Starting phenix.real_space_refine (version: 1.21rc1) on Sun Jul 9 09:01:12 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/07_2023/7bwm_30233.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/07_2023/7bwm_30233.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/07_2023/7bwm_30233.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/07_2023/7bwm_30233.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/07_2023/7bwm_30233.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7bwm_30233/07_2023/7bwm_30233.pdb" } resolution = 2.9 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= 0.001 sd= 0.010 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9352 atoms to isotropic. Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 8 5.16 5 C 5997 2.51 5 N 1674 2.21 5 O 1853 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 139": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 275": "NH1" <-> "NH2" Residue "A ARG 317": "NH1" <-> "NH2" Residue "A ARG 385": "NH1" <-> "NH2" Residue "A PHE 442": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 484": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A GLU 607": "OE1" <-> "OE2" Residue "A GLU 624": "OE1" <-> "OE2" Residue "A TYR 658": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 696": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 707": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 755": "OE1" <-> "OE2" Residue "A PHE 766": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 794": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 807": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 822": "NH1" <-> "NH2" Residue "A ASP 826": "OD1" <-> "OD2" Residue "A ARG 848": "NH1" <-> "NH2" Residue "A PHE 854": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 909": "OD1" <-> "OD2" Residue "A PHE 915": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 984": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 1010": "NH1" <-> "NH2" Residue "A PHE 1115": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 1205": "OE1" <-> "OE2" Residue "A ARG 1272": "NH1" <-> "NH2" Residue "A ASP 1362": "OD1" <-> "OD2" Residue "A ARG 1368": "NH1" <-> "NH2" Residue "A GLU 1371": "OE1" <-> "OE2" Residue "A GLU 1371": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 9532 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 9532 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 1219, 9473 Classifications: {'peptide': 1219} Link IDs: {'PCIS': 2, 'PTRANS': 75, 'TRANS': 1141} Chain breaks: 12 Conformer: "B" Number of residues, atoms: 1219, 9473 Classifications: {'peptide': 1219} Link IDs: {'PCIS': 2, 'PTRANS': 75, 'TRANS': 1141} Chain breaks: 12 bond proxies already assigned to first conformer: 9640 Residues with excluded nonbonded symmetry interactions: 6 residue: pdb=" N AARG A 385 " occ=0.70 ... (20 atoms not shown) pdb=" NH2BARG A 385 " occ=0.30 residue: pdb=" N AASN A 911 " occ=0.50 ... (14 atoms not shown) pdb=" ND2BASN A 911 " occ=0.50 residue: pdb=" N ATRP A1025 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A1025 " occ=0.50 residue: pdb=" N AGLN A1188 " occ=0.70 ... (16 atoms not shown) pdb=" NE2BGLN A1188 " occ=0.30 residue: pdb=" N AASP A1257 " occ=0.50 ... (14 atoms not shown) pdb=" OD2BASP A1257 " occ=0.50 residue: pdb=" N AGLU A1371 " occ=0.70 ... (16 atoms not shown) pdb=" OE2BGLU A1371 " occ=0.30 Time building chain proxies: 8.97, per 1000 atoms: 0.94 Number of scatterers: 9532 At special positions: 0 Unit cell: (80.04, 100.05, 120.06, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 8 16.00 O 1853 8.00 N 1674 7.00 C 5997 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: 3.83 Conformation dependent library (CDL) restraints added in 2.7 seconds 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2258 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 15 sheets defined 25.6% alpha, 14.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.73 Creating SS restraints... Processing helix chain 'A' and resid 112 through 124 Processing helix chain 'A' and resid 176 through 181 removed outlier: 3.619A pdb=" N VAL A 180 " --> pdb=" O GLN A 176 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 209 removed outlier: 3.835A pdb=" N VAL A 208 " --> pdb=" O PRO A 204 " (cutoff:3.500A) removed outlier: 3.601A pdb=" N TYR A 209 " --> pdb=" O ARG A 205 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 204 through 209' Processing helix chain 'A' and resid 210 through 213 Processing helix chain 'A' and resid 248 through 254 removed outlier: 3.607A pdb=" N SER A 251 " --> pdb=" O THR A 248 " (cutoff:3.500A) removed outlier: 4.994A pdb=" N ASN A 252 " --> pdb=" O ALA A 249 " (cutoff:3.500A) removed outlier: 4.003A pdb=" N LYS A 254 " --> pdb=" O SER A 251 " (cutoff:3.500A) Processing helix chain 'A' and resid 310 through 312 No H-bonds generated for 'chain 'A' and resid 310 through 312' Processing helix chain 'A' and resid 328 through 333 removed outlier: 3.744A pdb=" N PHE A 332 " --> pdb=" O ALA A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 358 through 365 removed outlier: 3.556A pdb=" N ILE A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 395 through 401 removed outlier: 3.899A pdb=" N MET A 399 " --> pdb=" O ASP A 395 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 409 removed outlier: 3.777A pdb=" N THR A 409 " --> pdb=" O SER A 406 " (cutoff:3.500A) Processing helix chain 'A' and resid 415 through 426 removed outlier: 4.105A pdb=" N ASP A 419 " --> pdb=" O HIS A 415 " (cutoff:3.500A) Processing helix chain 'A' and resid 438 through 442 removed outlier: 3.821A pdb=" N TRP A 441 " --> pdb=" O HIS A 438 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N PHE A 442 " --> pdb=" O PRO A 439 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 438 through 442' Processing helix chain 'A' and resid 483 through 490 Processing helix chain 'A' and resid 542 through 546 Processing helix chain 'A' and resid 607 through 610 removed outlier: 3.572A pdb=" N SER A 610 " --> pdb=" O GLU A 607 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 607 through 610' Processing helix chain 'A' and resid 611 through 619 Processing helix chain 'A' and resid 630 through 634 removed outlier: 3.894A pdb=" N GLY A 633 " --> pdb=" O THR A 630 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N TRP A 634 " --> pdb=" O PRO A 631 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 630 through 634' Processing helix chain 'A' and resid 641 through 645 Processing helix chain 'A' and resid 662 through 666 removed outlier: 3.772A pdb=" N GLN A 666 " --> pdb=" O PRO A 663 " (cutoff:3.500A) Processing helix chain 'A' and resid 670 through 678 Processing helix chain 'A' and resid 701 through 710 Processing helix chain 'A' and resid 739 through 744 Processing helix chain 'A' and resid 753 through 757 removed outlier: 3.511A pdb=" N ASN A 756 " --> pdb=" O GLY A 753 " (cutoff:3.500A) removed outlier: 3.540A pdb=" N GLU A 757 " --> pdb=" O LYS A 754 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 753 through 757' Processing helix chain 'A' and resid 761 through 767 removed outlier: 3.676A pdb=" N ARG A 765 " --> pdb=" O ASN A 761 " (cutoff:3.500A) removed outlier: 3.617A pdb=" N PHE A 766 " --> pdb=" O GLU A 762 " (cutoff:3.500A) removed outlier: 3.696A pdb=" N ASN A 767 " --> pdb=" O TYR A 763 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 761 through 767' Processing helix chain 'A' and resid 779 through 785 removed outlier: 3.932A pdb=" N PHE A 783 " --> pdb=" O TRP A 780 " (cutoff:3.500A) removed outlier: 3.966A pdb=" N SER A 784 " --> pdb=" O SER A 781 " (cutoff:3.500A) Proline residue: A 785 - end of helix Processing helix chain 'A' and resid 797 through 808 removed outlier: 3.624A pdb=" N ASP A 802 " --> pdb=" O GLY A 798 " (cutoff:3.500A) removed outlier: 4.454A pdb=" N GLN A 803 " --> pdb=" O SER A 799 " (cutoff:3.500A) removed outlier: 3.828A pdb=" N VAL A 804 " --> pdb=" O VAL A 800 " (cutoff:3.500A) removed outlier: 3.847A pdb=" N ASP A 806 " --> pdb=" O ASP A 802 " (cutoff:3.500A) Processing helix chain 'A' and resid 822 through 826 removed outlier: 3.557A pdb=" N ASP A 826 " --> pdb=" O GLY A 823 " (cutoff:3.500A) Processing helix chain 'A' and resid 915 through 919 Processing helix chain 'A' and resid 981 through 985 removed outlier: 3.524A pdb=" N PHE A 984 " --> pdb=" O ALA A 981 " (cutoff:3.500A) Processing helix chain 'A' and resid 988 through 1002 removed outlier: 3.929A pdb=" N GLN A 994 " --> pdb=" O ALA A 990 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1023 removed outlier: 3.605A pdb=" N GLN A1023 " --> pdb=" O ALA A1020 " (cutoff:3.500A) Processing helix chain 'A' and resid 1026 through 1031 Processing helix chain 'A' and resid 1049 through 1059 Processing helix chain 'A' and resid 1067 through 1071 removed outlier: 4.354A pdb=" N THR A1071 " --> pdb=" O SER A1068 " (cutoff:3.500A) Processing helix chain 'A' and resid 1146 through 1154 Processing helix chain 'A' and resid 1179 through 1187 Processing helix chain 'A' and resid 1195 through 1201 Processing helix chain 'A' and resid 1218 through 1223 removed outlier: 3.580A pdb=" N LYS A1223 " --> pdb=" O SER A1220 " (cutoff:3.500A) Processing helix chain 'A' and resid 1255 through 1260 Processing helix chain 'A' and resid 1263 through 1275 removed outlier: 3.780A pdb=" N VAL A1267 " --> pdb=" O ASP A1263 " (cutoff:3.500A) Processing helix chain 'A' and resid 1302 through 1307 removed outlier: 3.534A pdb=" N SER A1307 " --> pdb=" O SER A1303 " (cutoff:3.500A) Processing helix chain 'A' and resid 1326 through 1338 Processing sheet with id=AA1, first strand: chain 'A' and resid 67 through 68 Processing sheet with id=AA2, first strand: chain 'A' and resid 67 through 68 removed outlier: 3.574A pdb=" N VAL A 92 " --> pdb=" O ALA A 127 " (cutoff:3.500A) removed outlier: 6.379A pdb=" N LEU A 128 " --> pdb=" O ASP A 140 " (cutoff:3.500A) removed outlier: 4.408A pdb=" N ASP A 140 " --> pdb=" O LEU A 128 " (cutoff:3.500A) removed outlier: 6.825A pdb=" N ARG A 130 " --> pdb=" O LEU A 138 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 161 through 162 Processing sheet with id=AA4, first strand: chain 'A' and resid 184 through 191 removed outlier: 6.577A pdb=" N LEU A 201 " --> pdb=" O VAL A 186 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N VAL A 188 " --> pdb=" O ALA A 199 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N ALA A 199 " --> pdb=" O VAL A 188 " (cutoff:3.500A) removed outlier: 5.044A pdb=" N GLN A 190 " --> pdb=" O ARG A 197 " (cutoff:3.500A) removed outlier: 7.553A pdb=" N ARG A 197 " --> pdb=" O GLN A 190 " (cutoff:3.500A) removed outlier: 5.127A pdb=" N TYR A 196 " --> pdb=" O ASP A 378 " (cutoff:3.500A) removed outlier: 4.245A pdb=" N ARG A 390 " --> pdb=" O ILE A 375 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N TYR A 377 " --> pdb=" O ILE A 388 " (cutoff:3.500A) removed outlier: 5.609A pdb=" N ILE A 388 " --> pdb=" O TYR A 377 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 245 through 246 Processing sheet with id=AA6, first strand: chain 'A' and resid 257 through 259 removed outlier: 5.857A pdb=" N ALA A 286 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 257 through 259 removed outlier: 5.857A pdb=" N ALA A 286 " --> pdb=" O ALA A 258 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 319 through 320 removed outlier: 3.681A pdb=" N GLN A 323 " --> pdb=" O GLU A 320 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 494 through 497 Processing sheet with id=AB1, first strand: chain 'A' and resid 574 through 582 removed outlier: 5.110A pdb=" N VAL A 576 " --> pdb=" O THR A 591 " (cutoff:3.500A) removed outlier: 6.618A pdb=" N THR A 591 " --> pdb=" O VAL A 576 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N GLY A 578 " --> pdb=" O ALA A 589 " (cutoff:3.500A) removed outlier: 3.995A pdb=" N LEU A 586 " --> pdb=" O LEU A 738 " (cutoff:3.500A) removed outlier: 3.948A pdb=" N ARG A 789 " --> pdb=" O ILE A 737 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 862 through 863 Processing sheet with id=AB3, first strand: chain 'A' and resid 913 through 914 Processing sheet with id=AB4, first strand: chain 'A' and resid 1006 through 1008 Processing sheet with id=AB5, first strand: chain 'A' and resid 1107 through 1109 removed outlier: 8.658A pdb=" N GLY A1367 " --> pdb=" O LEU A1137 " (cutoff:3.500A) removed outlier: 5.783A pdb=" N LEU A1139 " --> pdb=" O GLY A1367 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 1162 through 1167 removed outlier: 5.466A pdb=" N VAL A1176 " --> pdb=" O ARG A1163 " (cutoff:3.500A) removed outlier: 4.465A pdb=" N SER A1165 " --> pdb=" O GLU A1174 " (cutoff:3.500A) removed outlier: 6.578A pdb=" N GLU A1174 " --> pdb=" O SER A1165 " (cutoff:3.500A) removed outlier: 3.978A pdb=" N SER A1287 " --> pdb=" O MET A1377 " (cutoff:3.500A) 223 hydrogen bonds defined for protein. 567 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: 3.32 Time building geometry restraints manager: 4.13 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: 3173 1.34 - 1.46: 1638 1.46 - 1.57: 4947 1.57 - 1.69: 0 1.69 - 1.80: 16 Bond restraints: 9774 Sorted by residual: bond pdb=" C PHE A 850 " pdb=" N LEU A 851 " ideal model delta sigma weight residual 1.329 1.270 0.059 1.86e-02 2.89e+03 1.01e+01 bond pdb=" C PHE A 722 " pdb=" N VAL A 723 " ideal model delta sigma weight residual 1.329 1.301 0.028 1.31e-02 5.83e+03 4.42e+00 bond pdb=" C SER A 784 " pdb=" N PRO A 785 " ideal model delta sigma weight residual 1.334 1.351 -0.017 8.40e-03 1.42e+04 4.27e+00 bond pdb=" CA SER A 799 " pdb=" C SER A 799 " ideal model delta sigma weight residual 1.523 1.500 0.023 1.35e-02 5.49e+03 2.99e+00 bond pdb=" N HIS A 653 " pdb=" CA HIS A 653 " ideal model delta sigma weight residual 1.456 1.476 -0.020 1.25e-02 6.40e+03 2.65e+00 ... (remaining 9769 not shown) Histogram of bond angle deviations from ideal: 100.23 - 106.99: 378 106.99 - 113.75: 5345 113.75 - 120.52: 3610 120.52 - 127.28: 3841 127.28 - 134.04: 157 Bond angle restraints: 13331 Sorted by residual: angle pdb=" N VAL A1363 " pdb=" CA VAL A1363 " pdb=" C VAL A1363 " ideal model delta sigma weight residual 113.71 107.50 6.21 9.50e-01 1.11e+00 4.27e+01 angle pdb=" C THR A 950 " pdb=" CA THR A 950 " pdb=" CB THR A 950 " ideal model delta sigma weight residual 109.83 105.02 4.81 9.90e-01 1.02e+00 2.36e+01 angle pdb=" C SER A 948 " pdb=" N LEU A 949 " pdb=" CA LEU A 949 " ideal model delta sigma weight residual 121.54 130.73 -9.19 1.91e+00 2.74e-01 2.32e+01 angle pdb=" N THR A 950 " pdb=" CA THR A 950 " pdb=" C THR A 950 " ideal model delta sigma weight residual 113.51 120.67 -7.16 1.52e+00 4.33e-01 2.22e+01 angle pdb=" C ASP A 667 " pdb=" N ARG A 668 " pdb=" CA ARG A 668 " ideal model delta sigma weight residual 122.21 111.72 10.49 2.87e+00 1.21e-01 1.34e+01 ... (remaining 13326 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 19.57: 5373 19.57 - 39.14: 287 39.14 - 58.71: 92 58.71 - 78.29: 15 78.29 - 97.86: 6 Dihedral angle restraints: 5773 sinusoidal: 2261 harmonic: 3512 Sorted by residual: dihedral pdb=" CA GLN A1282 " pdb=" C GLN A1282 " pdb=" N PRO A1283 " pdb=" CA PRO A1283 " ideal model delta harmonic sigma weight residual 0.00 34.48 -34.48 0 5.00e+00 4.00e-02 4.76e+01 dihedral pdb=" CA THR A 951 " pdb=" C THR A 951 " pdb=" N GLN A 952 " pdb=" CA GLN A 952 " ideal model delta harmonic sigma weight residual 180.00 146.58 33.42 0 5.00e+00 4.00e-02 4.47e+01 dihedral pdb=" CA THR A 950 " pdb=" C THR A 950 " pdb=" N THR A 951 " pdb=" CA THR A 951 " ideal model delta harmonic sigma weight residual 180.00 149.25 30.75 0 5.00e+00 4.00e-02 3.78e+01 ... (remaining 5770 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 1005 0.043 - 0.086: 324 0.086 - 0.128: 108 0.128 - 0.171: 6 0.171 - 0.214: 3 Chirality restraints: 1446 Sorted by residual: chirality pdb=" CA GLN A 960 " pdb=" N GLN A 960 " pdb=" C GLN A 960 " pdb=" CB GLN A 960 " both_signs ideal model delta sigma weight residual False 2.51 2.30 0.21 2.00e-01 2.50e+01 1.14e+00 chirality pdb=" CA THR A 950 " pdb=" N THR A 950 " pdb=" C THR A 950 " pdb=" CB THR A 950 " both_signs ideal model delta sigma weight residual False 2.53 2.32 0.20 2.00e-01 2.50e+01 1.04e+00 chirality pdb=" CA PRO A1283 " pdb=" N PRO A1283 " pdb=" C PRO A1283 " pdb=" CB PRO A1283 " both_signs ideal model delta sigma weight residual False 2.72 2.53 0.19 2.00e-01 2.50e+01 9.02e-01 ... (remaining 1443 not shown) Planarity restraints: 1761 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 973 " 0.028 5.00e-02 4.00e+02 4.20e-02 2.83e+00 pdb=" N PRO A 974 " -0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 974 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 974 " 0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A1099 " 0.027 5.00e-02 4.00e+02 4.10e-02 2.68e+00 pdb=" N PRO A1100 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A1100 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A1100 " 0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ALA A 478 " 0.024 5.00e-02 4.00e+02 3.63e-02 2.11e+00 pdb=" N PRO A 479 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.020 5.00e-02 4.00e+02 ... (remaining 1758 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 139 2.62 - 3.19: 8094 3.19 - 3.76: 14707 3.76 - 4.33: 22272 4.33 - 4.90: 35629 Nonbonded interactions: 80841 Sorted by model distance: nonbonded pdb=" O THR A 950 " pdb=" OG1 THR A 951 " model vdw 2.048 2.440 nonbonded pdb=" OH TYR A 139 " pdb=" OD1 ASP A 378 " model vdw 2.102 2.440 nonbonded pdb=" O LEU A1271 " pdb=" OG SER A1274 " model vdw 2.150 2.440 nonbonded pdb=" O LEU A 120 " pdb=" OG1 THR A 124 " model vdw 2.174 2.440 nonbonded pdb=" OD1 ASP A 142 " pdb=" OG SER A 144 " model vdw 2.193 2.440 ... (remaining 80836 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=0.30 max=1.00 mean=0.99 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.410 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.100 Construct map_model_manager: 0.010 Extract box with map and model: 5.200 Check model and map are aligned: 0.160 Set scattering table: 0.090 Process input model: 33.540 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 52.450 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8331 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 : 0.005 0.059 9774 Z= 0.328 Angle : 0.784 10.810 13331 Z= 0.467 Chirality : 0.046 0.214 1446 Planarity : 0.005 0.042 1761 Dihedral : 14.238 97.857 3515 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 7.32 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.78 % Favored : 93.96 % Rotamer Outliers : 7.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.18 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.28 (0.20), residues: 1211 helix: -2.75 (0.26), residues: 213 sheet: -1.23 (0.36), residues: 169 loop : -2.38 (0.18), residues: 829 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 74 poor density : 118 time to evaluate : 1.005 Fit side-chains revert: symmetry clash outliers start: 74 outliers final: 23 residues processed: 183 average time/residue: 1.1419 time to fit residues: 224.5603 Evaluate side-chains 100 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 77 time to evaluate : 1.034 Switching outliers to nearest non-outliers outliers start: 23 outliers final: 19 residues processed: 4 average time/residue: 0.1337 time to fit residues: 2.2713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 102 optimal weight: 3.9990 chunk 91 optimal weight: 1.9990 chunk 50 optimal weight: 1.9990 chunk 31 optimal weight: 0.3980 chunk 61 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 94 optimal weight: 7.9990 chunk 36 optimal weight: 0.9980 chunk 57 optimal weight: 0.8980 chunk 70 optimal weight: 2.9990 chunk 109 optimal weight: 7.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 162 ASN A 274 GLN A 469 GLN A 490 ASN A 661 ASN A 685 ASN A 716 GLN ** A 803 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A1192 GLN A1279 HIS A1352 ASN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.1477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9774 Z= 0.163 Angle : 0.594 10.328 13331 Z= 0.303 Chirality : 0.044 0.210 1446 Planarity : 0.004 0.049 1761 Dihedral : 5.253 33.010 1308 Min Nonbonded Distance : 2.029 Molprobity Statistics. All-atom Clashscore : 7.74 Ramachandran Plot: Outliers : 0.08 % Allowed : 4.95 % Favored : 94.97 % Rotamer Outliers : 3.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.22), residues: 1211 helix: -1.49 (0.31), residues: 218 sheet: -0.64 (0.38), residues: 158 loop : -1.68 (0.19), residues: 835 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 85 time to evaluate : 1.132 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 39 outliers final: 19 residues processed: 114 average time/residue: 1.1343 time to fit residues: 140.2353 Evaluate side-chains 93 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 74 time to evaluate : 1.093 Switching outliers to nearest non-outliers outliers start: 19 outliers final: 18 residues processed: 1 average time/residue: 0.0897 time to fit residues: 1.7086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 61 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 91 optimal weight: 3.9990 chunk 74 optimal weight: 0.7980 chunk 30 optimal weight: 7.9990 chunk 110 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 98 optimal weight: 4.9990 chunk 109 optimal weight: 6.9990 chunk 37 optimal weight: 8.9990 chunk 88 optimal weight: 10.0000 overall best weight: 2.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 803 GLN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8326 moved from start: 0.1554 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 9774 Z= 0.282 Angle : 0.640 10.619 13331 Z= 0.326 Chirality : 0.046 0.211 1446 Planarity : 0.004 0.041 1761 Dihedral : 5.313 34.556 1308 Min Nonbonded Distance : 2.033 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.54 % Favored : 93.38 % Rotamer Outliers : 3.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.87 (0.22), residues: 1211 helix: -1.15 (0.32), residues: 217 sheet: -0.39 (0.40), residues: 158 loop : -1.51 (0.20), residues: 836 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 80 time to evaluate : 0.993 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 40 outliers final: 21 residues processed: 110 average time/residue: 1.1446 time to fit residues: 136.3884 Evaluate side-chains 96 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 75 time to evaluate : 0.960 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 17 residues processed: 4 average time/residue: 0.0862 time to fit residues: 2.0783 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9990 chunk 82 optimal weight: 5.9990 chunk 57 optimal weight: 0.9990 chunk 12 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 73 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 116 optimal weight: 4.9990 chunk 104 optimal weight: 6.9990 chunk 31 optimal weight: 0.7980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8276 moved from start: 0.1897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 9774 Z= 0.155 Angle : 0.567 9.440 13331 Z= 0.288 Chirality : 0.043 0.194 1446 Planarity : 0.004 0.058 1761 Dihedral : 4.936 32.275 1308 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 7.42 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.11 % Favored : 94.80 % Rotamer Outliers : 3.02 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.47 (0.22), residues: 1211 helix: -0.70 (0.34), residues: 217 sheet: -0.15 (0.41), residues: 156 loop : -1.27 (0.20), residues: 838 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 77 time to evaluate : 1.048 Fit side-chains revert: symmetry clash outliers start: 31 outliers final: 22 residues processed: 103 average time/residue: 1.1508 time to fit residues: 128.8411 Evaluate side-chains 95 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 73 time to evaluate : 1.136 Switching outliers to nearest non-outliers outliers start: 22 outliers final: 21 residues processed: 1 average time/residue: 0.0898 time to fit residues: 1.7172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 66 optimal weight: 7.9990 chunk 1 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 48 optimal weight: 3.9990 chunk 99 optimal weight: 0.9990 chunk 80 optimal weight: 3.9990 chunk 0 optimal weight: 8.9990 chunk 59 optimal weight: 6.9990 chunk 104 optimal weight: 7.9990 chunk 29 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 overall best weight: 2.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8335 moved from start: 0.1774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.055 9774 Z= 0.340 Angle : 0.649 10.548 13331 Z= 0.329 Chirality : 0.047 0.201 1446 Planarity : 0.005 0.046 1761 Dihedral : 5.273 32.827 1308 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.08 % Allowed : 6.45 % Favored : 93.46 % Rotamer Outliers : 3.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.56 (0.22), residues: 1211 helix: -0.85 (0.33), residues: 216 sheet: -0.21 (0.41), residues: 158 loop : -1.32 (0.20), residues: 837 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 73 time to evaluate : 1.156 Fit side-chains outliers start: 35 outliers final: 24 residues processed: 103 average time/residue: 1.1154 time to fit residues: 125.0102 Evaluate side-chains 96 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 72 time to evaluate : 1.044 Switching outliers to nearest non-outliers outliers start: 24 outliers final: 21 residues processed: 3 average time/residue: 0.0912 time to fit residues: 2.0275 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 0.8980 chunk 28 optimal weight: 3.9990 chunk 117 optimal weight: 6.9990 chunk 97 optimal weight: 0.9980 chunk 54 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 38 optimal weight: 0.8980 chunk 61 optimal weight: 0.8980 chunk 112 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 960 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 9774 Z= 0.165 Angle : 0.564 9.361 13331 Z= 0.286 Chirality : 0.043 0.192 1446 Planarity : 0.004 0.041 1761 Dihedral : 4.917 31.050 1308 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 7.37 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer Outliers : 2.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 1.30 % Cis-general : 0.00 % Twisted Proline : 1.30 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.28 (0.23), residues: 1211 helix: -0.52 (0.35), residues: 216 sheet: -0.10 (0.41), residues: 156 loop : -1.14 (0.20), residues: 839 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 28 poor density : 73 time to evaluate : 1.069 Fit side-chains outliers start: 28 outliers final: 21 residues processed: 98 average time/residue: 1.1231 time to fit residues: 119.6087 Evaluate side-chains 89 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 1.049 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.1818 time to fit residues: 2.0297 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 13 optimal weight: 7.9990 chunk 66 optimal weight: 7.9990 chunk 85 optimal weight: 2.9990 chunk 98 optimal weight: 5.9990 chunk 65 optimal weight: 0.8980 chunk 116 optimal weight: 7.9990 chunk 72 optimal weight: 5.9990 chunk 71 optimal weight: 0.8980 chunk 53 optimal weight: 3.9990 chunk 46 optimal weight: 0.8980 chunk 69 optimal weight: 0.7980 overall best weight: 1.2982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8297 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.039 9774 Z= 0.201 Angle : 0.579 9.524 13331 Z= 0.293 Chirality : 0.044 0.189 1446 Planarity : 0.004 0.047 1761 Dihedral : 4.908 29.884 1308 Min Nonbonded Distance : 2.140 Molprobity Statistics. All-atom Clashscore : 6.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer Outliers : 2.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.22 (0.23), residues: 1211 helix: -0.40 (0.35), residues: 216 sheet: -0.05 (0.41), residues: 156 loop : -1.11 (0.20), residues: 839 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 72 time to evaluate : 1.137 Fit side-chains outliers start: 29 outliers final: 21 residues processed: 97 average time/residue: 1.2157 time to fit residues: 127.9758 Evaluate side-chains 89 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 68 time to evaluate : 0.986 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 19 residues processed: 2 average time/residue: 0.1031 time to fit residues: 2.0176 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 74 optimal weight: 0.8980 chunk 79 optimal weight: 6.9990 chunk 57 optimal weight: 3.9990 chunk 10 optimal weight: 10.0000 chunk 91 optimal weight: 0.8980 chunk 106 optimal weight: 3.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 1.9990 chunk 108 optimal weight: 0.8980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8287 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 9774 Z= 0.184 Angle : 0.565 9.328 13331 Z= 0.286 Chirality : 0.043 0.191 1446 Planarity : 0.004 0.067 1761 Dihedral : 4.857 29.405 1308 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.45 % Favored : 94.55 % Rotamer Outliers : 2.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.16 (0.23), residues: 1211 helix: -0.34 (0.35), residues: 216 sheet: -0.08 (0.41), residues: 156 loop : -1.06 (0.20), residues: 839 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 74 time to evaluate : 1.034 Fit side-chains outliers start: 24 outliers final: 18 residues processed: 98 average time/residue: 1.0906 time to fit residues: 116.4196 Evaluate side-chains 90 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 72 time to evaluate : 1.041 Switching outliers to nearest non-outliers outliers start: 18 outliers final: 18 residues processed: 0 time to fit residues: 1.4785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 111 optimal weight: 3.9990 chunk 65 optimal weight: 3.9990 chunk 47 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 chunk 98 optimal weight: 5.9990 chunk 102 optimal weight: 0.0970 chunk 108 optimal weight: 0.8980 chunk 71 optimal weight: 0.0470 chunk 114 optimal weight: 9.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.6078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.2391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.038 9774 Z= 0.141 Angle : 0.536 8.675 13331 Z= 0.271 Chirality : 0.042 0.189 1446 Planarity : 0.004 0.040 1761 Dihedral : 4.572 29.048 1308 Min Nonbonded Distance : 2.136 Molprobity Statistics. All-atom Clashscore : 6.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.03 % Favored : 94.97 % Rotamer Outliers : 1.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.00 (0.23), residues: 1211 helix: -0.13 (0.36), residues: 216 sheet: -0.04 (0.41), residues: 156 loop : -0.96 (0.20), residues: 839 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 82 time to evaluate : 0.996 Fit side-chains outliers start: 19 outliers final: 17 residues processed: 101 average time/residue: 1.0517 time to fit residues: 116.0413 Evaluate side-chains 87 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 70 time to evaluate : 1.081 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.5798 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 54 optimal weight: 0.0670 chunk 79 optimal weight: 5.9990 chunk 120 optimal weight: 0.5980 chunk 110 optimal weight: 1.9990 chunk 95 optimal weight: 5.9990 chunk 9 optimal weight: 8.9990 chunk 74 optimal weight: 0.4980 chunk 58 optimal weight: 0.5980 chunk 76 optimal weight: 3.9990 chunk 102 optimal weight: 2.9990 chunk 29 optimal weight: 5.9990 overall best weight: 0.7520 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 9774 Z= 0.153 Angle : 0.550 10.406 13331 Z= 0.277 Chirality : 0.043 0.191 1446 Planarity : 0.004 0.071 1761 Dihedral : 4.569 28.772 1308 Min Nonbonded Distance : 2.135 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.94 (0.23), residues: 1211 helix: -0.10 (0.36), residues: 216 sheet: -0.02 (0.41), residues: 156 loop : -0.92 (0.21), residues: 839 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2422 Ramachandran restraints generated. 1211 Oldfield, 0 Emsley, 1211 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 1.062 Fit side-chains outliers start: 18 outliers final: 17 residues processed: 87 average time/residue: 1.0587 time to fit residues: 100.8981 Evaluate side-chains 84 residues out of total 1014 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 67 time to evaluate : 1.083 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 17 residues processed: 0 time to fit residues: 1.5013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 88 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 26 optimal weight: 3.9990 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 6.9990 chunk 98 optimal weight: 0.7980 chunk 12 optimal weight: 4.9990 chunk 17 optimal weight: 1.9990 chunk 84 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 chunk 69 optimal weight: 0.3980 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 490 ASN ** A 941 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1260 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3891 r_free = 0.3891 target = 0.164332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 30)----------------| | r_work = 0.3473 r_free = 0.3473 target = 0.129014 restraints weight = 39221.082| |-----------------------------------------------------------------------------| r_work (start): 0.3444 rms_B_bonded: 6.68 r_work: 0.3053 rms_B_bonded: 6.45 restraints_weight: 2.0000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3025 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3025 r_free = 0.3025 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.30 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3024 r_free = 0.3024 target_work(ls_wunit_k1) = 0.098 | | occupancies: max = 1.00 min = 0.33 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.3024 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8589 moved from start: 0.2376 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 9774 Z= 0.189 Angle : 0.565 10.758 13331 Z= 0.285 Chirality : 0.044 0.191 1446 Planarity : 0.004 0.041 1761 Dihedral : 4.649 28.525 1308 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer Outliers : 1.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 2.60 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.97 (0.23), residues: 1211 helix: -0.16 (0.36), residues: 216 sheet: -0.00 (0.41), residues: 156 loop : -0.93 (0.20), residues: 839 =============================================================================== Job complete usr+sys time: 3023.86 seconds wall clock time: 54 minutes 50.13 seconds (3290.13 seconds total)