Starting phenix.real_space_refine (version: dev) on Thu May 12 19:08:53 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/05_2022/6npy_0476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/05_2022/6npy_0476.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/05_2022/6npy_0476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/05_2022/6npy_0476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/05_2022/6npy_0476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/05_2022/6npy_0476_updated.pdb" } resolution = 3.8 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= 0.002 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 "A PHE 207": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 210": "OD1" <-> "OD2" Residue "A ASP 211": "OD1" <-> "OD2" Residue "A PHE 255": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 256": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 302": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 303": "OD1" <-> "OD2" Residue "A PHE 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 441": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 531": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 548": "NH1" <-> "NH2" Residue "A PHE 566": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 573": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 577": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 634": "OE1" <-> "OE2" Residue "A TYR 647": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 648": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 727": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 844": "OD1" <-> "OD2" Residue "A TYR 859": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 924": "OD1" <-> "OD2" Residue "A ASP 981": "OD1" <-> "OD2" Residue "A PHE 987": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 1008": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 1010": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1022": "OE1" <-> "OE2" Residue "A PHE 1030": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 126": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 213": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 215": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4597/modules/chem_data/mon_lib" Total number of atoms: 7586 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 6192 Number of conformers: 1 Conformer: "" Number of residues, atoms: 798, 6192 Classifications: {'peptide': 798} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 25, 'TRANS': 772} Chain breaks: 7 Unresolved non-hydrogen bonds: 153 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 131 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'GLN:plan1': 4, 'HIS:plan': 1, 'TYR:plan': 1, 'TRP:plan': 1, 'ASP:plan': 3, 'PHE:plan': 2, 'GLU:plan': 3, 'ARG:plan': 7} Unresolved non-hydrogen planarities: 105 Chain: "B" Number of atoms: 1367 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 Conformer: "B" Number of residues, atoms: 167, 1359 Classifications: {'peptide': 167} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 11, 'TRANS': 155} Chain breaks: 2 Unresolved non-hydrogen bonds: 9 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 3 bond proxies already assigned to first conformer: 1385 Chain: "A" Number of atoms: 27 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 27 Unusual residues: {'ADP': 1} Classifications: {'undetermined': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N AASP B 284 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP B 284 " occ=0.50 Time building chain proxies: 5.37, per 1000 atoms: 0.71 Number of scatterers: 7586 At special positions: 0 Unit cell: (115.08, 89.88, 100.8, 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 70 16.00 P 2 15.00 O 1405 8.00 N 1286 7.00 C 4823 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: 3.02 Conformation dependent library (CDL) restraints added in 1.4 seconds 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1830 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 43 helices and 4 sheets defined 40.4% alpha, 3.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.95 Creating SS restraints... Processing helix chain 'A' and resid 135 through 147 Processing helix chain 'A' and resid 230 through 242 Processing helix chain 'A' and resid 287 through 290 No H-bonds generated for 'chain 'A' and resid 287 through 290' Processing helix chain 'A' and resid 302 through 304 No H-bonds generated for 'chain 'A' and resid 302 through 304' Processing helix chain 'A' and resid 332 through 337 Processing helix chain 'A' and resid 351 through 358 removed outlier: 3.904A pdb=" N GLU A 354 " --> pdb=" O VAL A 351 " (cutoff:3.500A) removed outlier: 3.981A pdb=" N LYS A 355 " --> pdb=" O ALA A 352 " (cutoff:3.500A) removed outlier: 4.597A pdb=" N HIS A 358 " --> pdb=" O LYS A 355 " (cutoff:3.500A) Processing helix chain 'A' and resid 373 through 383 Processing helix chain 'A' and resid 392 through 398 Processing helix chain 'A' and resid 406 through 408 No H-bonds generated for 'chain 'A' and resid 406 through 408' Processing helix chain 'A' and resid 410 through 417 Processing helix chain 'A' and resid 437 through 448 removed outlier: 3.826A pdb=" N TYR A 441 " --> pdb=" O THR A 437 " (cutoff:3.500A) Processing helix chain 'A' and resid 460 through 470 removed outlier: 4.042A pdb=" N TRP A 465 " --> pdb=" O CYS A 461 " (cutoff:3.500A) removed outlier: 3.834A pdb=" N LEU A 470 " --> pdb=" O GLY A 466 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 476 No H-bonds generated for 'chain 'A' and resid 473 through 476' Processing helix chain 'A' and resid 486 through 490 Processing helix chain 'A' and resid 495 through 504 Processing helix chain 'A' and resid 522 through 534 Processing helix chain 'A' and resid 544 through 553 Proline residue: A 552 - end of helix Processing helix chain 'A' and resid 562 through 576 removed outlier: 3.706A pdb=" N ILE A 572 " --> pdb=" O LYS A 568 " (cutoff:3.500A) removed outlier: 3.964A pdb=" N PHE A 573 " --> pdb=" O GLY A 569 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 585 No H-bonds generated for 'chain 'A' and resid 583 through 585' Processing helix chain 'A' and resid 618 through 633 Proline residue: A 623 - end of helix Processing helix chain 'A' and resid 647 through 650 No H-bonds generated for 'chain 'A' and resid 647 through 650' Processing helix chain 'A' and resid 705 through 711 Processing helix chain 'A' and resid 729 through 735 removed outlier: 5.093A pdb=" N VAL A 734 " --> pdb=" O GLY A 730 " (cutoff:3.500A) Processing helix chain 'A' and resid 753 through 756 No H-bonds generated for 'chain 'A' and resid 753 through 756' Processing helix chain 'A' and resid 760 through 763 No H-bonds generated for 'chain 'A' and resid 760 through 763' Processing helix chain 'A' and resid 782 through 793 removed outlier: 4.699A pdb=" N PHE A 786 " --> pdb=" O GLU A 783 " (cutoff:3.500A) Processing helix chain 'A' and resid 812 through 822 Processing helix chain 'A' and resid 842 through 851 removed outlier: 4.264A pdb=" N SER A 847 " --> pdb=" O GLN A 843 " (cutoff:3.500A) removed outlier: 3.906A pdb=" N VAL A 848 " --> pdb=" O ASP A 844 " (cutoff:3.500A) removed outlier: 4.211A pdb=" N LEU A 849 " --> pdb=" O LEU A 845 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N SER A 850 " --> pdb=" O ALA A 846 " (cutoff:3.500A) Processing helix chain 'A' and resid 870 through 875 Processing helix chain 'A' and resid 895 through 908 removed outlier: 3.754A pdb=" N SER A 904 " --> pdb=" O SER A 900 " (cutoff:3.500A) removed outlier: 3.626A pdb=" N VAL A 905 " --> pdb=" O ALA A 901 " (cutoff:3.500A) Processing helix chain 'A' and resid 924 through 934 Processing helix chain 'A' and resid 955 through 965 Processing helix chain 'A' and resid 980 through 992 removed outlier: 3.686A pdb=" N VAL A 984 " --> pdb=" O GLY A 980 " (cutoff:3.500A) Processing helix chain 'A' and resid 1010 through 1018 removed outlier: 4.062A pdb=" N ALA A1015 " --> pdb=" O GLU A1011 " (cutoff:3.500A) Processing helix chain 'B' and resid 119 through 129 removed outlier: 3.886A pdb=" N PHE B 126 " --> pdb=" O MET B 122 " (cutoff:3.500A) Processing helix chain 'B' and resid 135 through 154 removed outlier: 4.202A pdb=" N GLN B 144 " --> pdb=" O LYS B 140 " (cutoff:3.500A) removed outlier: 3.605A pdb=" N ALA B 148 " --> pdb=" O GLN B 144 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 166 No H-bonds generated for 'chain 'B' and resid 164 through 166' Processing helix chain 'B' and resid 205 through 208 No H-bonds generated for 'chain 'B' and resid 205 through 208' Processing helix chain 'B' and resid 215 through 231 Processing helix chain 'B' and resid 244 through 252 Processing helix chain 'B' and resid 265 through 274 Processing helix chain 'B' and resid 279 through 281 No H-bonds generated for 'chain 'B' and resid 279 through 281' Processing helix chain 'B' and resid 285 through 299 removed outlier: 4.170A pdb=" N ASP B 290 " --> pdb=" O THR B 286 " (cutoff:3.500A) removed outlier: 3.789A pdb=" N ARG B 294 " --> pdb=" O ASP B 290 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N THR B 299 " --> pdb=" O MET B 295 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 170 through 172 removed outlier: 6.411A pdb=" N LEU A 344 " --> pdb=" O VAL A 220 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N PHE A 222 " --> pdb=" O LEU A 344 " (cutoff:3.500A) removed outlier: 6.774A pdb=" N ILE A 346 " --> pdb=" O PHE A 222 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 253 through 258 Processing sheet with id= C, first strand: chain 'A' and resid 800 through 802 removed outlier: 7.435A pdb=" N LYS A 829 " --> pdb=" O LEU A 801 " (cutoff:3.500A) removed outlier: 6.421A pdb=" N ARG A 857 " --> pdb=" O LEU A 830 " (cutoff:3.500A) No H-bonds generated for sheet with id= C Processing sheet with id= D, first strand: chain 'A' and resid 971 through 974 removed outlier: 6.162A pdb=" N ASN A1000 " --> pdb=" O LEU A 972 " (cutoff:3.500A) removed outlier: 8.368A pdb=" N LEU A 974 " --> pdb=" O ASN A1000 " (cutoff:3.500A) removed outlier: 5.776A pdb=" N GLY A1002 " --> pdb=" O LEU A 974 " (cutoff:3.500A) No H-bonds generated for sheet with id= D 210 hydrogen bonds defined for protein. 594 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: 1.86 Time building geometry restraints manager: 3.27 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2435 1.34 - 1.46: 1641 1.46 - 1.58: 3564 1.58 - 1.70: 3 1.70 - 1.82: 96 Bond restraints: 7739 Sorted by residual: bond pdb=" C MET A 685 " pdb=" N PRO A 686 " ideal model delta sigma weight residual 1.334 1.381 -0.047 8.40e-03 1.42e+04 3.18e+01 bond pdb=" N THR A 433 " pdb=" CA THR A 433 " ideal model delta sigma weight residual 1.460 1.486 -0.026 1.54e-02 4.22e+03 2.93e+00 bond pdb=" C LYS A 291 " pdb=" N PRO A 292 " ideal model delta sigma weight residual 1.334 1.373 -0.039 2.34e-02 1.83e+03 2.82e+00 bond pdb=" CB TRP A 831 " pdb=" CG TRP A 831 " ideal model delta sigma weight residual 1.498 1.449 0.049 3.10e-02 1.04e+03 2.54e+00 bond pdb=" CA LEU A 746 " pdb=" CB LEU A 746 " ideal model delta sigma weight residual 1.531 1.480 0.051 3.28e-02 9.30e+02 2.39e+00 ... (remaining 7734 not shown) Histogram of bond angle deviations from ideal: 99.24 - 106.64: 226 106.64 - 114.03: 4394 114.03 - 121.42: 3960 121.42 - 128.81: 1812 128.81 - 136.20: 71 Bond angle restraints: 10463 Sorted by residual: angle pdb=" N VAL A 860 " pdb=" CA VAL A 860 " pdb=" C VAL A 860 " ideal model delta sigma weight residual 111.77 105.80 5.97 1.04e+00 9.25e-01 3.30e+01 angle pdb=" C GLN A 432 " pdb=" N THR A 433 " pdb=" CA THR A 433 " ideal model delta sigma weight residual 122.46 129.31 -6.85 1.41e+00 5.03e-01 2.36e+01 angle pdb=" N ILE A 475 " pdb=" CA ILE A 475 " pdb=" C ILE A 475 " ideal model delta sigma weight residual 113.71 109.13 4.58 9.50e-01 1.11e+00 2.33e+01 angle pdb=" C VAL A 262 " pdb=" N SER A 263 " pdb=" CA SER A 263 " ideal model delta sigma weight residual 121.54 130.63 -9.09 1.91e+00 2.74e-01 2.27e+01 angle pdb=" N LEU A 551 " pdb=" CA LEU A 551 " pdb=" C LEU A 551 " ideal model delta sigma weight residual 109.81 118.79 -8.98 2.21e+00 2.05e-01 1.65e+01 ... (remaining 10458 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.56: 4019 17.56 - 35.13: 530 35.13 - 52.69: 93 52.69 - 70.25: 14 70.25 - 87.81: 15 Dihedral angle restraints: 4671 sinusoidal: 1853 harmonic: 2818 Sorted by residual: dihedral pdb=" CA VAL A 860 " pdb=" C VAL A 860 " pdb=" N GLY A 861 " pdb=" CA GLY A 861 " ideal model delta harmonic sigma weight residual -180.00 -151.56 -28.44 0 5.00e+00 4.00e-02 3.23e+01 dihedral pdb=" CA CYS A 784 " pdb=" C CYS A 784 " pdb=" N CYS A 785 " pdb=" CA CYS A 785 " ideal model delta harmonic sigma weight residual -180.00 -154.38 -25.62 0 5.00e+00 4.00e-02 2.62e+01 dihedral pdb=" CA PRO A 363 " pdb=" C PRO A 363 " pdb=" N ARG A 364 " pdb=" CA ARG A 364 " ideal model delta harmonic sigma weight residual 180.00 154.44 25.56 0 5.00e+00 4.00e-02 2.61e+01 ... (remaining 4668 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.073: 944 0.073 - 0.146: 202 0.146 - 0.218: 30 0.218 - 0.291: 4 0.291 - 0.364: 3 Chirality restraints: 1183 Sorted by residual: chirality pdb=" CB ILE A 480 " pdb=" CA ILE A 480 " pdb=" CG1 ILE A 480 " pdb=" CG2 ILE A 480 " both_signs ideal model delta sigma weight residual False 2.64 2.28 0.36 2.00e-01 2.50e+01 3.31e+00 chirality pdb=" CB VAL A 791 " pdb=" CA VAL A 791 " pdb=" CG1 VAL A 791 " pdb=" CG2 VAL A 791 " both_signs ideal model delta sigma weight residual False -2.63 -2.30 -0.33 2.00e-01 2.50e+01 2.64e+00 chirality pdb=" CB VAL A 860 " pdb=" CA VAL A 860 " pdb=" CG1 VAL A 860 " pdb=" CG2 VAL A 860 " both_signs ideal model delta sigma weight residual False -2.63 -2.33 -0.30 2.00e-01 2.50e+01 2.30e+00 ... (remaining 1180 not shown) Planarity restraints: 1327 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO A 283 " -0.063 5.00e-02 4.00e+02 9.41e-02 1.42e+01 pdb=" N PRO A 284 " 0.163 5.00e-02 4.00e+02 pdb=" CA PRO A 284 " -0.047 5.00e-02 4.00e+02 pdb=" CD PRO A 284 " -0.052 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 648 " -0.058 5.00e-02 4.00e+02 8.80e-02 1.24e+01 pdb=" N PRO A 649 " 0.152 5.00e-02 4.00e+02 pdb=" CA PRO A 649 " -0.044 5.00e-02 4.00e+02 pdb=" CD PRO A 649 " -0.049 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE A 648 " 0.028 2.00e-02 2.50e+03 2.08e-02 7.57e+00 pdb=" CG PHE A 648 " -0.045 2.00e-02 2.50e+03 pdb=" CD1 PHE A 648 " -0.001 2.00e-02 2.50e+03 pdb=" CD2 PHE A 648 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 PHE A 648 " 0.009 2.00e-02 2.50e+03 pdb=" CE2 PHE A 648 " 0.011 2.00e-02 2.50e+03 pdb=" CZ PHE A 648 " 0.002 2.00e-02 2.50e+03 ... (remaining 1324 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 1659 2.77 - 3.31: 7362 3.31 - 3.84: 12770 3.84 - 4.37: 14291 4.37 - 4.90: 23159 Nonbonded interactions: 59241 Sorted by model distance: nonbonded pdb=" O MET B 295 " pdb=" OG1 THR B 299 " model vdw 2.244 2.440 nonbonded pdb=" O SER A1014 " pdb=" OG1 THR A1018 " model vdw 2.251 2.440 nonbonded pdb=" O PRO B 134 " pdb=" OG1 THR B 137 " model vdw 2.254 2.440 nonbonded pdb=" O LEU A 706 " pdb=" OG SER A 709 " model vdw 2.277 2.440 nonbonded pdb=" OH TYR A 570 " pdb=" O GLU A 585 " model vdw 2.278 2.440 ... (remaining 59236 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 70 5.16 5 C 4823 2.51 5 N 1286 2.21 5 O 1405 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.550 Check model and map are aligned: 0.110 Convert atoms to be neutral: 0.060 Process input model: 23.790 Find NCS groups from input model: 0.200 Set up NCS constraints: 0.030 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:2.700 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 30.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7114 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 : 0.006 0.061 7739 Z= 0.415 Angle : 1.160 10.488 10463 Z= 0.608 Chirality : 0.063 0.364 1183 Planarity : 0.007 0.094 1327 Dihedral : 16.443 87.813 2841 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.63 % Favored : 85.26 % Rotamer Outliers : 0.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.90 (0.22), residues: 946 helix: -3.04 (0.17), residues: 402 sheet: -3.72 (0.52), residues: 74 loop : -3.36 (0.25), residues: 470 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 173 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 166 time to evaluate : 0.924 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 6 residues processed: 172 average time/residue: 0.2420 time to fit residues: 53.3783 Evaluate side-chains 130 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 0.917 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0758 time to fit residues: 2.1634 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 80 optimal weight: 2.9990 chunk 72 optimal weight: 1.9990 chunk 39 optimal weight: 10.0000 chunk 24 optimal weight: 0.5980 chunk 48 optimal weight: 6.9990 chunk 38 optimal weight: 0.8980 chunk 74 optimal weight: 5.9990 chunk 28 optimal weight: 0.3980 chunk 45 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 86 optimal weight: 4.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 GLN A 909 ASN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7080 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 7739 Z= 0.195 Angle : 0.782 9.006 10463 Z= 0.388 Chirality : 0.044 0.228 1183 Planarity : 0.006 0.097 1327 Dihedral : 7.417 37.901 1040 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer Outliers : 2.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.25), residues: 946 helix: -1.70 (0.23), residues: 400 sheet: -3.36 (0.55), residues: 69 loop : -2.93 (0.27), residues: 477 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 167 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 145 time to evaluate : 0.935 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 22 outliers final: 12 residues processed: 158 average time/residue: 0.2096 time to fit residues: 44.0743 Evaluate side-chains 138 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0758 time to fit residues: 2.8852 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 47 optimal weight: 0.9990 chunk 26 optimal weight: 0.0870 chunk 71 optimal weight: 10.0000 chunk 58 optimal weight: 0.0020 chunk 23 optimal weight: 0.3980 chunk 86 optimal weight: 8.9990 chunk 93 optimal weight: 7.9990 chunk 76 optimal weight: 8.9990 chunk 85 optimal weight: 5.9990 chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 1.9990 overall best weight: 0.6970 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 218 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7004 moved from start: 0.2368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 7739 Z= 0.171 Angle : 0.739 8.987 10463 Z= 0.363 Chirality : 0.044 0.250 1183 Planarity : 0.005 0.078 1327 Dihedral : 6.650 40.038 1040 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 15.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.71 % Favored : 89.29 % Rotamer Outliers : 1.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.02 (0.26), residues: 946 helix: -1.08 (0.25), residues: 403 sheet: -3.03 (0.56), residues: 71 loop : -2.71 (0.28), residues: 472 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 131 time to evaluate : 0.972 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 16 outliers final: 6 residues processed: 143 average time/residue: 0.2057 time to fit residues: 39.6373 Evaluate side-chains 131 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0707 time to fit residues: 1.9836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 8.9990 chunk 64 optimal weight: 2.9990 chunk 44 optimal weight: 0.0970 chunk 9 optimal weight: 8.9990 chunk 41 optimal weight: 5.9990 chunk 58 optimal weight: 5.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.2980 chunk 45 optimal weight: 0.0060 chunk 82 optimal weight: 1.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 620 GLN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7020 moved from start: 0.2690 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.094 7739 Z= 0.194 Angle : 0.739 9.651 10463 Z= 0.362 Chirality : 0.044 0.205 1183 Planarity : 0.005 0.087 1327 Dihedral : 6.422 39.710 1040 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 16.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer Outliers : 1.80 % 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: -2.65 (0.27), residues: 946 helix: -0.70 (0.26), residues: 394 sheet: -2.95 (0.56), residues: 71 loop : -2.53 (0.28), residues: 481 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 127 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 15 outliers final: 7 residues processed: 138 average time/residue: 0.2122 time to fit residues: 39.7655 Evaluate side-chains 131 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 124 time to evaluate : 0.940 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0889 time to fit residues: 2.3797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 76 optimal weight: 9.9990 chunk 52 optimal weight: 10.0000 chunk 1 optimal weight: 9.9990 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 10.0000 chunk 78 optimal weight: 10.0000 chunk 63 optimal weight: 0.0980 chunk 0 optimal weight: 10.0000 chunk 46 optimal weight: 4.9990 chunk 82 optimal weight: 2.9990 chunk 23 optimal weight: 9.9990 overall best weight: 5.0188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 400 ASN ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7238 moved from start: 0.2706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.057 7739 Z= 0.387 Angle : 0.888 11.460 10463 Z= 0.446 Chirality : 0.049 0.182 1183 Planarity : 0.006 0.075 1327 Dihedral : 7.190 35.745 1040 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 25.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.16 % Favored : 84.84 % Rotamer Outliers : 3.85 % 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: -2.86 (0.27), residues: 946 helix: -0.85 (0.25), residues: 392 sheet: -3.21 (0.56), residues: 71 loop : -2.64 (0.29), residues: 483 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 158 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 32 poor density : 126 time to evaluate : 0.937 Fit side-chains revert: symmetry clash outliers start: 32 outliers final: 20 residues processed: 150 average time/residue: 0.1865 time to fit residues: 38.9197 Evaluate side-chains 135 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 115 time to evaluate : 0.925 Switching outliers to nearest non-outliers outliers start: 20 outliers final: 0 residues processed: 20 average time/residue: 0.0759 time to fit residues: 4.0411 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 30 optimal weight: 3.9990 chunk 82 optimal weight: 1.9990 chunk 18 optimal weight: 0.9990 chunk 53 optimal weight: 0.8980 chunk 22 optimal weight: 6.9990 chunk 91 optimal weight: 0.0270 chunk 76 optimal weight: 0.0040 chunk 42 optimal weight: 0.8980 chunk 7 optimal weight: 0.9980 chunk 48 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5650 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 400 ASN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7040 moved from start: 0.2974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.048 7739 Z= 0.178 Angle : 0.754 11.730 10463 Z= 0.367 Chirality : 0.045 0.196 1183 Planarity : 0.005 0.070 1327 Dihedral : 6.409 40.445 1040 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 16.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer Outliers : 1.56 % 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: -2.51 (0.27), residues: 946 helix: -0.55 (0.26), residues: 392 sheet: -2.82 (0.60), residues: 71 loop : -2.50 (0.29), residues: 483 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 136 time to evaluate : 1.040 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 147 average time/residue: 0.2000 time to fit residues: 39.8233 Evaluate side-chains 129 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 124 time to evaluate : 0.959 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0834 time to fit residues: 2.0667 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 10 optimal weight: 10.0000 chunk 52 optimal weight: 9.9990 chunk 67 optimal weight: 0.1980 chunk 77 optimal weight: 8.9990 chunk 51 optimal weight: 0.0270 chunk 91 optimal weight: 10.0000 chunk 57 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 42 optimal weight: 7.9990 chunk 56 optimal weight: 4.9990 chunk 36 optimal weight: 0.9980 overall best weight: 1.8442 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7094 moved from start: 0.3056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.124 7739 Z= 0.225 Angle : 0.786 11.027 10463 Z= 0.381 Chirality : 0.045 0.169 1183 Planarity : 0.006 0.118 1327 Dihedral : 6.314 38.448 1040 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer Outliers : 2.04 % 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: -2.44 (0.28), residues: 946 helix: -0.50 (0.26), residues: 390 sheet: -2.57 (0.61), residues: 76 loop : -2.46 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 128 time to evaluate : 1.005 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 17 outliers final: 9 residues processed: 139 average time/residue: 0.2007 time to fit residues: 38.0442 Evaluate side-chains 132 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.853 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0821 time to fit residues: 2.5125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 54 optimal weight: 0.9990 chunk 27 optimal weight: 0.3980 chunk 17 optimal weight: 0.0020 chunk 58 optimal weight: 5.9990 chunk 62 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 71 optimal weight: 6.9990 chunk 83 optimal weight: 7.9990 chunk 87 optimal weight: 6.9990 chunk 80 optimal weight: 7.9990 overall best weight: 2.6794 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7133 moved from start: 0.3172 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.090 7739 Z= 0.256 Angle : 0.842 13.580 10463 Z= 0.405 Chirality : 0.047 0.218 1183 Planarity : 0.006 0.091 1327 Dihedral : 6.534 37.454 1040 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 21.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.83 % Favored : 87.17 % Rotamer Outliers : 1.08 % 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: -2.49 (0.28), residues: 946 helix: -0.58 (0.26), residues: 393 sheet: -2.67 (0.61), residues: 76 loop : -2.46 (0.30), residues: 477 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 122 time to evaluate : 0.922 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 4 residues processed: 129 average time/residue: 0.1964 time to fit residues: 34.8426 Evaluate side-chains 123 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 119 time to evaluate : 0.898 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0788 time to fit residues: 1.7894 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 85 optimal weight: 3.9990 chunk 87 optimal weight: 9.9990 chunk 51 optimal weight: 4.9990 chunk 37 optimal weight: 1.9990 chunk 67 optimal weight: 5.9990 chunk 26 optimal weight: 0.0670 chunk 77 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 overall best weight: 1.6124 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 357 GLN ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 153 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.3333 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.081 7739 Z= 0.209 Angle : 0.836 14.227 10463 Z= 0.394 Chirality : 0.046 0.213 1183 Planarity : 0.005 0.082 1327 Dihedral : 6.361 38.565 1040 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 18.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.24 % Favored : 88.76 % Rotamer Outliers : 0.96 % 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: -2.45 (0.28), residues: 946 helix: -0.53 (0.26), residues: 390 sheet: -2.63 (0.61), residues: 76 loop : -2.44 (0.29), residues: 480 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 130 time to evaluate : 0.995 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 5 residues processed: 132 average time/residue: 0.2075 time to fit residues: 37.2412 Evaluate side-chains 131 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 126 time to evaluate : 0.961 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0965 time to fit residues: 2.0859 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 42 optimal weight: 0.0050 chunk 62 optimal weight: 10.0000 chunk 94 optimal weight: 0.6980 chunk 87 optimal weight: 3.9990 chunk 75 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 46 optimal weight: 0.0570 chunk 59 optimal weight: 4.9990 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.9514 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.084 7739 Z= 0.194 Angle : 0.846 14.147 10463 Z= 0.396 Chirality : 0.046 0.187 1183 Planarity : 0.005 0.075 1327 Dihedral : 6.207 39.380 1040 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 17.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.82 % Favored : 89.18 % Rotamer Outliers : 0.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.11 % 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: -2.37 (0.28), residues: 946 helix: -0.41 (0.27), residues: 387 sheet: -2.40 (0.63), residues: 67 loop : -2.49 (0.29), residues: 492 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1892 Ramachandran restraints generated. 946 Oldfield, 0 Emsley, 946 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 134 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 3 outliers final: 1 residues processed: 136 average time/residue: 0.2099 time to fit residues: 38.6829 Evaluate side-chains 125 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 124 time to evaluate : 0.912 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0713 time to fit residues: 1.3846 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 95 random chunks: chunk 69 optimal weight: 7.9990 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 3.9990 chunk 75 optimal weight: 6.9990 chunk 31 optimal weight: 7.9990 chunk 77 optimal weight: 4.9990 chunk 9 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 66 optimal weight: 7.9990 chunk 4 optimal weight: 9.9990 chunk 54 optimal weight: 8.9990 overall best weight: 3.8988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 223 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4097 r_free = 0.4097 target = 0.102388 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.082291 restraints weight = 56138.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3780 r_free = 0.3780 target = 0.085614 restraints weight = 26409.578| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3822 r_free = 0.3822 target = 0.087753 restraints weight = 16541.004| |-----------------------------------------------------------------------------| r_work (final): 0.3782 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.4097 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.4097 r_free = 0.4097 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.4095 r_free = 0.4095 target_work(ls_wunit_k1) = 0.102 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.4095 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7222 moved from start: 0.3471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.078 7739 Z= 0.321 Angle : 0.917 13.002 10463 Z= 0.443 Chirality : 0.049 0.218 1183 Planarity : 0.006 0.077 1327 Dihedral : 6.710 35.870 1040 Min Nonbonded Distance : 2.127 Molprobity Statistics. All-atom Clashscore : 25.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.47 % Favored : 86.53 % Rotamer Outliers : 0.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.55 (0.28), residues: 946 helix: -0.64 (0.26), residues: 389 sheet: -2.93 (0.58), residues: 76 loop : -2.41 (0.30), residues: 481 =============================================================================== Job complete usr+sys time: 1798.53 seconds wall clock time: 33 minutes 23.31 seconds (2003.31 seconds total)