Starting phenix.real_space_refine (version: dev) on Tue Apr 5 16:29:06 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/04_2022/7d1z_30551.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/04_2022/7d1z_30551.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.15 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/04_2022/7d1z_30551.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/04_2022/7d1z_30551.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/04_2022/7d1z_30551.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7d1z_30551/04_2022/7d1z_30551.pdb" } resolution = 3.15 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped Residue "H TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "K TYR 277": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4553/modules/chem_data/mon_lib" Total number of atoms: 13327 Number of models: 1 Model: "" Number of chains: 11 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 801 Classifications: {'peptide': 97} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "B" Number of atoms: 646 Number of conformers: 1 Conformer: "" Number of residues, atoms: 81, 646 Classifications: {'peptide': 81} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 79} Chain: "C" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 824 Classifications: {'peptide': 107} Link IDs: {'PTRANS': 5, 'TRANS': 101} Chain: "D" Number of atoms: 729 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 729 Classifications: {'peptide': 93} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "E" Number of atoms: 800 Number of conformers: 1 Conformer: "" Number of residues, atoms: 97, 800 Classifications: {'peptide': 97} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 3, 'TRANS': 93} Chain: "G" Number of atoms: 840 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 840 Classifications: {'peptide': 109} Link IDs: {'PTRANS': 5, 'TRANS': 103} Chain: "H" Number of atoms: 719 Number of conformers: 1 Conformer: "" Number of residues, atoms: 92, 719 Classifications: {'peptide': 92} Link IDs: {'PTRANS': 2, 'TRANS': 89} Chain: "I" Number of atoms: 2952 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2952 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "J" Number of atoms: 2987 Number of conformers: 1 Conformer: "" Number of residues, atoms: 145, 2987 Classifications: {'DNA': 145} Modifications used: {'5*END': 1} Link IDs: {'rna3p': 144} Chain: "K" Number of atoms: 1330 Number of conformers: 1 Conformer: "" Number of residues, atoms: 166, 1330 Classifications: {'peptide': 166} Link IDs: {'PTRANS': 3, 'TRANS': 162} Chain: "F" Number of atoms: 699 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 699 Classifications: {'peptide': 87} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 1, 'TRANS': 85} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Time building chain proxies: 8.05, per 1000 atoms: 0.60 Number of scatterers: 13327 At special positions: 0 Unit cell: (118.65, 99.75, 123.9, 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 20 16.00 P 288 15.00 O 3057 8.00 N 2499 7.00 C 7463 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 6.68 Conformation dependent library (CDL) restraints added in 1.0 seconds 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1728 Finding SS restraints... Secondary structure from input PDB file: 39 helices and 15 sheets defined 64.5% alpha, 5.6% beta 138 base pairs and 259 stacking pairs defined. Time for finding SS restraints: 5.84 Creating SS restraints... Processing helix chain 'A' and resid 44 through 57 Processing helix chain 'A' and resid 63 through 79 removed outlier: 3.805A pdb=" N PHE A 78 " --> pdb=" O ILE A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 132 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: 3.544A pdb=" N GLU B 53 " --> pdb=" O LEU B 49 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 22 Processing helix chain 'C' and resid 26 through 37 Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.399A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 90 through 97 Processing helix chain 'C' and resid 112 through 116 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 103 through 124 removed outlier: 3.557A pdb=" N ALA D 124 " --> pdb=" O LYS D 120 " (cutoff:3.500A) Processing helix chain 'E' and resid 44 through 57 Processing helix chain 'E' and resid 63 through 76 Processing helix chain 'E' and resid 85 through 114 Processing helix chain 'E' and resid 120 through 132 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 36 Processing helix chain 'G' and resid 45 through 73 removed outlier: 4.409A pdb=" N VAL G 49 " --> pdb=" O ALA G 45 " (cutoff:3.500A) removed outlier: 3.796A pdb=" N LEU G 65 " --> pdb=" O GLU G 61 " (cutoff:3.500A) Processing helix chain 'G' and resid 79 through 90 Processing helix chain 'G' and resid 92 through 97 Processing helix chain 'G' and resid 112 through 116 removed outlier: 3.632A pdb=" N LEU G 116 " --> pdb=" O ALA G 113 " (cutoff:3.500A) Processing helix chain 'H' and resid 37 through 49 Processing helix chain 'H' and resid 55 through 84 Processing helix chain 'H' and resid 90 through 102 Processing helix chain 'H' and resid 103 through 124 Processing helix chain 'K' and resid 194 through 211 Processing helix chain 'K' and resid 254 through 264 removed outlier: 3.805A pdb=" N GLU K 259 " --> pdb=" O ALA K 255 " (cutoff:3.500A) removed outlier: 5.278A pdb=" N ALA K 260 " --> pdb=" O LYS K 256 " (cutoff:3.500A) Processing helix chain 'K' and resid 340 through 347 Processing helix chain 'K' and resid 348 through 352 removed outlier: 3.729A pdb=" N LYS K 351 " --> pdb=" O PRO K 348 " (cutoff:3.500A) Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 Processing helix chain 'F' and resid 82 through 94 removed outlier: 3.595A pdb=" N VAL F 86 " --> pdb=" O THR F 82 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 83 through 84 removed outlier: 6.784A 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 98 Processing sheet with id=AA4, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.876A pdb=" N ARG C 42 " --> pdb=" O ILE D 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 77 through 78 Processing sheet with id=AA6, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.807A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'E' and resid 83 through 84 removed outlier: 6.863A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA9, first strand: chain 'G' and resid 42 through 43 removed outlier: 7.199A pdb=" N ARG G 42 " --> pdb=" O ILE H 89 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AB2, first strand: chain 'K' and resid 218 through 223 removed outlier: 3.735A pdb=" N GLY K 227 " --> pdb=" O ILE K 223 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU K 330 " --> pdb=" O ALA K 232 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'K' and resid 240 through 244 removed outlier: 3.693A pdb=" N ASP K 240 " --> pdb=" O ALA K 322 " (cutoff:3.500A) removed outlier: 6.843A pdb=" N LEU K 320 " --> pdb=" O VAL K 242 " (cutoff:3.500A) removed outlier: 4.530A pdb=" N ILE K 321 " --> pdb=" O GLN K 306 " (cutoff:3.500A) removed outlier: 4.329A pdb=" N GLN K 306 " --> pdb=" O ILE K 321 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'K' and resid 248 through 250 removed outlier: 3.849A pdb=" N CYS K 283 " --> pdb=" O ILE K 250 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'K' and resid 276 through 277 Processing sheet with id=AB6, first strand: chain 'K' and resid 310 through 312 removed outlier: 3.966A pdb=" N VAL K 315 " --> pdb=" O ILE K 312 " (cutoff:3.500A) 458 hydrogen bonds defined for protein. 1347 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 356 hydrogen bonds 712 hydrogen bond angles 0 basepair planarities 138 basepair parallelities 259 stacking parallelities Total time for adding SS restraints: 5.99 Time building geometry restraints manager: 7.12 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: 2477 1.33 - 1.45: 4477 1.45 - 1.57: 6590 1.57 - 1.69: 576 1.69 - 1.81: 32 Bond restraints: 14152 Sorted by residual: bond pdb=" CA ALA F 76 " pdb=" C ALA F 76 " ideal model delta sigma weight residual 1.523 1.491 0.033 1.80e-02 3.09e+03 3.26e+00 bond pdb=" C LEU E 61 " pdb=" N ILE E 62 " ideal model delta sigma weight residual 1.334 1.315 0.019 1.29e-02 6.01e+03 2.08e+00 bond pdb=" CB ARG A 131 " pdb=" CG ARG A 131 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.62e+00 bond pdb=" CB ARG D 79 " pdb=" CG ARG D 79 " ideal model delta sigma weight residual 1.520 1.482 0.038 3.00e-02 1.11e+03 1.60e+00 bond pdb=" CB THR C 59 " pdb=" CG2 THR C 59 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.59e+00 ... (remaining 14147 not shown) Histogram of bond angle deviations from ideal: 80.88 - 91.50: 2 91.50 - 102.12: 331 102.12 - 112.74: 9026 112.74 - 123.36: 9604 123.36 - 133.97: 1376 Bond angle restraints: 20339 Sorted by residual: angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP1 DG J 21 " ideal model delta sigma weight residual 108.00 80.88 27.12 3.00e+00 1.11e-01 8.17e+01 angle pdb=" N VAL A 117 " pdb=" CA VAL A 117 " pdb=" C VAL A 117 " ideal model delta sigma weight residual 113.71 106.59 7.12 9.50e-01 1.11e+00 5.61e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" OP2 DG J 21 " ideal model delta sigma weight residual 108.00 87.24 20.76 3.00e+00 1.11e-01 4.79e+01 angle pdb=" O3' DG J 20 " pdb=" P DG J 21 " pdb=" O5' DG J 21 " ideal model delta sigma weight residual 104.00 97.98 6.02 1.50e+00 4.44e-01 1.61e+01 angle pdb=" C HIS F 75 " pdb=" N ALA F 76 " pdb=" CA ALA F 76 " ideal model delta sigma weight residual 122.31 114.58 7.73 2.00e+00 2.50e-01 1.49e+01 ... (remaining 20334 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 31.83: 5851 31.83 - 63.67: 1626 63.67 - 95.50: 49 95.50 - 127.34: 0 127.34 - 159.17: 2 Dihedral angle restraints: 7528 sinusoidal: 4841 harmonic: 2687 Sorted by residual: dihedral pdb=" CA ALA G 12 " pdb=" C ALA G 12 " pdb=" N LYS G 13 " pdb=" CA LYS G 13 " ideal model delta harmonic sigma weight residual 180.00 -157.79 -22.21 0 5.00e+00 4.00e-02 1.97e+01 dihedral pdb=" CA PRO H 103 " pdb=" C PRO H 103 " pdb=" N GLY H 104 " pdb=" CA GLY H 104 " ideal model delta harmonic sigma weight residual -180.00 -160.33 -19.67 0 5.00e+00 4.00e-02 1.55e+01 dihedral pdb=" C4' DT J -17 " pdb=" C3' DT J -17 " pdb=" O3' DT J -17 " pdb=" P DT J -16 " ideal model delta sinusoidal sigma weight residual 220.00 60.83 159.17 1 3.50e+01 8.16e-04 1.52e+01 ... (remaining 7525 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.410: 2296 0.410 - 0.819: 0 0.819 - 1.229: 0 1.229 - 1.639: 0 1.639 - 2.048: 1 Chirality restraints: 2297 Sorted by residual: chirality pdb=" P DG J 21 " pdb=" OP1 DG J 21 " pdb=" OP2 DG J 21 " pdb=" O5' DG J 21 " both_signs ideal model delta sigma weight residual True 2.35 0.30 2.05 2.00e-01 2.50e+01 1.05e+02 chirality pdb=" CA ILE F 29 " pdb=" N ILE F 29 " pdb=" C ILE F 29 " pdb=" CB ILE F 29 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.40e-01 chirality pdb=" CA VAL A 117 " pdb=" N VAL A 117 " pdb=" C VAL A 117 " pdb=" CB VAL A 117 " both_signs ideal model delta sigma weight residual False 2.44 2.58 -0.14 2.00e-01 2.50e+01 4.57e-01 ... (remaining 2294 not shown) Planarity restraints: 1578 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' DA I -35 " 0.028 2.00e-02 2.50e+03 1.22e-02 4.09e+00 pdb=" N9 DA I -35 " -0.026 2.00e-02 2.50e+03 pdb=" C8 DA I -35 " -0.004 2.00e-02 2.50e+03 pdb=" N7 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" C5 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DA I -35 " 0.002 2.00e-02 2.50e+03 pdb=" N6 DA I -35 " 0.010 2.00e-02 2.50e+03 pdb=" N1 DA I -35 " 0.001 2.00e-02 2.50e+03 pdb=" C2 DA I -35 " -0.002 2.00e-02 2.50e+03 pdb=" N3 DA I -35 " -0.006 2.00e-02 2.50e+03 pdb=" C4 DA I -35 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 28 " 0.027 2.00e-02 2.50e+03 1.12e-02 3.76e+00 pdb=" N9 DG I 28 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" N7 DG I 28 " -0.005 2.00e-02 2.50e+03 pdb=" C5 DG I 28 " 0.000 2.00e-02 2.50e+03 pdb=" C6 DG I 28 " 0.006 2.00e-02 2.50e+03 pdb=" O6 DG I 28 " 0.008 2.00e-02 2.50e+03 pdb=" N1 DG I 28 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 28 " -0.002 2.00e-02 2.50e+03 pdb=" N2 DG I 28 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 28 " -0.003 2.00e-02 2.50e+03 pdb=" C4 DG I 28 " -0.002 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C1' DG I 26 " 0.026 2.00e-02 2.50e+03 1.09e-02 3.57e+00 pdb=" N9 DG I 26 " -0.025 2.00e-02 2.50e+03 pdb=" C8 DG I 26 " -0.005 2.00e-02 2.50e+03 pdb=" N7 DG I 26 " -0.003 2.00e-02 2.50e+03 pdb=" C5 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C6 DG I 26 " 0.003 2.00e-02 2.50e+03 pdb=" O6 DG I 26 " 0.009 2.00e-02 2.50e+03 pdb=" N1 DG I 26 " 0.002 2.00e-02 2.50e+03 pdb=" C2 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" N2 DG I 26 " -0.004 2.00e-02 2.50e+03 pdb=" N3 DG I 26 " -0.001 2.00e-02 2.50e+03 pdb=" C4 DG I 26 " -0.002 2.00e-02 2.50e+03 ... (remaining 1575 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 453 2.67 - 3.23: 11697 3.23 - 3.79: 25151 3.79 - 4.34: 32751 4.34 - 4.90: 46742 Nonbonded interactions: 116794 Sorted by model distance: nonbonded pdb=" O ALA K 255 " pdb=" OH TYR K 274 " model vdw 2.118 2.440 nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.179 2.520 nonbonded pdb=" OG1 THR F 73 " pdb=" OD2 ASP F 85 " model vdw 2.194 2.440 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.247 2.440 nonbonded pdb=" OG1 THR B 73 " pdb=" OD2 ASP B 85 " model vdw 2.254 2.440 ... (remaining 116789 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' and resid 39 through 134) selection = (chain 'E' and resid 39 through 134) } ncs_group { reference = chain 'B' selection = (chain 'F' and resid 22 through 102) } ncs_group { reference = chain 'C' selection = (chain 'G' and resid 12 through 118) } ncs_group { reference = (chain 'D' and resid 33 through 124) selection = chain 'H' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 288 5.49 5 S 20 5.16 5 C 7463 2.51 5 N 2499 2.21 5 O 3057 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.280 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 2.630 Check model and map are aligned: 0.210 Convert atoms to be neutral: 0.120 Process input model: 43.980 Find NCS groups from input model: 0.530 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Set scattering table: 0.010 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:2.980 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 50.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8553 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 : 0.007 0.047 14152 Z= 0.440 Angle : 0.731 27.121 20339 Z= 0.423 Chirality : 0.058 2.048 2297 Planarity : 0.003 0.035 1578 Dihedral : 28.144 159.170 5800 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 8.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.61 % Favored : 95.39 % Rotamer Outliers : 0.00 % 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: -2.13 (0.24), residues: 911 helix: -0.32 (0.19), residues: 582 sheet: -3.86 (0.67), residues: 28 loop : -3.32 (0.28), residues: 301 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 1.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 202 average time/residue: 0.3865 time to fit residues: 100.2347 Evaluate side-chains 155 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.175 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 30.0000 chunk 87 optimal weight: 7.9990 chunk 48 optimal weight: 0.1980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 90 optimal weight: 10.0000 chunk 35 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 67 optimal weight: 7.9990 chunk 105 optimal weight: 20.0000 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 75 HIS B 93 GLN D 82 HIS D 84 ASN D 95 GLN E 68 GLN E 113 HIS ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN H 84 ASN K 347 HIS F 75 HIS F 93 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.1457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 14152 Z= 0.178 Angle : 0.620 27.011 20339 Z= 0.350 Chirality : 0.054 2.039 2297 Planarity : 0.004 0.030 1578 Dihedral : 31.068 160.672 3955 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 8.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.45 (0.27), residues: 911 helix: 1.68 (0.20), residues: 589 sheet: -3.22 (0.63), residues: 43 loop : -2.22 (0.33), residues: 279 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 182 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 176 time to evaluate : 1.289 Fit side-chains outliers start: 6 outliers final: 1 residues processed: 179 average time/residue: 0.3239 time to fit residues: 78.0770 Evaluate side-chains 156 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 155 time to evaluate : 1.122 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1105 time to fit residues: 1.5761 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 3.9990 chunk 32 optimal weight: 7.9990 chunk 87 optimal weight: 7.9990 chunk 71 optimal weight: 7.9990 chunk 29 optimal weight: 1.9990 chunk 105 optimal weight: 50.0000 chunk 114 optimal weight: 3.9990 chunk 93 optimal weight: 8.9990 chunk 104 optimal weight: 7.9990 chunk 35 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 overall best weight: 3.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN H 49 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1447 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.045 14152 Z= 0.356 Angle : 0.665 27.174 20339 Z= 0.369 Chirality : 0.056 2.025 2297 Planarity : 0.004 0.026 1578 Dihedral : 31.340 160.344 3955 Min Nonbonded Distance : 2.068 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.28), residues: 911 helix: 1.98 (0.21), residues: 587 sheet: -3.09 (0.65), residues: 43 loop : -1.90 (0.34), residues: 281 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 160 time to evaluate : 1.170 Fit side-chains outliers start: 13 outliers final: 10 residues processed: 165 average time/residue: 0.3093 time to fit residues: 69.5203 Evaluate side-chains 162 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 152 time to evaluate : 1.178 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1705 time to fit residues: 4.2439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 9.9990 chunk 79 optimal weight: 10.0000 chunk 54 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 0.7980 chunk 70 optimal weight: 7.9990 chunk 105 optimal weight: 8.9990 chunk 112 optimal weight: 0.8980 chunk 55 optimal weight: 3.9990 chunk 100 optimal weight: 30.0000 chunk 30 optimal weight: 0.9980 overall best weight: 1.1382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 47 GLN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 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 14152 Z= 0.184 Angle : 0.608 26.921 20339 Z= 0.340 Chirality : 0.054 2.035 2297 Planarity : 0.003 0.032 1578 Dihedral : 30.898 161.654 3955 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 9.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.28), residues: 911 helix: 2.46 (0.21), residues: 590 sheet: -2.93 (0.67), residues: 46 loop : -1.47 (0.35), residues: 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 170 time to evaluate : 1.214 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 172 average time/residue: 0.3065 time to fit residues: 71.8946 Evaluate side-chains 165 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 162 time to evaluate : 1.186 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1215 time to fit residues: 1.9665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 5.9990 chunk 63 optimal weight: 0.9990 chunk 1 optimal weight: 4.9990 chunk 83 optimal weight: 8.9990 chunk 46 optimal weight: 0.0980 chunk 95 optimal weight: 50.0000 chunk 77 optimal weight: 20.0000 chunk 0 optimal weight: 10.0000 chunk 57 optimal weight: 0.9990 chunk 100 optimal weight: 50.0000 chunk 28 optimal weight: 3.9990 overall best weight: 2.2188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8512 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 14152 Z= 0.248 Angle : 0.625 27.139 20339 Z= 0.346 Chirality : 0.054 2.022 2297 Planarity : 0.004 0.031 1578 Dihedral : 31.056 161.874 3955 Min Nonbonded Distance : 2.098 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.16 % 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: 1.71 (0.28), residues: 911 helix: 2.53 (0.21), residues: 587 sheet: -2.79 (0.68), residues: 46 loop : -1.31 (0.36), residues: 278 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 166 time to evaluate : 1.178 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 171 average time/residue: 0.3651 time to fit residues: 86.6845 Evaluate side-chains 158 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 153 time to evaluate : 1.077 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1053 time to fit residues: 2.3419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 2.9990 chunk 100 optimal weight: 30.0000 chunk 22 optimal weight: 8.9990 chunk 65 optimal weight: 10.0000 chunk 27 optimal weight: 0.9980 chunk 112 optimal weight: 0.8980 chunk 93 optimal weight: 3.9990 chunk 51 optimal weight: 5.9990 chunk 9 optimal weight: 3.9990 chunk 58 optimal weight: 2.9990 chunk 108 optimal weight: 7.9990 overall best weight: 2.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** H 47 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8515 moved from start: 0.2054 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 14152 Z= 0.257 Angle : 0.628 27.095 20339 Z= 0.346 Chirality : 0.055 2.025 2297 Planarity : 0.004 0.035 1578 Dihedral : 31.023 162.164 3955 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.62 % Favored : 96.38 % Rotamer Outliers : 1.03 % 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: 1.75 (0.28), residues: 911 helix: 2.51 (0.21), residues: 585 sheet: -2.73 (0.68), residues: 46 loop : -1.16 (0.35), residues: 280 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 161 time to evaluate : 1.164 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 163 average time/residue: 0.2966 time to fit residues: 66.6697 Evaluate side-chains 159 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 154 time to evaluate : 1.131 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1146 time to fit residues: 2.4327 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.6980 chunk 63 optimal weight: 3.9990 chunk 81 optimal weight: 8.9990 chunk 94 optimal weight: 0.0570 chunk 62 optimal weight: 0.8980 chunk 111 optimal weight: 0.7980 chunk 69 optimal weight: 7.9990 chunk 68 optimal weight: 7.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 66 optimal weight: 10.0000 overall best weight: 0.8900 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: E 108 ASN ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2198 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14152 Z= 0.166 Angle : 0.621 27.053 20339 Z= 0.341 Chirality : 0.054 2.031 2297 Planarity : 0.003 0.035 1578 Dihedral : 30.989 162.663 3955 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.28), residues: 911 helix: 2.54 (0.21), residues: 590 sheet: -2.67 (0.68), residues: 46 loop : -1.04 (0.36), residues: 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 164 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 158 time to evaluate : 1.150 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 161 average time/residue: 0.2870 time to fit residues: 63.9590 Evaluate side-chains 158 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 155 time to evaluate : 1.017 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1081 time to fit residues: 1.8169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 0.6980 chunk 71 optimal weight: 7.9990 chunk 76 optimal weight: 10.0000 chunk 55 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 87 optimal weight: 7.9990 chunk 101 optimal weight: 9.9990 chunk 107 optimal weight: 40.0000 chunk 97 optimal weight: 40.0000 chunk 104 optimal weight: 20.0000 overall best weight: 2.8984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8525 moved from start: 0.2120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.041 14152 Z= 0.296 Angle : 0.646 27.173 20339 Z= 0.353 Chirality : 0.055 2.021 2297 Planarity : 0.004 0.053 1578 Dihedral : 31.072 162.785 3955 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.06 % Favored : 95.94 % Rotamer Outliers : 0.65 % 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: 1.76 (0.28), residues: 911 helix: 2.48 (0.21), residues: 585 sheet: -2.60 (0.69), residues: 46 loop : -1.08 (0.35), residues: 280 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 149 time to evaluate : 1.147 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 152 average time/residue: 0.3023 time to fit residues: 63.2395 Evaluate side-chains 149 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 148 time to evaluate : 1.224 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.1265 time to fit residues: 1.6352 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 40.0000 chunk 62 optimal weight: 0.9990 chunk 45 optimal weight: 0.1980 chunk 81 optimal weight: 6.9990 chunk 31 optimal weight: 0.9990 chunk 94 optimal weight: 0.0030 chunk 98 optimal weight: 0.4980 chunk 103 optimal weight: 50.0000 chunk 68 optimal weight: 8.9990 chunk 110 optimal weight: 0.4980 chunk 67 optimal weight: 8.9990 overall best weight: 0.4392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 14152 Z= 0.154 Angle : 0.627 27.019 20339 Z= 0.344 Chirality : 0.055 2.034 2297 Planarity : 0.004 0.041 1578 Dihedral : 31.058 163.360 3955 Min Nonbonded Distance : 2.130 Molprobity Statistics. All-atom Clashscore : 9.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 0.52 % 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: 1.86 (0.28), residues: 911 helix: 2.54 (0.21), residues: 587 sheet: -2.43 (0.72), residues: 46 loop : -1.04 (0.36), residues: 278 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 156 time to evaluate : 1.181 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 158 average time/residue: 0.2950 time to fit residues: 65.0605 Evaluate side-chains 156 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 154 time to evaluate : 1.129 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.1080 time to fit residues: 1.7020 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.9980 chunk 76 optimal weight: 10.0000 chunk 115 optimal weight: 1.9990 chunk 106 optimal weight: 6.9990 chunk 92 optimal weight: 0.8980 chunk 9 optimal weight: 0.4980 chunk 71 optimal weight: 7.9990 chunk 56 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 98 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8489 moved from start: 0.2365 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14152 Z= 0.188 Angle : 0.623 26.968 20339 Z= 0.340 Chirality : 0.054 2.030 2297 Planarity : 0.004 0.037 1578 Dihedral : 30.863 163.630 3955 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 9.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.26 % 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: 2.00 (0.28), residues: 911 helix: 2.63 (0.21), residues: 587 sheet: -2.32 (0.74), residues: 46 loop : -0.94 (0.36), residues: 278 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1822 Ramachandran restraints generated. 911 Oldfield, 0 Emsley, 911 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 159 time to evaluate : 1.107 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 159 average time/residue: 0.2954 time to fit residues: 65.2063 Evaluate side-chains 148 residues out of total 775 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 147 time to evaluate : 1.228 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.4102 time to fit residues: 1.9026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 7.9990 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 0.9990 chunk 92 optimal weight: 10.0000 chunk 38 optimal weight: 0.9990 chunk 94 optimal weight: 20.0000 chunk 11 optimal weight: 0.0980 chunk 16 optimal weight: 1.9990 chunk 80 optimal weight: 10.0000 chunk 5 optimal weight: 0.7980 chunk 66 optimal weight: 10.0000 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** G 31 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** G 104 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4021 r_free = 0.4021 target = 0.152393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3208 r_free = 0.3208 target = 0.093838 restraints weight = 20626.537| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 1.88 r_work: 0.3136 rms_B_bonded: 1.71 restraints_weight: 0.5000 r_work: 0.3118 rms_B_bonded: 1.72 restraints_weight: 0.2500 r_work: 0.3099 rms_B_bonded: 1.81 restraints_weight: 0.1250 r_work: 0.3079 rms_B_bonded: 1.96 restraints_weight: 0.0625 r_work: 0.3057 rms_B_bonded: 2.17 restraints_weight: 0.0312 r_work: 0.3033 rms_B_bonded: 2.43 restraints_weight: 0.0156 r_work: 0.3007 rms_B_bonded: 2.75 restraints_weight: 0.0078 r_work: 0.2977 rms_B_bonded: 3.14 restraints_weight: 0.0039 r_work: 0.2944 rms_B_bonded: 3.60 restraints_weight: 0.0020 r_work: 0.2907 rms_B_bonded: 4.16 restraints_weight: 0.0010 r_work: 0.2865 rms_B_bonded: 4.82 restraints_weight: 0.0005 r_work (final): 0.2865 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8677 moved from start: 0.2457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 14152 Z= 0.160 Angle : 0.624 27.124 20339 Z= 0.340 Chirality : 0.055 2.028 2297 Planarity : 0.005 0.112 1578 Dihedral : 30.851 163.889 3955 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 9.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.29 % Favored : 96.71 % Rotamer Outliers : 0.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.08 (0.28), residues: 911 helix: 2.63 (0.21), residues: 592 sheet: -2.27 (0.75), residues: 46 loop : -0.85 (0.36), residues: 273 =============================================================================== Job complete usr+sys time: 2198.17 seconds wall clock time: 40 minutes 54.86 seconds (2454.86 seconds total)