000 atoms: 0.54 Number of scatterers: 15266 At special positions: 0 Unit cell: (132.6, 137.8, 114.4, 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 29 16.00 P 289 15.00 O 3413 8.00 N 2824 7.00 C 8711 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.69 Conformation dependent library (CDL) restraints added in 1.1 seconds 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2194 Finding SS restraints... Secondary structure from input PDB file: 49 helices and 10 sheets defined 62.3% alpha, 3.9% beta 143 base pairs and 248 stacking pairs defined. Time for finding SS restraints: 6.81 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 removed outlier: 4.928A pdb=" N GLU A 50 " --> pdb=" O VAL A 46 " (cutoff:3.500A) removed outlier: 6.171A pdb=" N ARG A 53 " --> pdb=" O ARG A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 63 through 77 removed outlier: 3.508A pdb=" N ASP A 77 " --> pdb=" O GLU A 73 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 removed outlier: 3.841A pdb=" N ILE A 124 " --> pdb=" O MET A 120 " (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: 3.794A pdb=" N ASP B 68 " --> pdb=" O ASN B 64 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 93 removed outlier: 3.649A 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: 4.347A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) removed outlier: 3.508A pdb=" N LEU C 65 " --> pdb=" O GLU C 61 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 removed outlier: 3.793A pdb=" N LEU C 83 " --> pdb=" O ILE C 79 " (cutoff:3.500A) removed outlier: 3.684A 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 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 120 removed outlier: 3.973A pdb=" N SER D 109 " --> pdb=" O LYS D 105 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N SER D 120 " --> pdb=" O THR D 116 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 removed outlier: 4.928A pdb=" N GLU E 50 " --> pdb=" O VAL E 46 " (cutoff:3.500A) removed outlier: 6.172A pdb=" N ARG E 53 " --> pdb=" O ARG E 49 " (cutoff:3.500A) Processing helix chain 'E' and resid 63 through 77 removed outlier: 3.507A pdb=" N ASP E 77 " --> pdb=" O GLU E 73 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 removed outlier: 3.840A pdb=" N ILE E 124 " --> pdb=" O MET E 120 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 3.749A pdb=" N ASP F 68 " --> pdb=" O ASN F 64 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 93 removed outlier: 3.852A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing helix chain 'G' and resid 16 through 21 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.651A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.639A pdb=" N ASN G 68 " --> pdb=" O GLU G 64 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N ALA G 69 " --> pdb=" O LEU G 65 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 91 through 97 Processing helix chain 'H' and resid 34 through 46 Processing helix chain 'H' and resid 52 through 81 Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 100 through 121 Processing helix chain 'L' and resid 22 through 35 removed outlier: 3.588A pdb=" N VAL L 26 " --> pdb=" O THR L 22 " (cutoff:3.500A) Processing helix chain 'K' and resid 32 through 46 removed outlier: 3.548A pdb=" N ILE K 37 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 3.737A pdb=" N ILE K 38 " --> pdb=" O ALA K 34 " (cutoff:3.500A) Processing helix chain 'K' and resid 51 through 56 Processing helix chain 'K' and resid 67 through 90 Processing helix chain 'K' and resid 103 through 119 Processing helix chain 'K' and resid 121 through 127 removed outlier: 3.625A pdb=" N LEU K 125 " --> pdb=" O ASP K 121 " (cutoff:3.500A) Processing helix chain 'K' and resid 140 through 151 removed outlier: 4.054A pdb=" N VAL K 144 " --> pdb=" O SER K 140 " (cutoff:3.500A) Processing helix chain 'K' and resid 167 through 177 Processing helix chain 'K' and resid 188 through 209 Processing helix chain 'K' and resid 225 through 235 Processing helix chain 'K' and resid 241 through 245 removed outlier: 4.552A pdb=" N ALA K 244 " --> pdb=" O ASN K 241 " (cutoff:3.500A) Processing helix chain 'K' and resid 246 through 258 Processing helix chain 'K' and resid 281 through 285 removed outlier: 3.960A pdb=" N LEU K 284 " --> pdb=" O SER K 281 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N SER K 285 " --> pdb=" O ARG K 282 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 281 through 285' Processing helix chain 'K' and resid 287 through 289 No H-bonds generated for 'chain 'K' and resid 287 through 289' Processing helix chain 'K' and resid 319 through 331 Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 7.398A pdb=" N ARG A 83 " --> pdb=" O VAL B 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 118 through 119 Processing sheet with id=AA3, first strand: chain 'B' and resid 96 through 97 removed outlier: 6.260A pdb=" N THR B 96 " --> pdb=" O THR G 101 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 7.448A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.089A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'L' and resid 4 through 6 removed outlier: 3.639A pdb=" N LEU L 69 " --> pdb=" O LYS L 6 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 217 through 218 removed outlier: 6.583A pdb=" N HIS K 182 " --> pdb=" O THR K 217 " (cutoff:3.500A) removed outlier: 6.404A pdb=" N PHE K 159 " --> pdb=" O TYR K 183 " (cutoff:3.500A) removed outlier: 8.449A pdb=" N VAL K 185 " --> pdb=" O PHE K 159 " (cutoff:3.500A) removed outlier: 6.902A pdb=" N ASP K 161 " --> pdb=" O VAL K 185 " (cutoff:3.500A) removed outlier: 5.710A pdb=" N VAL K 160 " --> pdb=" O PHE K 239 " (cutoff:3.500A) removed outlier: 5.891A pdb=" N ILE K 238 " --> pdb=" O VAL K 267 " (cutoff:3.500A) 521 hydrogen bonds defined for protein. 1542 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 366 hydrogen bonds 728 hydrogen bond angles 0 basepair planarities 143 basepair parallelities 248 stacking parallelities Total time for adding SS restraints: 6.09 Time building geometry restraints manager: 4.30 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: 2782 1.33 - 1.45: 5098 1.45 - 1.57: 7638 1.57 - 1.69: 577 1.69 - 1.81: 50 Bond restraints: 16145 Sorted by residual: bond pdb=" C8 SAH K 501 " pdb=" N7 SAH K 501 " ideal model delta sigma weight residual 1.299 1.357 -0.058 2.00e-02 2.50e+03 8.29e+00 bond pdb=" C2 SAH K 501 " pdb=" N3 SAH K 501 " ideal model delta sigma weight residual 1.322 1.367 -0.045 2.00e-02 2.50e+03 5.02e+00 bond pdb=" C3' DT J 15 " pdb=" O3' DT J 15 " ideal model delta sigma weight residual 1.422 1.488 -0.066 3.00e-02 1.11e+03 4.78e+00 bond pdb=" C3' DC J 126 " pdb=" O3' DC J 126 " ideal model delta sigma weight residual 1.422 1.487 -0.065 3.00e-02 1.11e+03 4.74e+00 bond pdb=" C LYS B 31 " pdb=" N PRO B 32 " ideal model delta sigma weight residual 1.337 1.361 -0.024 1.24e-02 6.50e+03 3.78e+00 ... (remaining 16140 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.38: 22306 2.38 - 4.76: 680 4.76 - 7.14: 47 7.14 - 9.52: 18 9.52 - 11.90: 4 Bond angle restraints: 23055 Sorted by residual: angle pdb=" C LEU K 299 " pdb=" N LYS K 300 " pdb=" CA LYS K 300 " ideal model delta sigma weight residual 121.70 132.86 -11.16 1.80e+00 3.09e-01 3.84e+01 angle pdb=" N GLY L 75 " pdb=" CA GLY L 75 " pdb=" C GLY L 75 " ideal model delta sigma weight residual 113.18 102.30 10.88 2.37e+00 1.78e-01 2.11e+01 angle pdb=" C THR B 30 " pdb=" N LYS B 31 " pdb=" CA LYS B 31 " ideal model delta sigma weight residual 120.97 127.28 -6.31 1.48e+00 4.57e-01 1.82e+01 angle pdb=" C ARG E 49 " pdb=" N GLU E 50 " pdb=" CA GLU E 50 " ideal model delta sigma weight residual 126.45 133.50 -7.05 1.77e+00 3.19e-01 1.59e+01 angle pdb=" C ARG A 49 " pdb=" N GLU A 50 " pdb=" CA GLU A 50 " ideal model delta sigma weight residual 126.45 133.46 -7.01 1.77e+00 3.19e-01 1.57e+01 ... (remaining 23050 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 30.05: 7058 30.05 - 60.09: 1830 60.09 - 90.14: 85 90.14 - 120.18: 1 120.18 - 150.23: 2 Dihedral angle restraints: 8976 sinusoidal: 5583 harmonic: 3393 Sorted by residual: dihedral pdb=" CA PRO H 100 " pdb=" C PRO H 100 " pdb=" N GLY H 101 " pdb=" CA GLY H 101 " ideal model delta harmonic sigma weight residual -180.00 -145.87 -34.13 0 5.00e+00 4.00e-02 4.66e+01 dihedral pdb=" CA SER K 304 " pdb=" C SER K 304 " pdb=" N TRP K 305 " pdb=" CA TRP K 305 " ideal model delta harmonic sigma weight residual 180.00 148.77 31.23 0 5.00e+00 4.00e-02 3.90e+01 dihedral pdb=" CA ARG L 74 " pdb=" C ARG L 74 " pdb=" N GLY L 75 " pdb=" CA GLY L 75 " ideal model delta harmonic sigma weight residual 180.00 150.47 29.53 0 5.00e+00 4.00e-02 3.49e+01 ... (remaining 8973 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1840 0.050 - 0.100: 620 0.100 - 0.150: 121 0.150 - 0.200: 21 0.200 - 0.250: 5 Chirality restraints: 2607 Sorted by residual: chirality pdb=" P DT J 83 " pdb=" OP1 DT J 83 " pdb=" OP2 DT J 83 " pdb=" O5' DT J 83 " both_signs ideal model delta sigma weight residual True 2.35 -2.60 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" C1' DG J 82 " pdb=" O4' DG J 82 " pdb=" C2' DG J 82 " pdb=" N9 DG J 82 " both_signs ideal model delta sigma weight residual False 2.42 2.18 0.23 2.00e-01 2.50e+01 1.38e+00 chirality pdb=" CB ILE L 13 " pdb=" CA ILE L 13 " pdb=" CG1 ILE L 13 " pdb=" CG2 ILE L 13 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.21 2.00e-01 2.50e+01 1.15e+00 ... (remaining 2604 not shown) Planarity restraints: 1920 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR E 45 " 0.014 2.00e-02 2.50e+03 2.87e-02 8.22e+00 pdb=" C THR E 45 " -0.050 2.00e-02 2.50e+03 pdb=" O THR E 45 " 0.019 2.00e-02 2.50e+03 pdb=" N VAL E 46 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU A 50 " 0.014 2.00e-02 2.50e+03 2.84e-02 8.05e+00 pdb=" C GLU A 50 " -0.049 2.00e-02 2.50e+03 pdb=" O GLU A 50 " 0.018 2.00e-02 2.50e+03 pdb=" N ILE A 51 " 0.017 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLU E 50 " -0.014 2.00e-02 2.50e+03 2.83e-02 8.01e+00 pdb=" C GLU E 50 " 0.049 2.00e-02 2.50e+03 pdb=" O GLU E 50 " -0.018 2.00e-02 2.50e+03 pdb=" N ILE E 51 " -0.017 2.00e-02 2.50e+03 ... (remaining 1917 not shown) Histogram of nonbonded interaction distances: 2.20 - 2.74: 1901 2.74 - 3.28: 14252 3.28 - 3.82: 32196 3.82 - 4.36: 36012 4.36 - 4.90: 51791 Nonbonded interactions: 136152 Sorted by model distance: nonbonded pdb=" OD1 ASP A 123 " pdb=" NE2 HIS E 113 " model vdw 2.204 3.120 nonbonded pdb=" OG1 THR H 87 " pdb=" OE1 GLU H 90 " model vdw 2.250 3.040 nonbonded pdb=" OD1 ASN K 242 " pdb=" OG SER K 269 " model vdw 2.252 3.040 nonbonded pdb=" O2 DC I 95 " pdb=" N2 DG J 53 " model vdw 2.260 2.496 nonbonded pdb=" OH TYR D 37 " pdb=" OP1 DG J 122 " model vdw 2.271 3.040 ... (remaining 136147 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'E' } ncs_group { reference = (chain 'B' and resid 21 through 101) selection = chain 'F' } ncs_group { reference = (chain 'C' and resid 13 through 117) selection = chain 'G' } ncs_group { reference = (chain 'D' and resid 28 through 120) selection = (chain 'H' and resid 28 through 120) } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.130 Construct map_model_manager: 0.010 Extract box with map and model: 0.570 Check model and map are aligned: 0.110 Set scattering table: 0.150 Process input model: 38.800 Find NCS groups from input model: 0.310 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5209 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 : 0.008 0.066 16145 Z= 0.451 Angle : 0.978 11.900 23055 Z= 0.559 Chirality : 0.051 0.250 2607 Planarity : 0.007 0.066 1920 Dihedral : 27.095 150.230 6782 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.05 % Favored : 91.95 % Rotamer: Outliers : 0.00 % Allowed : 1.40 % Favored : 98.60 % Cbeta Deviations : 0.09 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.18 % 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: -2.88 (0.21), residues: 1143 helix: -1.35 (0.16), residues: 694 sheet: -3.97 (0.63), residues: 37 loop : -2.49 (0.28), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.004 TRP K 228 HIS 0.019 0.003 HIS C 82 PHE 0.027 0.004 PHE K 245 TYR 0.041 0.004 TYR G 39 ARG 0.008 0.001 ARG K 80 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 379 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 379 time to evaluate : 1.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 62 ILE cc_start: 0.5261 (mt) cc_final: 0.4326 (mt) REVERT: A 93 GLN cc_start: 0.4178 (tt0) cc_final: 0.3786 (tt0) REVERT: B 100 PHE cc_start: 0.7406 (m-80) cc_final: 0.7027 (m-10) REVERT: C 57 TYR cc_start: 0.8736 (t80) cc_final: 0.8119 (t80) REVERT: C 75 LYS cc_start: 0.7886 (mmtp) cc_final: 0.7656 (mmtt) REVERT: D 90 GLU cc_start: 0.7424 (mp0) cc_final: 0.7194 (mp0) REVERT: D 106 HIS cc_start: 0.7983 (m-70) cc_final: 0.7287 (m-70) REVERT: G 68 ASN cc_start: 0.8396 (m-40) cc_final: 0.8053 (m-40) REVERT: G 72 ASP cc_start: 0.9244 (m-30) cc_final: 0.8830 (m-30) REVERT: G 115 LEU cc_start: 0.6386 (mt) cc_final: 0.5923 (tt) REVERT: H 90 GLU cc_start: 0.6325 (mp0) cc_final: 0.5988 (mt-10) REVERT: H 100 PRO cc_start: 0.4871 (Cg_endo) cc_final: 0.4583 (Cg_exo) REVERT: L 1 MET cc_start: 0.2615 (ttp) cc_final: 0.1893 (ttt) REVERT: L 6 LYS cc_start: 0.8999 (tttt) cc_final: 0.8754 (tptt) REVERT: L 71 LEU cc_start: 0.8587 (mp) cc_final: 0.7860 (mt) REVERT: K 53 LEU cc_start: 0.5821 (tp) cc_final: 0.5539 (pp) REVERT: K 66 LYS cc_start: 0.7634 (mppt) cc_final: 0.7178 (pttt) REVERT: K 96 MET cc_start: -0.0461 (ttp) cc_final: -0.1120 (tpt) outliers start: 0 outliers final: 0 residues processed: 379 average time/residue: 0.4057 time to fit residues: 201.4802 Evaluate side-chains 236 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 236 time to evaluate : 1.275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 117 optimal weight: 6.9990 chunk 105 optimal weight: 6.9990 chunk 58 optimal weight: 8.9990 chunk 35 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 56 optimal weight: 0.9990 chunk 108 optimal weight: 4.9990 chunk 42 optimal weight: 0.8980 chunk 66 optimal weight: 0.9990 chunk 81 optimal weight: 4.9990 chunk 126 optimal weight: 6.9990 overall best weight: 1.9788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 108 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 18 HIS C 24 GLN C 68 ASN D 46 HIS D 79 HIS D 81 ASN ** D 106 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN G 31 HIS G 38 ASN G 84 GLN K 35 HIS K 126 ASN K 213 HIS K 234 ASN K 251 HIS K 252 GLN K 315 HIS Total number of N/Q/H flips: 17 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5877 moved from start: 0.3982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 16145 Z= 0.284 Angle : 0.759 8.325 23055 Z= 0.427 Chirality : 0.044 0.283 2607 Planarity : 0.006 0.073 1920 Dihedral : 32.059 147.677 4447 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.25 % Favored : 94.75 % Rotamer: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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 (0.24), residues: 1143 helix: 0.17 (0.18), residues: 708 sheet: -3.30 (0.57), residues: 55 loop : -2.10 (0.31), residues: 380 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP K 208 HIS 0.012 0.002 HIS E 113 PHE 0.037 0.003 PHE E 67 TYR 0.013 0.002 TYR E 99 ARG 0.012 0.001 ARG K 319 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 319 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 319 time to evaluate : 1.200 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8443 (tp30) cc_final: 0.8110 (tp30) REVERT: A 62 ILE cc_start: 0.6862 (mt) cc_final: 0.6567 (mt) REVERT: A 93 GLN cc_start: 0.6473 (tt0) cc_final: 0.6149 (tt0) REVERT: A 120 MET cc_start: 0.5884 (mpp) cc_final: 0.5581 (mpp) REVERT: B 88 TYR cc_start: 0.8636 (m-80) cc_final: 0.8306 (m-80) REVERT: B 100 PHE cc_start: 0.8083 (m-80) cc_final: 0.7679 (m-10) REVERT: C 23 LEU cc_start: 0.8197 (mm) cc_final: 0.7783 (mm) REVERT: C 61 GLU cc_start: 0.8488 (mm-30) cc_final: 0.7828 (tp30) REVERT: C 75 LYS cc_start: 0.7609 (mmtp) cc_final: 0.7396 (mmtt) REVERT: C 91 GLU cc_start: 0.7833 (tm-30) cc_final: 0.7466 (tp30) REVERT: C 104 GLN cc_start: 0.8233 (tp-100) cc_final: 0.8022 (tp-100) REVERT: D 82 LYS cc_start: 0.9064 (mtpt) cc_final: 0.8599 (mmtt) REVERT: D 106 HIS cc_start: 0.8309 (m-70) cc_final: 0.7621 (m-70) REVERT: D 112 THR cc_start: 0.9131 (m) cc_final: 0.8899 (m) REVERT: E 105 GLU cc_start: 0.9252 (tm-30) cc_final: 0.8686 (tm-30) REVERT: E 125 GLN cc_start: 0.7893 (pt0) cc_final: 0.7646 (pm20) REVERT: F 51 TYR cc_start: 0.5787 (m-10) cc_final: 0.4334 (m-80) REVERT: F 84 MET cc_start: 0.7295 (mmp) cc_final: 0.6691 (mmp) REVERT: G 82 HIS cc_start: 0.8486 (m170) cc_final: 0.8279 (m-70) REVERT: G 99 ARG cc_start: 0.7011 (mmp80) cc_final: 0.6623 (mmt180) REVERT: H 98 LEU cc_start: 0.7827 (tp) cc_final: 0.7385 (tt) REVERT: L 1 MET cc_start: 0.3253 (ttp) cc_final: 0.2561 (ttt) REVERT: L 24 GLU cc_start: 0.8214 (tt0) cc_final: 0.7804 (mm-30) REVERT: L 27 LYS cc_start: 0.8688 (ptpp) cc_final: 0.8380 (mmtm) REVERT: K 53 LEU cc_start: 0.6032 (tp) cc_final: 0.5604 (mt) REVERT: K 66 LYS cc_start: 0.7854 (mppt) cc_final: 0.7430 (pttt) REVERT: K 96 MET cc_start: -0.0028 (ttp) cc_final: -0.0867 (tpt) REVERT: K 147 MET cc_start: 0.6901 (mtm) cc_final: 0.6593 (ttp) REVERT: K 205 TRP cc_start: 0.7158 (m100) cc_final: 0.6875 (m100) outliers start: 0 outliers final: 0 residues processed: 319 average time/residue: 0.3615 time to fit residues: 155.9917 Evaluate side-chains 244 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 244 time to evaluate : 1.225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 70 optimal weight: 2.9990 chunk 39 optimal weight: 2.9990 chunk 105 optimal weight: 30.0000 chunk 85 optimal weight: 10.0000 chunk 34 optimal weight: 2.9990 chunk 126 optimal weight: 20.0000 chunk 136 optimal weight: 0.8980 chunk 112 optimal weight: 30.0000 chunk 125 optimal weight: 7.9990 chunk 43 optimal weight: 0.0870 chunk 101 optimal weight: 0.0570 overall best weight: 1.4080 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 46 HIS D 106 HIS ** E 55 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN F 93 GLN G 38 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6104 moved from start: 0.5179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 16145 Z= 0.237 Angle : 0.695 7.111 23055 Z= 0.394 Chirality : 0.041 0.211 2607 Planarity : 0.005 0.056 1920 Dihedral : 31.735 144.697 4447 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 14.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.42 % Favored : 94.58 % Rotamer: Outliers : 0.20 % Allowed : 3.81 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.24), residues: 1143 helix: 0.63 (0.19), residues: 720 sheet: -2.92 (0.62), residues: 55 loop : -2.03 (0.31), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP K 305 HIS 0.004 0.001 HIS K 251 PHE 0.020 0.002 PHE K 326 TYR 0.023 0.002 TYR H 80 ARG 0.010 0.001 ARG D 96 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 320 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 318 time to evaluate : 1.606 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 50 GLU cc_start: 0.8243 (tp30) cc_final: 0.7748 (tp30) REVERT: A 115 LYS cc_start: 0.7420 (mptt) cc_final: 0.7080 (mmtm) REVERT: A 119 ILE cc_start: 0.3351 (pt) cc_final: 0.2980 (pt) REVERT: B 52 GLU cc_start: 0.7320 (mm-30) cc_final: 0.6896 (mp0) REVERT: B 100 PHE cc_start: 0.8218 (m-80) cc_final: 0.7922 (m-10) REVERT: C 17 ARG cc_start: 0.7349 (ptp-110) cc_final: 0.6975 (ptm160) REVERT: C 56 GLU cc_start: 0.8577 (mm-30) cc_final: 0.8220 (mm-30) REVERT: C 75 LYS cc_start: 0.7842 (mmtp) cc_final: 0.7411 (mmmt) REVERT: C 95 LYS cc_start: 0.9305 (tptp) cc_final: 0.8931 (tppt) REVERT: D 82 LYS cc_start: 0.9167 (mtpt) cc_final: 0.8567 (mmtt) REVERT: D 83 ARG cc_start: 0.8424 (mmp80) cc_final: 0.8212 (mmp80) REVERT: D 103 LEU cc_start: 0.9212 (tp) cc_final: 0.8965 (tp) REVERT: F 84 MET cc_start: 0.8108 (mmp) cc_final: 0.7816 (mmp) REVERT: G 82 HIS cc_start: 0.8639 (m170) cc_final: 0.8326 (m-70) REVERT: G 84 GLN cc_start: 0.8522 (tp40) cc_final: 0.7389 (tm-30) REVERT: G 85 LEU cc_start: 0.8641 (mm) cc_final: 0.8354 (mm) REVERT: G 101 THR cc_start: 0.8858 (m) cc_final: 0.8614 (p) REVERT: H 103 LEU cc_start: 0.7748 (pp) cc_final: 0.7440 (pt) REVERT: L 1 MET cc_start: 0.2669 (ttp) cc_final: 0.1889 (ttt) REVERT: L 6 LYS cc_start: 0.9018 (tttt) cc_final: 0.8782 (tptp) REVERT: L 24 GLU cc_start: 0.8213 (tt0) cc_final: 0.7655 (mm-30) REVERT: K 53 LEU cc_start: 0.5964 (tp) cc_final: 0.5562 (mt) REVERT: K 66 LYS cc_start: 0.7928 (mppt) cc_final: 0.7508 (pttt) REVERT: K 96 MET cc_start: 0.0179 (ttp) cc_final: -0.0461 (tpp) REVERT: K 179 CYS cc_start: 0.1942 (m) cc_final: 0.0959 (m) REVERT: K 205 TRP cc_start: 0.6935 (m100) cc_final: 0.6593 (m100) outliers start: 2 outliers final: 1 residues processed: 318 average time/residue: 0.3472 time to fit residues: 153.1968 Evaluate side-chains 252 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 251 time to evaluate : 1.241 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 124 optimal weight: 0.0470 chunk 95 optimal weight: 8.9990 chunk 65 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 60 optimal weight: 7.9990 chunk 84 optimal weight: 10.9990 chunk 126 optimal weight: 5.9990 chunk 134 optimal weight: 0.7980 chunk 66 optimal weight: 0.8980 chunk 120 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 overall best weight: 1.3482 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 94 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 108 ASN ** E 113 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 25 ASN G 38 ASN G 68 ASN K 181 HIS K 234 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6356 moved from start: 0.6419 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.087 16145 Z= 0.236 Angle : 0.666 10.692 23055 Z= 0.377 Chirality : 0.041 0.242 2607 Planarity : 0.005 0.074 1920 Dihedral : 31.466 144.859 4447 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 15.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.07 % Favored : 94.93 % Rotamer: Outliers : 0.20 % Allowed : 3.51 % Favored : 96.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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: -0.23 (0.25), residues: 1143 helix: 0.88 (0.19), residues: 712 sheet: -2.39 (0.74), residues: 48 loop : -1.79 (0.32), residues: 383 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP K 208 HIS 0.012 0.001 HIS K 251 PHE 0.035 0.002 PHE K 326 TYR 0.042 0.002 TYR F 51 ARG 0.011 0.001 ARG F 92 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 327 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 325 time to evaluate : 1.476 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.7704 (mptt) cc_final: 0.7468 (mmtm) REVERT: B 52 GLU cc_start: 0.7757 (mm-30) cc_final: 0.7459 (mp0) REVERT: B 100 PHE cc_start: 0.8317 (m-80) cc_final: 0.8089 (m-10) REVERT: C 23 LEU cc_start: 0.8270 (mm) cc_final: 0.8056 (mm) REVERT: C 57 TYR cc_start: 0.8818 (t80) cc_final: 0.8275 (t80) REVERT: C 75 LYS cc_start: 0.8123 (mmtp) cc_final: 0.7706 (mmmt) REVERT: C 95 LYS cc_start: 0.9294 (tptp) cc_final: 0.9020 (tppt) REVERT: D 37 TYR cc_start: 0.8420 (m-80) cc_final: 0.7858 (m-80) REVERT: D 82 LYS cc_start: 0.9210 (mtpt) cc_final: 0.8678 (mmtt) REVERT: D 83 ARG cc_start: 0.8452 (mmp80) cc_final: 0.8142 (mmp80) REVERT: D 103 LEU cc_start: 0.9327 (tp) cc_final: 0.8919 (tp) REVERT: D 110 GLU cc_start: 0.8483 (mm-30) cc_final: 0.8137 (mm-30) REVERT: E 62 ILE cc_start: 0.5693 (mt) cc_final: 0.5396 (mt) REVERT: E 63 ARG cc_start: 0.6626 (mmt-90) cc_final: 0.6170 (mmt180) REVERT: F 78 ARG cc_start: 0.7512 (ptt180) cc_final: 0.6997 (ptt-90) REVERT: F 82 THR cc_start: 0.8021 (p) cc_final: 0.7817 (p) REVERT: F 84 MET cc_start: 0.8242 (mmp) cc_final: 0.7134 (mmm) REVERT: G 76 THR cc_start: 0.9061 (p) cc_final: 0.8767 (t) REVERT: G 81 ARG cc_start: 0.7987 (tpt-90) cc_final: 0.6803 (tpt170) REVERT: G 82 HIS cc_start: 0.8626 (m170) cc_final: 0.8311 (m-70) REVERT: G 84 GLN cc_start: 0.8496 (tp40) cc_final: 0.7603 (tm-30) REVERT: G 85 LEU cc_start: 0.8761 (mm) cc_final: 0.8402 (mm) REVERT: G 101 THR cc_start: 0.8963 (m) cc_final: 0.8609 (t) REVERT: H 52 SER cc_start: 0.6680 (m) cc_final: 0.6068 (m) REVERT: L 1 MET cc_start: 0.3175 (ttp) cc_final: 0.2546 (ttt) REVERT: L 6 LYS cc_start: 0.9026 (tttt) cc_final: 0.8791 (tptp) REVERT: L 24 GLU cc_start: 0.8198 (tt0) cc_final: 0.7607 (mm-30) REVERT: L 62 GLN cc_start: 0.7678 (tp40) cc_final: 0.7389 (tp40) REVERT: K 53 LEU cc_start: 0.5960 (tp) cc_final: 0.5520 (mt) REVERT: K 66 LYS cc_start: 0.7966 (mppt) cc_final: 0.7530 (pttt) REVERT: K 96 MET cc_start: 0.0796 (ttp) cc_final: -0.0255 (tpp) REVERT: K 153 MET cc_start: 0.4846 (ttp) cc_final: 0.4480 (ppp) REVERT: K 179 CYS cc_start: 0.3129 (m) cc_final: 0.0951 (m) REVERT: K 187 LYS cc_start: 0.6789 (tttt) cc_final: 0.6472 (tppt) outliers start: 2 outliers final: 1 residues processed: 326 average time/residue: 0.3319 time to fit residues: 149.6701 Evaluate side-chains 266 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 265 time to evaluate : 1.429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 111 optimal weight: 7.9990 chunk 76 optimal weight: 6.9990 chunk 1 optimal weight: 6.9990 chunk 100 optimal weight: 20.0000 chunk 55 optimal weight: 8.9990 chunk 114 optimal weight: 10.0000 chunk 92 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 68 optimal weight: 3.9990 chunk 120 optimal weight: 9.9990 chunk 33 optimal weight: 1.9990 overall best weight: 5.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 25 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 68 ASN C 112 GLN D 79 HIS E 85 GLN E 125 GLN F 25 ASN ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 82 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 84 GLN H 46 HIS ** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 331 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7434 moved from start: 1.0987 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.177 16145 Z= 0.560 Angle : 1.025 11.781 23055 Z= 0.565 Chirality : 0.057 0.436 2607 Planarity : 0.009 0.111 1920 Dihedral : 32.223 148.121 4447 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 28.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.86 % Favored : 94.14 % Rotamer: Outliers : 0.20 % Allowed : 3.81 % Favored : 95.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -1.68 (0.23), residues: 1143 helix: -0.30 (0.17), residues: 695 sheet: -3.21 (0.69), residues: 43 loop : -2.22 (0.29), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP K 208 HIS 0.008 0.002 HIS D 46 PHE 0.032 0.004 PHE A 67 TYR 0.046 0.004 TYR D 80 ARG 0.052 0.002 ARG L 72 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 376 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 374 time to evaluate : 1.180 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 54 TYR cc_start: 0.7674 (m-10) cc_final: 0.7171 (m-80) REVERT: A 60 LEU cc_start: 0.8928 (mm) cc_final: 0.8725 (mt) REVERT: A 93 GLN cc_start: 0.9120 (tt0) cc_final: 0.8892 (tt0) REVERT: B 50 ILE cc_start: 0.8643 (mm) cc_final: 0.8434 (mm) REVERT: B 74 GLU cc_start: 0.8506 (mm-30) cc_final: 0.8117 (mt-10) REVERT: B 84 MET cc_start: 0.8862 (tpp) cc_final: 0.8453 (tpp) REVERT: B 95 ARG cc_start: 0.8827 (ptp-110) cc_final: 0.8451 (ptp-110) REVERT: C 24 GLN cc_start: 0.8653 (mm-40) cc_final: 0.8265 (mt0) REVERT: C 75 LYS cc_start: 0.8932 (mmtp) cc_final: 0.8218 (mmmm) REVERT: C 91 GLU cc_start: 0.8757 (pp20) cc_final: 0.7989 (tp30) REVERT: C 92 GLU cc_start: 0.8754 (pp20) cc_final: 0.8287 (tm-30) REVERT: C 95 LYS cc_start: 0.9530 (tptp) cc_final: 0.9258 (tppt) REVERT: D 65 ASP cc_start: 0.9090 (t70) cc_final: 0.8751 (t0) REVERT: D 80 TYR cc_start: 0.7843 (m-10) cc_final: 0.7554 (m-10) REVERT: D 82 LYS cc_start: 0.9463 (mtpt) cc_final: 0.8782 (mmtt) REVERT: D 83 ARG cc_start: 0.9033 (mmp80) cc_final: 0.8623 (mmp80) REVERT: D 92 GLN cc_start: 0.8986 (pt0) cc_final: 0.8779 (pt0) REVERT: D 97 LEU cc_start: 0.9253 (mt) cc_final: 0.8938 (mt) REVERT: D 99 LEU cc_start: 0.9615 (mt) cc_final: 0.9395 (mt) REVERT: D 103 LEU cc_start: 0.9369 (tp) cc_final: 0.9104 (tp) REVERT: D 106 HIS cc_start: 0.8395 (m90) cc_final: 0.8015 (m-70) REVERT: E 93 GLN cc_start: 0.9424 (tm-30) cc_final: 0.9152 (tm-30) REVERT: E 94 GLU cc_start: 0.9019 (tp30) cc_final: 0.8709 (tm-30) REVERT: E 104 PHE cc_start: 0.9128 (m-80) cc_final: 0.8854 (m-10) REVERT: E 123 ASP cc_start: 0.9108 (m-30) cc_final: 0.8619 (t70) REVERT: F 53 GLU cc_start: 0.8870 (tp30) cc_final: 0.8668 (tp30) REVERT: G 39 TYR cc_start: 0.8459 (m-80) cc_final: 0.7992 (m-80) REVERT: G 57 TYR cc_start: 0.8864 (t80) cc_final: 0.8492 (t80) REVERT: G 71 ARG cc_start: 0.8619 (mmp80) cc_final: 0.8401 (mmp80) REVERT: G 82 HIS cc_start: 0.8868 (m170) cc_final: 0.8160 (m90) REVERT: G 84 GLN cc_start: 0.8804 (tp-100) cc_final: 0.8586 (tp40) REVERT: G 101 THR cc_start: 0.9005 (m) cc_final: 0.8569 (p) REVERT: G 112 GLN cc_start: 0.8737 (mm-40) cc_final: 0.8326 (mm-40) REVERT: H 96 ARG cc_start: 0.8568 (ptm160) cc_final: 0.8346 (ttp-110) REVERT: L 1 MET cc_start: 0.3554 (ttp) cc_final: 0.2822 (ttt) REVERT: L 62 GLN cc_start: 0.7659 (tp40) cc_final: 0.7433 (tp40) REVERT: K 66 LYS cc_start: 0.8164 (mppt) cc_final: 0.7719 (pttt) REVERT: K 96 MET cc_start: -0.0252 (ttp) cc_final: -0.0902 (tpp) REVERT: K 153 MET cc_start: 0.5068 (ttp) cc_final: 0.3910 (tmm) REVERT: K 179 CYS cc_start: 0.2751 (m) cc_final: 0.1206 (m) REVERT: K 229 ARG cc_start: 0.8728 (mmm-85) cc_final: 0.8520 (ttm-80) REVERT: K 291 MET cc_start: 0.7097 (ptp) cc_final: 0.6464 (pmm) outliers start: 2 outliers final: 0 residues processed: 375 average time/residue: 0.3332 time to fit residues: 172.4349 Evaluate side-chains 304 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 304 time to evaluate : 1.341 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 45 optimal weight: 0.0050 chunk 120 optimal weight: 7.9990 chunk 26 optimal weight: 0.8980 chunk 78 optimal weight: 5.9990 chunk 33 optimal weight: 0.8980 chunk 134 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 62 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 44 optimal weight: 0.9980 chunk 70 optimal weight: 0.7980 overall best weight: 0.6594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 113 HIS A 125 GLN B 25 ASN B 75 HIS B 93 GLN ** C 73 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 93 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 46 HIS ** K 146 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7274 moved from start: 1.1128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.075 16145 Z= 0.225 Angle : 0.724 9.117 23055 Z= 0.410 Chirality : 0.044 0.247 2607 Planarity : 0.006 0.063 1920 Dihedral : 32.109 147.091 4447 Min Nonbonded Distance : 2.084 Molprobity Statistics. All-atom Clashscore : 17.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 2.81 % Favored : 97.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.18 % 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 (0.24), residues: 1143 helix: 0.50 (0.19), residues: 707 sheet: -2.42 (0.79), residues: 43 loop : -2.13 (0.29), residues: 393 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP K 208 HIS 0.013 0.001 HIS F 75 PHE 0.053 0.003 PHE E 67 TYR 0.035 0.002 TYR B 98 ARG 0.008 0.001 ARG B 92 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2286 Ramachandran restraints generated. 1143 Oldfield, 0 Emsley, 1143 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 397 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 397 time to evaluate : 1.444 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 115 LYS cc_start: 0.9359 (ttmm) cc_final: 0.9016 (mmtm) REVERT: A 120 MET cc_start: 0.8159 (mmt) cc_final: 0.7954 (mmm) REVERT: B 74 GLU cc_start: 0.8355 (mm-30) cc_final: 0.8144 (mt-10) REVERT: B 84 MET cc_start: 0.8551 (tpp) cc_final: 0.8315 (tpp) REVERT: B 95 ARG cc_start: 0.8705 (ptp-110) cc_final: 0.8226 (ptp-110) REVERT: B 100 PHE cc_start: 0.8295 (m-10) cc_final: 0.7390 (m-10) REVERT: C 25 PHE cc_start: 0.7745 (m-10) cc_final: 0.7537 (m-10) REVERT: C 75 LYS cc_start: 0.8876 (mmtp) cc_final: 0.8199 (mmmm) REVERT: C 91 GLU cc_start: 0.8686 (pp20) cc_final: 0.8049 (tp30) REVERT: C 95 LYS cc_start: 0.9443 (tptp) cc_final: 0.9120 (tppt) REVERT: D 37 TYR cc_start: 0.7958 (m-80) cc_final: 0.7747 (m-80) REVERT: D 57 SER cc_start: 0.8881 (t) cc_final: 0.8561 (p) REVERT: D 58 ILE cc_start: 0.9123 (mm) cc_final: 0.8714 (mm) REVERT: D 65 ASP cc_start: 0.8981 (t70) cc_final: 0.8727 (t0) REVERT: D 82 LYS cc_start: 0.9350 (mtpt) cc_final: 0.8498 (mmtt) REVERT: D 83 ARG cc_start: 0.8969 (mmp80) cc_final: 0.8476 (mmp80) REVERT: D 103 LEU cc_start: 0.9268 (tp) cc_final: 0.9039 (tp) REVERT: D 106 HIS cc_start: 0.8299 (m90) cc_final: 0.8023 (m-70) REVERT: E 55 GLN cc_start: 0.7981 (pp30) cc_final: 0.7779 (pp30) REVERT: E 85 GLN cc_start: 0.8390 (tt0) cc_final: 0.8138 (tt0) REVERT: E 97 GLU cc_start: 0.8398 (tp30) cc_final: 0.8051 (tp30) REVERT: E 122 LYS cc_start: 0.9231 (ptmm) cc_final: 0.8974 (ptmm) REVERT: F 36 ARG cc_start: 0.8535 (mpt-90) cc_final: 0.8228 (mtt90) REVERT: F 45 ARG cc_start: 0.8003 (ttt180) cc_final: 0.7515 (ttt90) REVERT: F 84 MET cc_start: 0.8884 (mmp) cc_final: 0.8456 (mmm) REVERT: F 92 ARG cc_start: 0.8589 (ttp80) cc_final: 0.8367 (ttp80) REVERT: G 75 LYS cc_start: 0.7860 (tptt) cc_final: 0.7477 (mmtt) REVERT: G 76 THR cc_start: 0.9075 (p) cc_final: 0.8781 (t) REVERT: G 81 ARG cc_start: 0.8386 (tpt-90) cc_final: 0.8078 (tpt170) REVERT: G 84 GLN cc_start: 0.8760 (tp-100) cc_final: 0.7922 (tm-30) REVERT: G 101 THR cc_start: 0.8822 (m) cc_final: 0.8476 (t) REVERT: G 104 GLN cc_start: 0.7610 (mp10) cc_final: 0.7022 (mp10) REVERT: H 56 MET cc_start: 0.8935 (mmp) cc_final: 0.8424 (tmm) REVERT: H 76 ARG cc_start: 0.8006 (ttm110) cc_final: 0.7805 (ttm-80) REVERT: H 96 ARG cc_start: 0.8471 (ptm160) cc_final: 0.8249 (ttp-110) REVERT: L 1 MET cc_start: 0.3418 (ttp) cc_final: 0.2651 (ttt) REVERT: L 62 GLN cc_start: 0.7764 (tp40) cc_final: 0.7527 (tp40) REVERT: K 66 LYS cc_start: 0.8111 (mppt) cc_final: 0.7669 (pttt) REVERT: K 96 MET cc_start: -0.0016 (ttp) cc_final: -0.0432 (tpp) REVERT: K 153 MET cc_start: 0.4640 (ttp) cc_final: 0.4367 (ppp) REVERT: K 179 CYS cc_start: 0.3386 (m) cc_final: 0.1231 (m) REVERT: K 187 LYS cc_start: 0.6121 (tttt) cc_final: 0.5737 (tppt) REVERT: K 281 SER cc_start: 0.9050 (t) cc_final: 0.8668 (m) outliers start: 0 outliers final: 0 residues processed: 397 average time/residue: 0.3374 time to fit residues: 183.8407 Evaluate side-chains 327 residues out of total 998 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 327 time to evaluate : 1.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 129 optimal weight: 0.8980 chunk 15 optimal weight: 0.3980 chunk 76 optimal weight: 7.9990 chunk 98 optimal weight: 9.9990 chunk 113 optimal weight: 5.9990 chunk 75 optimal weight: 7.9990 chunk 133 optimal weight: 2.9990 chunk 83 optimal weight: 6.9990 chunk 81 optimal weight: 7.9990 chunk 61 optimal weight: 0.6980 chunk 82 optimal weight: 5.9990 overall best weight: 2.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Sorry: Reduce crashed with command 'molprobity.reduce -quiet -trim -'. Dumping stdin to file 'reduce_failure.pdb'. Return code: -15 Dumping stderr: