Starting phenix.real_space_refine (version: dev) on Mon Feb 20 18:14:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtm_27705/02_2023/8dtm_27705_neut.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtm_27705/02_2023/8dtm_27705.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtm_27705/02_2023/8dtm_27705.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtm_27705/02_2023/8dtm_27705.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtm_27705/02_2023/8dtm_27705_neut.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8dtm_27705/02_2023/8dtm_27705_neut.pdb" } resolution = 3.5 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= 0.003 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 6304 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Process input model Symmetric amino acids flipped Residue "A ASP 59": "OD1" <-> "OD2" Residue "A TYR 107": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 250": "OD1" <-> "OD2" Residue "A PHE 264": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 353": "OE1" <-> "OE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 471": "OE1" <-> "OE2" Residue "B ASP 483": "OD1" <-> "OD2" Residue "B TYR 633": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 6498 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 3560 Number of conformers: 1 Conformer: "" Number of residues, atoms: 444, 3560 Classifications: {'peptide': 444} Link IDs: {'PCIS': 1, 'PTRANS': 18, 'TRANS': 424} Chain breaks: 4 Chain: "B" Number of atoms: 2793 Number of conformers: 1 Conformer: "" Number of residues, atoms: 340, 2793 Classifications: {'peptide': 340} Link IDs: {'PTRANS': 23, 'TRANS': 316} Chain breaks: 4 Chain: "C" Number of atoms: 145 Number of conformers: 1 Conformer: "" Number of residues, atoms: 18, 145 Classifications: {'peptide': 18} Link IDs: {'TRANS': 17} Time building chain proxies: 3.98, per 1000 atoms: 0.61 Number of scatterers: 6498 At special positions: 0 Unit cell: (89.64, 89.64, 145.8, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 51 16.00 O 1205 8.00 N 1113 7.00 C 4129 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=18, symmetry=0 Simple disulfide: pdb=" SG CYS A 8 " - pdb=" SG CYS A 26 " distance=2.03 Simple disulfide: pdb=" SG CYS A 126 " - pdb=" SG CYS A 155 " distance=2.03 Simple disulfide: pdb=" SG CYS A 159 " - pdb=" SG CYS A 182 " distance=2.03 Simple disulfide: pdb=" SG CYS A 169 " - pdb=" SG CYS A 188 " distance=2.03 Simple disulfide: pdb=" SG CYS A 192 " - pdb=" SG CYS A 201 " distance=2.03 Simple disulfide: pdb=" SG CYS A 196 " - pdb=" SG CYS A 207 " distance=2.03 Simple disulfide: pdb=" SG CYS A 208 " - pdb=" SG CYS A 216 " distance=2.03 Simple disulfide: pdb=" SG CYS A 212 " - pdb=" SG CYS A 225 " distance=2.03 Simple disulfide: pdb=" SG CYS A 228 " - pdb=" SG CYS A 237 " distance=2.03 Simple disulfide: pdb=" SG CYS A 241 " - pdb=" SG CYS A 253 " distance=2.03 Simple disulfide: pdb=" SG CYS A 259 " - pdb=" SG CYS A 284 " distance=2.03 Simple disulfide: pdb=" SG CYS A 266 " - pdb=" SG CYS A 274 " distance=2.03 Simple disulfide: pdb=" SG CYS A 288 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 304 " - pdb=" SG CYS A 308 " distance=2.03 Simple disulfide: pdb=" SG CYS A 312 " - pdb=" SG CYS A 333 " distance=2.03 Simple disulfide: pdb=" SG CYS B 649 " - pdb=" SG CYS B 862 " distance=2.03 Simple disulfide: pdb=" SG CYS B 788 " - pdb=" SG CYS B 797 " distance=2.04 Simple disulfide: pdb=" SG CYS C 11 " - pdb=" SG CYS C 18 " distance=2.03 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: 2.23 Conformation dependent library (CDL) restraints added in 938.8 milliseconds 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1516 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 15 sheets defined 12.6% alpha, 23.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 18 through 24 removed outlier: 3.564A pdb=" N LEU A 23 " --> pdb=" O LEU A 20 " (cutoff:3.500A) Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.716A pdb=" N LYS A 224 " --> pdb=" O ASP A 221 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N CYS A 225 " --> pdb=" O PRO A 222 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 221 through 225' Processing helix chain 'A' and resid 255 through 265 removed outlier: 3.578A pdb=" N CYS A 259 " --> pdb=" O ASN A 255 " (cutoff:3.500A) Processing helix chain 'A' and resid 314 through 318 removed outlier: 3.619A pdb=" N GLY A 317 " --> pdb=" O ILE A 314 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 329 removed outlier: 4.344A pdb=" N GLU A 329 " --> pdb=" O THR A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 359 Processing helix chain 'A' and resid 435 through 447 removed outlier: 3.550A pdb=" N ILE A 439 " --> pdb=" O CYS A 435 " (cutoff:3.500A) Processing helix chain 'B' and resid 496 through 500 removed outlier: 3.768A pdb=" N LEU B 500 " --> pdb=" O PHE B 497 " (cutoff:3.500A) Processing helix chain 'B' and resid 642 through 646 removed outlier: 4.063A pdb=" N LEU B 646 " --> pdb=" O LEU B 643 " (cutoff:3.500A) Processing helix chain 'B' and resid 697 through 711 removed outlier: 4.006A pdb=" N LEU B 711 " --> pdb=" O PHE B 707 " (cutoff:3.500A) Processing helix chain 'B' and resid 865 through 872 Processing helix chain 'C' and resid 2 through 13 Processing sheet with id=AA1, first strand: chain 'A' and resid 7 through 14 removed outlier: 7.155A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 7 through 14 removed outlier: 7.155A pdb=" N CYS A 8 " --> pdb=" O GLU A 30 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N HIS A 32 " --> pdb=" O CYS A 8 " (cutoff:3.500A) removed outlier: 4.557A pdb=" N GLY A 10 " --> pdb=" O HIS A 32 " (cutoff:3.500A) removed outlier: 7.481A pdb=" N GLN A 34 " --> pdb=" O GLY A 10 " (cutoff:3.500A) removed outlier: 4.417A pdb=" N ASP A 12 " --> pdb=" O GLN A 34 " (cutoff:3.500A) removed outlier: 7.280A pdb=" N LEU A 36 " --> pdb=" O ASP A 12 " (cutoff:3.500A) removed outlier: 4.061A pdb=" N ARG A 14 " --> pdb=" O LEU A 36 " (cutoff:3.500A) removed outlier: 6.688A pdb=" N MET A 38 " --> pdb=" O ARG A 14 " (cutoff:3.500A) removed outlier: 8.775A pdb=" N LEU A 62 " --> pdb=" O GLY A 31 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N LEU A 33 " --> pdb=" O LEU A 62 " (cutoff:3.500A) removed outlier: 8.163A pdb=" N PHE A 64 " --> pdb=" O LEU A 33 " (cutoff:3.500A) removed outlier: 6.537A pdb=" N ILE A 35 " --> pdb=" O PHE A 64 " (cutoff:3.500A) removed outlier: 5.723A pdb=" N VAL A 66 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 7.596A pdb=" N LEU A 37 " --> pdb=" O VAL A 66 " (cutoff:3.500A) removed outlier: 6.335A pdb=" N LEU A 61 " --> pdb=" O VAL A 94 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N PHE A 96 " --> pdb=" O LEU A 61 " (cutoff:3.500A) removed outlier: 6.377A pdb=" N LEU A 63 " --> pdb=" O PHE A 96 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N VAL A 117 " --> pdb=" O TYR A 144 " (cutoff:3.500A) removed outlier: 7.833A pdb=" N VAL A 146 " --> pdb=" O VAL A 117 " (cutoff:3.500A) removed outlier: 6.632A pdb=" N ILE A 119 " --> pdb=" O VAL A 146 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 231 through 233 Processing sheet with id=AA4, first strand: chain 'A' and resid 246 through 248 Processing sheet with id=AA5, first strand: chain 'A' and resid 278 through 279 Processing sheet with id=AA6, first strand: chain 'A' and resid 292 through 294 Processing sheet with id=AA7, first strand: chain 'A' and resid 311 through 312 Processing sheet with id=AA8, first strand: chain 'A' and resid 320 through 321 removed outlier: 7.648A pdb=" N PHE A 427 " --> pdb=" O SER A 399 " (cutoff:3.500A) removed outlier: 4.570A pdb=" N TYR A 401 " --> pdb=" O PHE A 427 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N HIS A 429 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.205A pdb=" N LEU A 403 " --> pdb=" O HIS A 429 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 471 through 473 removed outlier: 3.668A pdb=" N LYS B 584 " --> pdb=" O GLU B 471 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'B' and resid 475 through 480 removed outlier: 3.889A pdb=" N PHE B 477 " --> pdb=" O ARG B 488 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'B' and resid 532 through 534 removed outlier: 3.765A pdb=" N GLY B 502 " --> pdb=" O LEU B 571 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 601 through 606 removed outlier: 5.533A pdb=" N ASP B 602 " --> pdb=" O LYS B 618 " (cutoff:3.500A) removed outlier: 3.945A pdb=" N LYS B 618 " --> pdb=" O ASP B 602 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'B' and resid 761 through 765 removed outlier: 4.318A pdb=" N GLY B 780 " --> pdb=" O GLN B 637 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'B' and resid 821 through 824 Processing sheet with id=AB6, first strand: chain 'B' and resid 859 through 864 removed outlier: 3.640A pdb=" N LEU B 846 " --> pdb=" O THR B 891 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N ARG B 852 " --> pdb=" O SER B 885 " (cutoff:3.500A) removed outlier: 3.958A pdb=" N SER B 885 " --> pdb=" O ARG B 852 " (cutoff:3.500A) 150 hydrogen bonds defined for protein. 384 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.02 Time building geometry restraints manager: 2.45 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.35: 2125 1.35 - 1.47: 1605 1.47 - 1.59: 2861 1.59 - 1.71: 0 1.71 - 1.83: 63 Bond restraints: 6654 Sorted by residual: bond pdb=" C ARG B 759 " pdb=" N PRO B 760 " ideal model delta sigma weight residual 1.333 1.323 0.010 1.01e-02 9.80e+03 1.06e+00 bond pdb=" CB ASP A 404 " pdb=" CG ASP A 404 " ideal model delta sigma weight residual 1.516 1.539 -0.023 2.50e-02 1.60e+03 8.75e-01 bond pdb=" CG LEU A 2 " pdb=" CD1 LEU A 2 " ideal model delta sigma weight residual 1.521 1.495 0.026 3.30e-02 9.18e+02 6.42e-01 bond pdb=" CA ASP B 483 " pdb=" CB ASP B 483 " ideal model delta sigma weight residual 1.533 1.550 -0.017 2.15e-02 2.16e+03 6.33e-01 bond pdb=" C SER B 792 " pdb=" N PRO B 793 " ideal model delta sigma weight residual 1.334 1.351 -0.017 2.34e-02 1.83e+03 5.34e-01 ... (remaining 6649 not shown) Histogram of bond angle deviations from ideal: 99.55 - 106.44: 207 106.44 - 113.32: 3526 113.32 - 120.21: 2336 120.21 - 127.10: 2853 127.10 - 133.98: 87 Bond angle restraints: 9009 Sorted by residual: angle pdb=" C ASP B 647 " pdb=" N TYR B 648 " pdb=" CA TYR B 648 " ideal model delta sigma weight residual 122.09 116.72 5.37 1.79e+00 3.12e-01 9.00e+00 angle pdb=" C ILE A 35 " pdb=" N LEU A 36 " pdb=" CA LEU A 36 " ideal model delta sigma weight residual 121.62 116.98 4.64 1.83e+00 2.99e-01 6.43e+00 angle pdb=" C TYR B 633 " pdb=" N TRP B 634 " pdb=" CA TRP B 634 " ideal model delta sigma weight residual 122.37 118.19 4.18 1.72e+00 3.38e-01 5.91e+00 angle pdb=" CA GLU C 12 " pdb=" CB GLU C 12 " pdb=" CG GLU C 12 " ideal model delta sigma weight residual 114.10 118.61 -4.51 2.00e+00 2.50e-01 5.08e+00 angle pdb=" CA CYS B 797 " pdb=" CB CYS B 797 " pdb=" SG CYS B 797 " ideal model delta sigma weight residual 114.40 119.49 -5.09 2.30e+00 1.89e-01 4.89e+00 ... (remaining 9004 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.75: 3496 17.75 - 35.50: 415 35.50 - 53.26: 95 53.26 - 71.01: 24 71.01 - 88.76: 11 Dihedral angle restraints: 4041 sinusoidal: 1698 harmonic: 2343 Sorted by residual: dihedral pdb=" CB CYS A 196 " pdb=" SG CYS A 196 " pdb=" SG CYS A 207 " pdb=" CB CYS A 207 " ideal model delta sinusoidal sigma weight residual -86.00 -143.51 57.51 1 1.00e+01 1.00e-02 4.44e+01 dihedral pdb=" CB CYS A 169 " pdb=" SG CYS A 169 " pdb=" SG CYS A 188 " pdb=" CB CYS A 188 " ideal model delta sinusoidal sigma weight residual -86.00 -28.88 -57.12 1 1.00e+01 1.00e-02 4.39e+01 dihedral pdb=" CB CYS B 649 " pdb=" SG CYS B 649 " pdb=" SG CYS B 862 " pdb=" CB CYS B 862 " ideal model delta sinusoidal sigma weight residual 93.00 38.78 54.22 1 1.00e+01 1.00e-02 3.99e+01 ... (remaining 4038 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 540 0.027 - 0.054: 244 0.054 - 0.081: 98 0.081 - 0.109: 53 0.109 - 0.136: 38 Chirality restraints: 973 Sorted by residual: chirality pdb=" CA ILE A 35 " pdb=" N ILE A 35 " pdb=" C ILE A 35 " pdb=" CB ILE A 35 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA ASP B 483 " pdb=" N ASP B 483 " pdb=" C ASP B 483 " pdb=" CB ASP B 483 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.53e-01 chirality pdb=" CA ILE A 112 " pdb=" N ILE A 112 " pdb=" C ILE A 112 " pdb=" CB ILE A 112 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 970 not shown) Planarity restraints: 1162 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP B 634 " 0.015 2.00e-02 2.50e+03 1.90e-02 9.07e+00 pdb=" CG TRP B 634 " -0.049 2.00e-02 2.50e+03 pdb=" CD1 TRP B 634 " 0.029 2.00e-02 2.50e+03 pdb=" CD2 TRP B 634 " -0.004 2.00e-02 2.50e+03 pdb=" NE1 TRP B 634 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TRP B 634 " -0.001 2.00e-02 2.50e+03 pdb=" CE3 TRP B 634 " 0.004 2.00e-02 2.50e+03 pdb=" CZ2 TRP B 634 " -0.002 2.00e-02 2.50e+03 pdb=" CZ3 TRP B 634 " 0.011 2.00e-02 2.50e+03 pdb=" CH2 TRP B 634 " -0.003 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB ASP B 483 " -0.008 2.00e-02 2.50e+03 1.54e-02 2.37e+00 pdb=" CG ASP B 483 " 0.027 2.00e-02 2.50e+03 pdb=" OD1 ASP B 483 " -0.010 2.00e-02 2.50e+03 pdb=" OD2 ASP B 483 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 404 " 0.006 2.00e-02 2.50e+03 1.32e-02 1.74e+00 pdb=" C ASP A 404 " -0.023 2.00e-02 2.50e+03 pdb=" O ASP A 404 " 0.009 2.00e-02 2.50e+03 pdb=" N ASN A 405 " 0.008 2.00e-02 2.50e+03 ... (remaining 1159 not shown) Histogram of nonbonded interaction distances: 2.13 - 2.69: 130 2.69 - 3.24: 5885 3.24 - 3.79: 9349 3.79 - 4.35: 12659 4.35 - 4.90: 21518 Nonbonded interactions: 49541 Sorted by model distance: nonbonded pdb=" OG1 THR A 41 " pdb=" O TYR A 67 " model vdw 2.132 2.440 nonbonded pdb=" O SER B 880 " pdb=" OH TYR B 884 " model vdw 2.142 2.440 nonbonded pdb=" O VAL B 888 " pdb=" OG1 THR B 900 " model vdw 2.204 2.440 nonbonded pdb=" NH2 ARG A 372 " pdb=" OD1 ASP B 533 " model vdw 2.235 2.520 nonbonded pdb=" OG SER A 339 " pdb=" O PHE A 367 " model vdw 2.262 2.440 ... (remaining 49536 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 4 Type Number sf(0) Gaussians S 51 5.16 5 C 4129 2.51 5 N 1113 2.21 5 O 1205 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.300 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.080 Construct map_model_manager: 0.000 Extract box with map and model: 6.250 Check model and map are aligned: 0.090 Process input model: 20.180 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Set scattering table: 0.060 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:2.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.640 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 6654 Z= 0.210 Angle : 0.564 7.103 9009 Z= 0.295 Chirality : 0.045 0.136 973 Planarity : 0.004 0.030 1162 Dihedral : 16.330 88.760 2471 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.77 % Favored : 94.23 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.79 (0.31), residues: 780 helix: 0.63 (0.62), residues: 73 sheet: 0.22 (0.38), residues: 196 loop : -1.04 (0.29), residues: 511 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 60 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 57 time to evaluate : 0.859 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 59 average time/residue: 0.1876 time to fit residues: 15.4849 Evaluate side-chains 57 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.822 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0650 time to fit residues: 1.5865 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 66 optimal weight: 0.0040 chunk 59 optimal weight: 4.9990 chunk 33 optimal weight: 0.7980 chunk 20 optimal weight: 0.9990 chunk 40 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 chunk 61 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 37 optimal weight: 0.0570 chunk 46 optimal weight: 0.7980 chunk 71 optimal weight: 0.5980 overall best weight: 0.4510 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8009 moved from start: 0.0382 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6654 Z= 0.158 Angle : 0.504 6.881 9009 Z= 0.261 Chirality : 0.044 0.145 973 Planarity : 0.003 0.030 1162 Dihedral : 4.381 22.880 874 Min Nonbonded Distance : 2.131 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.69 (0.31), residues: 780 helix: 0.70 (0.59), residues: 79 sheet: 0.31 (0.38), residues: 195 loop : -1.00 (0.29), residues: 506 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 57 time to evaluate : 0.722 Fit side-chains revert: symmetry clash outliers start: 14 outliers final: 9 residues processed: 67 average time/residue: 0.2069 time to fit residues: 18.6313 Evaluate side-chains 63 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 54 time to evaluate : 0.826 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0746 time to fit residues: 2.2063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 71 optimal weight: 0.8980 chunk 77 optimal weight: 0.9990 chunk 64 optimal weight: 0.0010 chunk 24 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 54 optimal weight: 0.9980 overall best weight: 0.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 337 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8025 moved from start: 0.0516 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 6654 Z= 0.216 Angle : 0.515 6.855 9009 Z= 0.267 Chirality : 0.044 0.148 973 Planarity : 0.003 0.029 1162 Dihedral : 4.402 23.251 874 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 1.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.72 (0.31), residues: 780 helix: 0.80 (0.60), residues: 79 sheet: 0.28 (0.38), residues: 195 loop : -1.04 (0.29), residues: 506 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 58 time to evaluate : 0.798 Fit side-chains revert: symmetry clash outliers start: 13 outliers final: 8 residues processed: 69 average time/residue: 0.1950 time to fit residues: 18.4004 Evaluate side-chains 62 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 54 time to evaluate : 0.798 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0656 time to fit residues: 2.0617 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 37 optimal weight: 0.0670 chunk 7 optimal weight: 0.0000 chunk 34 optimal weight: 0.9980 chunk 48 optimal weight: 0.9990 chunk 72 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 20 optimal weight: 2.9990 chunk 63 optimal weight: 2.9990 chunk 43 optimal weight: 7.9990 chunk 1 optimal weight: 0.7980 overall best weight: 0.5724 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.0653 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6654 Z= 0.178 Angle : 0.500 6.803 9009 Z= 0.259 Chirality : 0.044 0.143 973 Planarity : 0.003 0.029 1162 Dihedral : 4.397 22.047 874 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.64 % Favored : 94.36 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.69 (0.31), residues: 780 helix: 0.75 (0.59), residues: 79 sheet: 0.32 (0.38), residues: 195 loop : -1.01 (0.29), residues: 506 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 60 time to evaluate : 0.720 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 65 average time/residue: 0.1928 time to fit residues: 17.1062 Evaluate side-chains 57 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 54 time to evaluate : 0.723 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0594 time to fit residues: 1.3204 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 56 optimal weight: 0.5980 chunk 31 optimal weight: 0.7980 chunk 65 optimal weight: 0.7980 chunk 52 optimal weight: 1.9990 chunk 0 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 chunk 68 optimal weight: 1.9990 chunk 19 optimal weight: 4.9990 chunk 25 optimal weight: 2.9990 chunk 15 optimal weight: 0.0010 chunk 44 optimal weight: 1.9990 overall best weight: 0.8388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 32 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.0724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.027 6654 Z= 0.238 Angle : 0.520 6.806 9009 Z= 0.269 Chirality : 0.045 0.148 973 Planarity : 0.003 0.029 1162 Dihedral : 4.474 23.103 874 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.76 (0.31), residues: 780 helix: 0.78 (0.59), residues: 79 sheet: 0.18 (0.37), residues: 197 loop : -1.04 (0.29), residues: 504 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 57 time to evaluate : 0.868 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 65 average time/residue: 0.1846 time to fit residues: 16.6414 Evaluate side-chains 61 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 54 time to evaluate : 0.716 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0616 time to fit residues: 1.8806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 18 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 0.0060 chunk 6 optimal weight: 0.9980 chunk 25 optimal weight: 1.9990 chunk 40 optimal weight: 3.9990 chunk 73 optimal weight: 0.9990 chunk 8 optimal weight: 0.8980 chunk 43 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8030 moved from start: 0.0803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 6654 Z= 0.222 Angle : 0.516 6.800 9009 Z= 0.268 Chirality : 0.044 0.143 973 Planarity : 0.003 0.028 1162 Dihedral : 4.472 23.958 874 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 7.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 1.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.77 (0.31), residues: 780 helix: 0.77 (0.60), residues: 79 sheet: 0.24 (0.38), residues: 192 loop : -1.06 (0.28), residues: 509 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 56 time to evaluate : 0.817 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 3 residues processed: 61 average time/residue: 0.2000 time to fit residues: 16.9524 Evaluate side-chains 61 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 58 time to evaluate : 1.069 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1102 time to fit residues: 2.1504 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 43 optimal weight: 8.9990 chunk 64 optimal weight: 3.9990 chunk 42 optimal weight: 4.9990 chunk 76 optimal weight: 0.6980 chunk 47 optimal weight: 2.9990 chunk 46 optimal weight: 0.6980 chunk 35 optimal weight: 1.9990 chunk 30 optimal weight: 0.1980 chunk 45 optimal weight: 0.5980 chunk 22 optimal weight: 0.7980 chunk 14 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.0898 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6654 Z= 0.158 Angle : 0.496 6.700 9009 Z= 0.257 Chirality : 0.044 0.148 973 Planarity : 0.003 0.028 1162 Dihedral : 4.350 22.009 874 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.15 % Favored : 93.85 % Rotamer Outliers : 0.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.68 (0.31), residues: 780 helix: 0.75 (0.60), residues: 79 sheet: 0.35 (0.38), residues: 190 loop : -0.99 (0.29), residues: 511 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 62 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 58 time to evaluate : 0.697 Fit side-chains revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 60 average time/residue: 0.2029 time to fit residues: 16.5391 Evaluate side-chains 56 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.776 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0649 time to fit residues: 1.1978 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 14 optimal weight: 0.9990 chunk 48 optimal weight: 0.8980 chunk 51 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 7 optimal weight: 0.4980 chunk 59 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 66 optimal weight: 0.0270 chunk 70 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 overall best weight: 0.6840 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.0946 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 6654 Z= 0.202 Angle : 0.508 6.738 9009 Z= 0.263 Chirality : 0.044 0.148 973 Planarity : 0.003 0.028 1162 Dihedral : 4.407 23.039 874 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 6.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.28 % Favored : 93.72 % Rotamer Outliers : 0.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.72 (0.31), residues: 780 helix: 0.75 (0.60), residues: 79 sheet: 0.31 (0.38), residues: 190 loop : -1.03 (0.28), residues: 511 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 55 time to evaluate : 0.890 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 0 residues processed: 57 average time/residue: 0.2194 time to fit residues: 17.2238 Evaluate side-chains 52 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.715 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.0926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 30 optimal weight: 0.5980 chunk 55 optimal weight: 0.3980 chunk 21 optimal weight: 0.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 75 optimal weight: 0.9980 chunk 45 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 52 optimal weight: 0.0870 overall best weight: 0.4558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8002 moved from start: 0.1026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6654 Z= 0.159 Angle : 0.495 6.653 9009 Z= 0.257 Chirality : 0.044 0.145 973 Planarity : 0.003 0.028 1162 Dihedral : 4.309 21.335 874 Min Nonbonded Distance : 2.144 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.65 (0.31), residues: 780 helix: 0.81 (0.60), residues: 79 sheet: 0.36 (0.38), residues: 190 loop : -0.98 (0.28), residues: 511 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.755 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 57 average time/residue: 0.1848 time to fit residues: 14.9682 Evaluate side-chains 58 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 57 time to evaluate : 0.805 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0627 time to fit residues: 1.2210 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 78 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 48 optimal weight: 1.9990 chunk 38 optimal weight: 0.9980 chunk 49 optimal weight: 0.0000 chunk 66 optimal weight: 0.4980 chunk 19 optimal weight: 0.7980 chunk 57 optimal weight: 0.2980 chunk 9 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 15 ASN A 337 ASN B 786 GLN ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8000 moved from start: 0.1113 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.029 6654 Z= 0.160 Angle : 0.492 6.663 9009 Z= 0.255 Chirality : 0.044 0.148 973 Planarity : 0.003 0.028 1162 Dihedral : 4.279 21.054 874 Min Nonbonded Distance : 2.146 Molprobity Statistics. All-atom Clashscore : 6.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.65 (0.31), residues: 780 helix: 0.86 (0.60), residues: 79 sheet: 0.36 (0.38), residues: 190 loop : -1.00 (0.28), residues: 511 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1560 Ramachandran restraints generated. 780 Oldfield, 0 Emsley, 780 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 60 time to evaluate : 0.779 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 61 average time/residue: 0.1887 time to fit residues: 16.0694 Evaluate side-chains 59 residues out of total 730 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.837 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0645 time to fit residues: 1.2730 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 79 random chunks: chunk 17 optimal weight: 0.6980 chunk 62 optimal weight: 2.9990 chunk 26 optimal weight: 0.0770 chunk 64 optimal weight: 2.9990 chunk 7 optimal weight: 0.0270 chunk 11 optimal weight: 1.9990 chunk 55 optimal weight: 0.7980 chunk 3 optimal weight: 0.9980 chunk 45 optimal weight: 0.3980 chunk 71 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 0.3996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 281 ASN A 337 ASN B 786 GLN B 822 HIS ** B 831 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3682 r_free = 0.3682 target = 0.137334 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.107045 restraints weight = 9155.604| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3349 r_free = 0.3349 target = 0.110464 restraints weight = 5779.369| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.112743 restraints weight = 4311.786| |-----------------------------------------------------------------------------| r_work (final): 0.3382 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8118 moved from start: 0.1173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 6654 Z= 0.152 Angle : 0.500 6.719 9009 Z= 0.262 Chirality : 0.044 0.143 973 Planarity : 0.003 0.028 1162 Dihedral : 4.257 20.507 874 Min Nonbonded Distance : 2.129 Molprobity Statistics. All-atom Clashscore : 7.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.51 % Favored : 94.49 % Rotamer Outliers : 0.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.38 % 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: -0.64 (0.31), residues: 780 helix: 0.87 (0.60), residues: 79 sheet: 0.37 (0.38), residues: 190 loop : -0.99 (0.28), residues: 511 =============================================================================== Job complete usr+sys time: 1489.79 seconds wall clock time: 27 minutes 29.78 seconds (1649.78 seconds total)