Starting phenix.real_space_refine on Fri Dec 8 07:09:48 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/12_2023/6npy_0476_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/12_2023/6npy_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_0476/12_2023/6npy_0476.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/12_2023/6npy_0476.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/12_2023/6npy_0476_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6npy_0476/12_2023/6npy_0476_updated.pdb" } resolution = 3.8 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.002 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 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. 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: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/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: 2.95 Conformation dependent library (CDL) restraints added in 1.6 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: 1.53 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: 1.84 Time building geometry restraints manager: 3.17 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 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: 0.010 Normalize map: mean=0, sd=1: 0.620 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: 3.280 Check model and map are aligned: 0.120 Set scattering table: 0.070 Process input model: 24.600 Find NCS groups from input model: 0.190 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7273 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 : 8.58 Ramachandran Plot: Outliers : 0.11 % Allowed : 14.63 % Favored : 85.26 % Rotamer: Outliers : 0.84 % Allowed : 13.58 % Favored : 85.58 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 241 HIS 0.011 0.002 HIS A 698 PHE 0.045 0.003 PHE A 648 TYR 0.029 0.003 TYR A 531 ARG 0.005 0.001 ARG B 121 *********************** 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 : 0.903 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: 0.2635 time to fit residues: 57.3017 Evaluate side-chains 130 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 124 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0810 time to fit residues: 2.1692 ------------------------------------------------------------------------------- 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: 0.7233 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 7739 Z= 0.197 Angle : 0.783 8.938 10463 Z= 0.388 Chirality : 0.044 0.225 1183 Planarity : 0.005 0.079 1327 Dihedral : 7.421 37.839 1040 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.77 % Favored : 88.23 % Rotamer: Outliers : 2.64 % Allowed : 20.07 % Favored : 77.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.63 (0.25), residues: 946 helix: -1.71 (0.23), residues: 400 sheet: -3.35 (0.55), residues: 69 loop : -2.93 (0.27), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 957 HIS 0.005 0.001 HIS A 213 PHE 0.017 0.002 PHE A 648 TYR 0.020 0.002 TYR A 570 ARG 0.008 0.001 ARG B 121 *********************** 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 : 0.930 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: 0.2176 time to fit residues: 45.4755 Evaluate side-chains 138 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 126 time to evaluate : 0.955 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 0 residues processed: 12 average time/residue: 0.0893 time to fit residues: 3.0941 ------------------------------------------------------------------------------- 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: 20.0000 chunk 71 optimal weight: 8.9990 chunk 58 optimal weight: 0.0070 chunk 23 optimal weight: 2.9990 chunk 86 optimal weight: 10.0000 chunk 93 optimal weight: 5.9990 chunk 76 optimal weight: 0.9980 chunk 85 optimal weight: 7.9990 chunk 29 optimal weight: 7.9990 chunk 69 optimal weight: 0.6980 overall best weight: 1.1402 ------------------------------------------------------------------------------- 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: 0.7199 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 7739 Z= 0.180 Angle : 0.753 9.578 10463 Z= 0.371 Chirality : 0.044 0.253 1183 Planarity : 0.005 0.076 1327 Dihedral : 6.856 39.111 1040 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 16.50 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 2.28 % Allowed : 22.36 % Favored : 75.36 % 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: -3.05 (0.26), residues: 946 helix: -1.06 (0.25), residues: 398 sheet: -3.19 (0.55), residues: 71 loop : -2.73 (0.28), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 957 HIS 0.006 0.001 HIS A 782 PHE 0.015 0.001 PHE A 648 TYR 0.023 0.002 TYR A 630 ARG 0.006 0.000 ARG A 548 *********************** 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 151 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 132 time to evaluate : 0.882 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 6 residues processed: 146 average time/residue: 0.1933 time to fit residues: 38.4898 Evaluate side-chains 131 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 125 time to evaluate : 0.900 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0714 time to fit residues: 2.0061 ------------------------------------------------------------------------------- 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: 10.0000 chunk 64 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 9 optimal weight: 0.0980 chunk 41 optimal weight: 6.9990 chunk 58 optimal weight: 1.9990 chunk 86 optimal weight: 2.9990 chunk 91 optimal weight: 0.9990 chunk 45 optimal weight: 8.9990 chunk 82 optimal weight: 3.9990 chunk 24 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 620 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 0.7196 moved from start: 0.2559 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 7739 Z= 0.177 Angle : 0.736 10.300 10463 Z= 0.358 Chirality : 0.044 0.220 1183 Planarity : 0.005 0.075 1327 Dihedral : 6.561 39.437 1040 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 16.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.56 % Favored : 88.44 % Rotamer: Outliers : 2.52 % Allowed : 24.40 % Favored : 73.08 % 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: -2.73 (0.27), residues: 946 helix: -0.80 (0.26), residues: 397 sheet: -3.05 (0.55), residues: 71 loop : -2.54 (0.28), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP A 957 HIS 0.005 0.001 HIS A 782 PHE 0.032 0.001 PHE A 811 TYR 0.023 0.002 TYR A 570 ARG 0.006 0.000 ARG A 548 *********************** 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 152 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 131 time to evaluate : 0.868 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 21 outliers final: 10 residues processed: 143 average time/residue: 0.1982 time to fit residues: 38.3949 Evaluate side-chains 129 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 119 time to evaluate : 0.865 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.0803 time to fit residues: 2.5904 ------------------------------------------------------------------------------- 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: 10.0000 chunk 68 optimal weight: 6.9990 chunk 37 optimal weight: 9.9990 chunk 78 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 chunk 0 optimal weight: 7.9990 chunk 46 optimal weight: 3.9990 chunk 82 optimal weight: 0.9980 chunk 23 optimal weight: 10.0000 overall best weight: 4.1988 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 7739 Z= 0.339 Angle : 0.844 10.356 10463 Z= 0.423 Chirality : 0.047 0.201 1183 Planarity : 0.006 0.087 1327 Dihedral : 7.049 35.915 1040 Min Nonbonded Distance : 2.148 Molprobity Statistics. All-atom Clashscore : 25.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.42 % Favored : 85.58 % Rotamer: Outliers : 3.37 % Allowed : 25.36 % Favored : 71.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.85 (0.27), residues: 946 helix: -0.87 (0.25), residues: 398 sheet: -3.33 (0.54), residues: 71 loop : -2.60 (0.29), residues: 477 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.003 TRP A 241 HIS 0.006 0.001 HIS A 312 PHE 0.029 0.002 PHE A 648 TYR 0.019 0.002 TYR A 570 ARG 0.005 0.001 ARG A 548 *********************** 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 157 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 129 time to evaluate : 0.891 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 28 outliers final: 18 residues processed: 148 average time/residue: 0.2088 time to fit residues: 41.9531 Evaluate side-chains 133 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 115 time to evaluate : 0.895 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 0 residues processed: 18 average time/residue: 0.0739 time to fit residues: 3.6426 ------------------------------------------------------------------------------- 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: 5.9990 chunk 82 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 22 optimal weight: 4.9990 chunk 91 optimal weight: 2.9990 chunk 76 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 chunk 7 optimal weight: 0.7980 chunk 48 optimal weight: 3.9990 chunk 88 optimal weight: 1.9990 overall best weight: 1.1588 ------------------------------------------------------------------------------- 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: 0.7228 moved from start: 0.2835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7739 Z= 0.178 Angle : 0.763 10.934 10463 Z= 0.370 Chirality : 0.045 0.180 1183 Planarity : 0.005 0.083 1327 Dihedral : 6.556 39.419 1040 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 17.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.66 % Favored : 88.34 % Rotamer: Outliers : 1.68 % Allowed : 27.28 % Favored : 71.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.52 (0.28), residues: 946 helix: -0.59 (0.26), residues: 396 sheet: -3.01 (0.58), residues: 69 loop : -2.44 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 957 HIS 0.005 0.001 HIS B 125 PHE 0.027 0.001 PHE A 811 TYR 0.026 0.002 TYR A 630 ARG 0.006 0.000 ARG A 918 *********************** 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 143 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 129 time to evaluate : 0.899 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 8 residues processed: 142 average time/residue: 0.2023 time to fit residues: 38.7856 Evaluate side-chains 127 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 119 time to evaluate : 0.902 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 8 outliers final: 1 residues processed: 8 average time/residue: 0.0824 time to fit residues: 2.4200 ------------------------------------------------------------------------------- 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: 6.9990 chunk 52 optimal weight: 0.9980 chunk 67 optimal weight: 5.9990 chunk 77 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 91 optimal weight: 0.4980 chunk 57 optimal weight: 10.0000 chunk 55 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 56 optimal weight: 8.9990 chunk 36 optimal weight: 2.9990 overall best weight: 1.8584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 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: 0.7254 moved from start: 0.2964 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7739 Z= 0.208 Angle : 0.789 11.955 10463 Z= 0.383 Chirality : 0.046 0.212 1183 Planarity : 0.005 0.079 1327 Dihedral : 6.422 38.319 1040 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 19.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.62 % Favored : 87.38 % Rotamer: Outliers : 1.56 % Allowed : 28.49 % Favored : 69.95 % 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 (0.27), residues: 946 helix: -0.57 (0.26), residues: 399 sheet: -2.95 (0.59), residues: 69 loop : -2.44 (0.29), residues: 478 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 957 HIS 0.004 0.001 HIS A 312 PHE 0.030 0.001 PHE A 811 TYR 0.014 0.001 TYR B 213 ARG 0.011 0.000 ARG A 548 *********************** 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 138 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 125 time to evaluate : 1.463 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 5 residues processed: 136 average time/residue: 0.2070 time to fit residues: 38.1635 Evaluate side-chains 126 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 121 time to evaluate : 0.890 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0729 time to fit residues: 1.8749 ------------------------------------------------------------------------------- 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: 0.0980 chunk 27 optimal weight: 0.9980 chunk 17 optimal weight: 7.9990 chunk 58 optimal weight: 2.9990 chunk 62 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 8 optimal weight: 2.9990 chunk 71 optimal weight: 0.9980 chunk 83 optimal weight: 4.9990 chunk 87 optimal weight: 8.9990 chunk 80 optimal weight: 5.9990 overall best weight: 1.2182 ------------------------------------------------------------------------------- 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: 0.7210 moved from start: 0.3225 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 7739 Z= 0.185 Angle : 0.799 12.771 10463 Z= 0.381 Chirality : 0.046 0.176 1183 Planarity : 0.005 0.084 1327 Dihedral : 6.312 39.248 1040 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 18.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.45 % Favored : 88.55 % Rotamer: Outliers : 1.08 % Allowed : 30.17 % Favored : 68.75 % 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: -2.39 (0.27), residues: 946 helix: -0.38 (0.26), residues: 391 sheet: -2.31 (0.65), residues: 65 loop : -2.57 (0.28), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.002 TRP A 957 HIS 0.025 0.001 HIS A 213 PHE 0.035 0.001 PHE A 811 TYR 0.015 0.001 TYR B 213 ARG 0.011 0.000 ARG A 548 *********************** 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 138 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.913 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 3 residues processed: 135 average time/residue: 0.2057 time to fit residues: 37.4083 Evaluate side-chains 125 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 122 time to evaluate : 0.879 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0934 time to fit residues: 1.6780 ------------------------------------------------------------------------------- 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: 10.0000 chunk 87 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 67 optimal weight: 0.9980 chunk 26 optimal weight: 4.9990 chunk 77 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 56 optimal weight: 6.9990 chunk 90 optimal weight: 0.9980 chunk 55 optimal weight: 0.8980 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 422 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: 0.7179 moved from start: 0.3455 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 7739 Z= 0.178 Angle : 0.824 15.307 10463 Z= 0.387 Chirality : 0.045 0.173 1183 Planarity : 0.005 0.085 1327 Dihedral : 6.166 39.663 1040 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 17.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.35 % Favored : 88.65 % Rotamer: Outliers : 0.60 % Allowed : 30.05 % Favored : 69.35 % 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: -2.33 (0.28), residues: 946 helix: -0.37 (0.26), residues: 393 sheet: -2.19 (0.62), residues: 72 loop : -2.52 (0.29), residues: 481 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP A 957 HIS 0.027 0.001 HIS A 213 PHE 0.038 0.001 PHE A 811 TYR 0.015 0.001 TYR B 213 ARG 0.011 0.000 ARG A 548 *********************** 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 136 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.920 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: 5 outliers final: 1 residues processed: 136 average time/residue: 0.2138 time to fit residues: 38.6962 Evaluate side-chains 126 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 125 time to evaluate : 0.774 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0869 time to fit residues: 1.2893 ------------------------------------------------------------------------------- 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: 4.9990 chunk 62 optimal weight: 7.9990 chunk 94 optimal weight: 0.9990 chunk 87 optimal weight: 8.9990 chunk 75 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 58 optimal weight: 0.6980 chunk 46 optimal weight: 4.9990 chunk 59 optimal weight: 0.1980 chunk 80 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 overall best weight: 1.5786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 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: 0.7203 moved from start: 0.3576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 7739 Z= 0.210 Angle : 0.860 14.435 10463 Z= 0.404 Chirality : 0.047 0.218 1183 Planarity : 0.005 0.085 1327 Dihedral : 6.228 38.896 1040 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 19.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.98 % Favored : 88.02 % Rotamer: Outliers : 0.60 % Allowed : 30.89 % Favored : 68.51 % 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: -2.33 (0.28), residues: 946 helix: -0.34 (0.27), residues: 391 sheet: -2.32 (0.65), residues: 67 loop : -2.52 (0.29), residues: 488 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.034 0.002 TRP A 241 HIS 0.024 0.001 HIS A 213 PHE 0.016 0.001 PHE A 648 TYR 0.015 0.001 TYR B 213 ARG 0.006 0.000 ARG A 548 ********************** 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 136 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 131 time to evaluate : 0.912 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 135 average time/residue: 0.2188 time to fit residues: 39.8049 Evaluate side-chains 128 residues out of total 866 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 125 time to evaluate : 0.948 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0896 time to fit residues: 1.7156 ------------------------------------------------------------------------------- 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: 6.9990 chunk 11 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 75 optimal weight: 0.1980 chunk 31 optimal weight: 0.4980 chunk 77 optimal weight: 0.3980 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 0.5980 chunk 66 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 54 optimal weight: 2.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 213 HIS ** A 977 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4203 r_free = 0.4203 target = 0.108083 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3821 r_free = 0.3821 target = 0.087582 restraints weight = 55920.634| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3894 r_free = 0.3894 target = 0.091259 restraints weight = 25502.877| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.093629 restraints weight = 15601.722| |-----------------------------------------------------------------------------| r_work (final): 0.3919 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3919 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3919 r_free = 0.3919 target_work(ls_wunit_k1) = 0.093 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 2 | |-----------------------------------------------------------------------------| r_final: 0.3919 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7141 moved from start: 0.3827 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.059 7739 Z= 0.188 Angle : 0.860 14.805 10463 Z= 0.402 Chirality : 0.046 0.173 1183 Planarity : 0.005 0.084 1327 Dihedral : 6.037 39.951 1040 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 17.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.39 % Favored : 89.61 % Rotamer: Outliers : 0.48 % Allowed : 30.29 % Favored : 69.23 % 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: -2.29 (0.28), residues: 946 helix: -0.39 (0.26), residues: 392 sheet: -2.47 (0.56), residues: 85 loop : -2.37 (0.30), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP A 241 HIS 0.025 0.001 HIS A 213 PHE 0.042 0.001 PHE A 811 TYR 0.015 0.001 TYR B 213 ARG 0.007 0.000 ARG A 918 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1893.04 seconds wall clock time: 35 minutes 7.23 seconds (2107.23 seconds total)