Starting phenix.real_space_refine on Mon Mar 11 13:20:12 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/03_2024/8h8b_34541.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/03_2024/8h8b_34541.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.16 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/03_2024/8h8b_34541.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/03_2024/8h8b_34541.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/03_2024/8h8b_34541.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8h8b_34541/03_2024/8h8b_34541.pdb" } resolution = 3.16 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= 0.004 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: 4 Type Number sf(0) Gaussians S 13 5.16 5 C 5251 2.51 5 N 1439 2.21 5 O 1641 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 146": "OE1" <-> "OE2" Residue "A GLU 162": "OE1" <-> "OE2" Residue "A ASP 168": "OD1" <-> "OD2" Residue "A GLU 170": "OE1" <-> "OE2" Residue "A ARG 182": "NH1" <-> "NH2" Residue "A ARG 188": "NH1" <-> "NH2" Residue "A GLU 203": "OE1" <-> "OE2" Residue "A ASP 209": "OD1" <-> "OD2" Residue "A ASP 222": "OD1" <-> "OD2" Residue "A GLU 226": "OE1" <-> "OE2" Residue "A PHE 249": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 267": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 268": "OE1" <-> "OE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A ARG 293": "NH1" <-> "NH2" Residue "A ARG 296": "NH1" <-> "NH2" Residue "A GLU 299": "OE1" <-> "OE2" Residue "A ARG 305": "NH1" <-> "NH2" Residue "A GLU 309": "OE1" <-> "OE2" Residue "A GLU 320": "OE1" <-> "OE2" Residue "A GLU 337": "OE1" <-> "OE2" Residue "A ASP 339": "OD1" <-> "OD2" Residue "A ARG 367": "NH1" <-> "NH2" Residue "A PHE 371": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 376": "OE1" <-> "OE2" Residue "A PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 399": "NH1" <-> "NH2" Residue "A TYR 409": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 414": "OD1" <-> "OD2" Residue "A ASP 422": "OD1" <-> "OD2" Residue "A GLU 423": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A ARG 447": "NH1" <-> "NH2" Residue "A ASP 455": "OD1" <-> "OD2" Residue "A TYR 461": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 463": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 499": "OD1" <-> "OD2" Residue "A GLU 501": "OE1" <-> "OE2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A ARG 535": "NH1" <-> "NH2" Residue "A GLU 536": "OE1" <-> "OE2" Residue "A ASP 539": "OD1" <-> "OD2" Residue "A ASP 559": "OD1" <-> "OD2" Residue "A ARG 564": "NH1" <-> "NH2" Residue "A ASP 604": "OD1" <-> "OD2" Residue "A GLU 611": "OE1" <-> "OE2" Residue "A GLU 641": "OE1" <-> "OE2" Residue "A ASP 647": "OD1" <-> "OD2" Residue "A ARG 666": "NH1" <-> "NH2" Residue "A TYR 676": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 710": "OD1" <-> "OD2" Residue "A GLU 736": "OE1" <-> "OE2" Residue "A ARG 746": "NH1" <-> "NH2" Residue "A ARG 770": "NH1" <-> "NH2" Residue "A GLU 776": "OE1" <-> "OE2" Residue "A GLU 780": "OE1" <-> "OE2" Residue "A ARG 787": "NH1" <-> "NH2" Residue "A ASP 794": "OD1" <-> "OD2" Residue "A ASP 815": "OD1" <-> "OD2" Residue "A TYR 825": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 840": "NH1" <-> "NH2" Residue "A ARG 859": "NH1" <-> "NH2" Residue "A ASP 907": "OD1" <-> "OD2" Residue "A ASP 916": "OD1" <-> "OD2" Residue "A ARG 931": "NH1" <-> "NH2" Residue "A ARG 943": "NH1" <-> "NH2" Residue "A ARG 952": "NH1" <-> "NH2" Residue "A PHE 954": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 973": "OE1" <-> "OE2" Residue "A ARG 980": "NH1" <-> "NH2" Residue "A GLU 991": "OE1" <-> "OE2" Residue "A GLU 997": "OE1" <-> "OE2" Residue "A ARG 1009": "NH1" <-> "NH2" Residue "A GLU 1033": "OE1" <-> "OE2" Residue "A ASP 1035": "OD1" <-> "OD2" Residue "A ARG 1042": "NH1" <-> "NH2" Residue "A ARG 1070": "NH1" <-> "NH2" Residue "A ARG 1074": "NH1" <-> "NH2" Residue "A ARG 1100": "NH1" <-> "NH2" Residue "A ASP 1105": "OD1" <-> "OD2" Residue "A GLU 1134": "OE1" <-> "OE2" Residue "A GLU 1163": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 8344 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8344 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1027, 8344 Classifications: {'peptide': 1027} Link IDs: {'PTRANS': 24, 'TRANS': 1002} Time building chain proxies: 5.03, per 1000 atoms: 0.60 Number of scatterers: 8344 At special positions: 0 Unit cell: (76.56, 89.61, 119.19, 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 13 16.00 O 1641 8.00 N 1439 7.00 C 5251 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: 2.93 Conformation dependent library (CDL) restraints added in 1.5 seconds 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1884 Finding SS restraints... Secondary structure from input PDB file: 4 helices and 17 sheets defined 2.8% alpha, 31.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.21 Creating SS restraints... Processing helix chain 'A' and resid 380 through 384 removed outlier: 3.590A pdb=" N SER A 383 " --> pdb=" O GLU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 1107 through 1112 Processing helix chain 'A' and resid 1139 through 1144 Processing helix chain 'A' and resid 1154 through 1165 Processing sheet with id=AA1, first strand: chain 'A' and resid 163 through 170 removed outlier: 6.677A pdb=" N TRP A 177 " --> pdb=" O ASP A 168 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 205 through 207 removed outlier: 4.363A pdb=" N SER A 216 " --> pdb=" O VAL A 207 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N ASP A 225 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 251 removed outlier: 5.891A pdb=" N CYS A 247 " --> pdb=" O THR A 258 " (cutoff:3.500A) removed outlier: 7.496A pdb=" N THR A 258 " --> pdb=" O CYS A 247 " (cutoff:3.500A) removed outlier: 5.598A pdb=" N PHE A 249 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 7.273A pdb=" N ILE A 256 " --> pdb=" O PHE A 249 " (cutoff:3.500A) removed outlier: 3.693A pdb=" N ASN A 251 " --> pdb=" O ILE A 254 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 290 through 291 removed outlier: 3.503A pdb=" N ARG A 290 " --> pdb=" O ILE A 298 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 300 through 302 removed outlier: 7.072A pdb=" N VAL A 300 " --> pdb=" O VAL A 307 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 305 " --> pdb=" O HIS A 302 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 334 through 335 removed outlier: 3.665A pdb=" N ILE A 334 " --> pdb=" O GLY A 343 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N GLY A 343 " --> pdb=" O ILE A 334 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'A' and resid 353 through 356 Processing sheet with id=AA8, first strand: chain 'A' and resid 376 through 377 removed outlier: 3.554A pdb=" N GLU A 376 " --> pdb=" O ILE A 387 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 400 through 402 removed outlier: 5.513A pdb=" N LEU A 428 " --> pdb=" O TRP A 440 " (cutoff:3.500A) removed outlier: 6.002A pdb=" N GLU A 449 " --> pdb=" O TYR A 461 " (cutoff:3.500A) removed outlier: 5.293A pdb=" N ILE A 470 " --> pdb=" O TYR A 482 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N GLN A 481 " --> pdb=" O VAL A 494 " (cutoff:3.500A) removed outlier: 6.382A pdb=" N VAL A 491 " --> pdb=" O ALA A 503 " (cutoff:3.500A) removed outlier: 7.453A pdb=" N LYS A 502 " --> pdb=" O ASP A 514 " (cutoff:3.500A) removed outlier: 5.237A pdb=" N ASP A 514 " --> pdb=" O LYS A 502 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 544 through 547 removed outlier: 6.464A pdb=" N ARG A 544 " --> pdb=" O HIS A 556 " (cutoff:3.500A) removed outlier: 4.273A pdb=" N HIS A 556 " --> pdb=" O ARG A 544 " (cutoff:3.500A) removed outlier: 6.573A pdb=" N TRP A 546 " --> pdb=" O VAL A 554 " (cutoff:3.500A) removed outlier: 5.779A pdb=" N VAL A 554 " --> pdb=" O TYR A 565 " (cutoff:3.500A) removed outlier: 5.531A pdb=" N ASN A 574 " --> pdb=" O ILE A 586 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N THR A 595 " --> pdb=" O TYR A 612 " (cutoff:3.500A) removed outlier: 5.446A pdb=" N ALA A 621 " --> pdb=" O TYR A 632 " (cutoff:3.500A) removed outlier: 5.498A pdb=" N THR A 662 " --> pdb=" O PHE A 674 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 696 through 697 removed outlier: 6.916A pdb=" N LYS A 696 " --> pdb=" O ILE A 704 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 716 through 717 removed outlier: 4.579A pdb=" N GLN A 724 " --> pdb=" O PHE A 739 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ILE A 726 " --> pdb=" O ASN A 737 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 758 through 763 removed outlier: 7.257A pdb=" N GLN A 758 " --> pdb=" O ARG A 770 " (cutoff:3.500A) removed outlier: 5.203A pdb=" N ARG A 770 " --> pdb=" O GLN A 758 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N GLN A 760 " --> pdb=" O THR A 768 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N SER A 762 " --> pdb=" O HIS A 766 " (cutoff:3.500A) removed outlier: 7.211A pdb=" N HIS A 766 " --> pdb=" O SER A 762 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'A' and resid 799 through 803 removed outlier: 6.049A pdb=" N ASP A 803 " --> pdb=" O LEU A 808 " (cutoff:3.500A) removed outlier: 6.424A pdb=" N LEU A 808 " --> pdb=" O ASP A 803 " (cutoff:3.500A) removed outlier: 11.855A pdb=" N ARG A 807 " --> pdb=" O TYR A 825 " (cutoff:3.500A) removed outlier: 9.374A pdb=" N TYR A 825 " --> pdb=" O ARG A 807 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N SER A 809 " --> pdb=" O PHE A 823 " (cutoff:3.500A) removed outlier: 3.586A pdb=" N PHE A 823 " --> pdb=" O SER A 809 " (cutoff:3.500A) removed outlier: 5.416A pdb=" N SER A 832 " --> pdb=" O LYS A 843 " (cutoff:3.500A) removed outlier: 3.947A pdb=" N GLU A 853 " --> pdb=" O LEU A 844 " (cutoff:3.500A) removed outlier: 5.729A pdb=" N VAL A 852 " --> pdb=" O TYR A 863 " (cutoff:3.500A) removed outlier: 5.510A pdb=" N SER A 872 " --> pdb=" O TYR A 884 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 880 " --> pdb=" O ASP A 876 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'A' and resid 918 through 919 removed outlier: 6.526A pdb=" N LYS A 918 " --> pdb=" O GLU A 925 " (cutoff:3.500A) removed outlier: 5.087A pdb=" N GLU A 925 " --> pdb=" O TYR A 932 " (cutoff:3.500A) removed outlier: 5.760A pdb=" N VAL A 961 " --> pdb=" O TYR A 972 " (cutoff:3.500A) removed outlier: 6.835A pdb=" N HIS A 971 " --> pdb=" O LYS A 983 " (cutoff:3.500A) removed outlier: 4.804A pdb=" N LYS A 983 " --> pdb=" O HIS A 971 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N GLU A 973 " --> pdb=" O THR A 981 " (cutoff:3.500A) removed outlier: 5.667A pdb=" N THR A 981 " --> pdb=" O PHE A 992 " (cutoff:3.500A) removed outlier: 6.714A pdb=" N GLU A 991 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 4.692A pdb=" N GLU A1002 " --> pdb=" O GLU A 991 " (cutoff:3.500A) removed outlier: 4.250A pdb=" N LEU A 993 " --> pdb=" O LEU A1000 " (cutoff:3.500A) removed outlier: 3.821A pdb=" N ARG A 998 " --> pdb=" O GLU A 995 " (cutoff:3.500A) removed outlier: 3.652A pdb=" N ARG A1009 " --> pdb=" O GLU A1002 " (cutoff:3.500A) removed outlier: 3.579A pdb=" N ARG A1042 " --> pdb=" O GLU A1033 " (cutoff:3.500A) removed outlier: 5.373A pdb=" N GLU A1041 " --> pdb=" O ALA A1054 " (cutoff:3.500A) removed outlier: 6.602A pdb=" N ASP A1045 " --> pdb=" O ILE A1050 " (cutoff:3.500A) removed outlier: 6.593A pdb=" N ILE A1050 " --> pdb=" O ASP A1045 " (cutoff:3.500A) removed outlier: 3.775A pdb=" N VAL A1066 " --> pdb=" O SER A1053 " (cutoff:3.500A) removed outlier: 7.206A pdb=" N SER A1055 " --> pdb=" O ILE A1064 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N ILE A1064 " --> pdb=" O SER A1055 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'A' and resid 1013 through 1014 removed outlier: 6.205A pdb=" N ILE A1019 " --> pdb=" O GLN A1014 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'A' and resid 1079 through 1081 removed outlier: 3.597A pdb=" N ARG A1100 " --> pdb=" O ASP A1095 " (cutoff:3.500A) 219 hydrogen bonds defined for protein. 582 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: 3.62 Time building geometry restraints manager: 3.20 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 2805 1.34 - 1.46: 2083 1.46 - 1.58: 3641 1.58 - 1.69: 0 1.69 - 1.81: 17 Bond restraints: 8546 Sorted by residual: bond pdb=" CA GLU A 271 " pdb=" C GLU A 271 " ideal model delta sigma weight residual 1.519 1.529 -0.009 1.01e-02 9.80e+03 8.60e-01 bond pdb=" CA ILE A1019 " pdb=" CB ILE A1019 " ideal model delta sigma weight residual 1.537 1.525 0.012 1.29e-02 6.01e+03 8.25e-01 bond pdb=" N THR A 332 " pdb=" CA THR A 332 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.42e-02 4.96e+03 6.85e-01 bond pdb=" N TYR A 242 " pdb=" CA TYR A 242 " ideal model delta sigma weight residual 1.460 1.471 -0.011 1.39e-02 5.18e+03 6.13e-01 bond pdb=" CA VAL A 735 " pdb=" C VAL A 735 " ideal model delta sigma weight residual 1.524 1.531 -0.007 1.01e-02 9.80e+03 5.14e-01 ... (remaining 8541 not shown) Histogram of bond angle deviations from ideal: 100.79 - 107.43: 208 107.43 - 114.07: 4533 114.07 - 120.71: 3431 120.71 - 127.34: 3310 127.34 - 133.98: 88 Bond angle restraints: 11570 Sorted by residual: angle pdb=" N CYS A 147 " pdb=" CA CYS A 147 " pdb=" C CYS A 147 " ideal model delta sigma weight residual 108.24 112.24 -4.00 1.32e+00 5.74e-01 9.20e+00 angle pdb=" C HIS A 302 " pdb=" N ASN A 303 " pdb=" CA ASN A 303 " ideal model delta sigma weight residual 121.54 127.26 -5.72 1.91e+00 2.74e-01 8.98e+00 angle pdb=" N SER A 216 " pdb=" CA SER A 216 " pdb=" C SER A 216 " ideal model delta sigma weight residual 108.32 112.95 -4.63 1.64e+00 3.72e-01 7.98e+00 angle pdb=" N ASP A 397 " pdb=" CA ASP A 397 " pdb=" C ASP A 397 " ideal model delta sigma weight residual 107.93 111.54 -3.61 1.65e+00 3.67e-01 4.80e+00 angle pdb=" CA VAL A 319 " pdb=" C VAL A 319 " pdb=" N GLU A 320 " ideal model delta sigma weight residual 116.60 119.55 -2.95 1.45e+00 4.76e-01 4.14e+00 ... (remaining 11565 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 4587 17.86 - 35.71: 329 35.71 - 53.57: 58 53.57 - 71.43: 18 71.43 - 89.29: 6 Dihedral angle restraints: 4998 sinusoidal: 2018 harmonic: 2980 Sorted by residual: dihedral pdb=" CA LYS A 304 " pdb=" C LYS A 304 " pdb=" N ARG A 305 " pdb=" CA ARG A 305 " ideal model delta harmonic sigma weight residual -180.00 -160.03 -19.97 0 5.00e+00 4.00e-02 1.60e+01 dihedral pdb=" CB GLU A 429 " pdb=" CG GLU A 429 " pdb=" CD GLU A 429 " pdb=" OE1 GLU A 429 " ideal model delta sinusoidal sigma weight residual 0.00 -89.29 89.29 1 3.00e+01 1.11e-03 1.05e+01 dihedral pdb=" CA ASN A 303 " pdb=" C ASN A 303 " pdb=" N LYS A 304 " pdb=" CA LYS A 304 " ideal model delta harmonic sigma weight residual 180.00 164.26 15.74 0 5.00e+00 4.00e-02 9.91e+00 ... (remaining 4995 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 705 0.027 - 0.054: 322 0.054 - 0.081: 61 0.081 - 0.108: 68 0.108 - 0.135: 30 Chirality restraints: 1186 Sorted by residual: chirality pdb=" CA THR A 332 " pdb=" N THR A 332 " pdb=" C THR A 332 " pdb=" CB THR A 332 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.55e-01 chirality pdb=" CA ILE A 726 " pdb=" N ILE A 726 " pdb=" C ILE A 726 " pdb=" CB ILE A 726 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.11e-01 chirality pdb=" CA ILE A 597 " pdb=" N ILE A 597 " pdb=" C ILE A 597 " pdb=" CB ILE A 597 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 3.94e-01 ... (remaining 1183 not shown) Planarity restraints: 1528 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C ASN A 251 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.14e+00 pdb=" N PRO A 252 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A 252 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A 252 " 0.020 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PHE A 453 " 0.023 5.00e-02 4.00e+02 3.42e-02 1.87e+00 pdb=" N PRO A 454 " -0.059 5.00e-02 4.00e+02 pdb=" CA PRO A 454 " 0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 454 " 0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLN A1014 " 0.019 5.00e-02 4.00e+02 2.82e-02 1.27e+00 pdb=" N PRO A1015 " -0.049 5.00e-02 4.00e+02 pdb=" CA PRO A1015 " 0.014 5.00e-02 4.00e+02 pdb=" CD PRO A1015 " 0.016 5.00e-02 4.00e+02 ... (remaining 1525 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1165 2.76 - 3.30: 7163 3.30 - 3.83: 12974 3.83 - 4.37: 15555 4.37 - 4.90: 27797 Nonbonded interactions: 64654 Sorted by model distance: nonbonded pdb=" O SER A 587 " pdb=" OG1 THR A 595 " model vdw 2.226 2.440 nonbonded pdb=" OG1 THR A 742 " pdb=" O GLY A 745 " model vdw 2.246 2.440 nonbonded pdb=" O ILE A 871 " pdb=" OH TYR A 886 " model vdw 2.265 2.440 nonbonded pdb=" O THR A 796 " pdb=" OG SER A 814 " model vdw 2.287 2.440 nonbonded pdb=" O GLY A 938 " pdb=" OH TYR A1116 " model vdw 2.317 2.440 ... (remaining 64649 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=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.310 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: 4.240 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 26.940 Find NCS groups from input model: 0.240 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: 0.000 Load rotamer database and sin/cos tables:2.610 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.610 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7368 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 : 0.001 0.016 8546 Z= 0.096 Angle : 0.457 8.138 11570 Z= 0.276 Chirality : 0.040 0.135 1186 Planarity : 0.002 0.037 1528 Dihedral : 12.997 89.286 3114 Min Nonbonded Distance : 2.226 Molprobity Statistics. All-atom Clashscore : 6.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.34 % Favored : 93.66 % Rotamer: Outliers : 0.67 % Allowed : 6.86 % Favored : 92.46 % 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: -2.99 (0.23), residues: 1025 helix: -1.91 (1.51), residues: 12 sheet: -0.79 (0.37), residues: 188 loop : -2.52 (0.18), residues: 825 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 438 HIS 0.004 0.000 HIS A 444 PHE 0.006 0.000 PHE A 267 TYR 0.009 0.001 TYR A 242 ARG 0.001 0.000 ARG A 979 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 160 time to evaluate : 1.066 Fit side-chains REVERT: A 226 GLU cc_start: 0.5483 (pt0) cc_final: 0.5206 (pt0) REVERT: A 228 GLU cc_start: 0.7729 (mm-30) cc_final: 0.7265 (mm-30) REVERT: A 403 GLU cc_start: 0.6716 (tp30) cc_final: 0.6347 (mm-30) REVERT: A 918 LYS cc_start: 0.7893 (tttt) cc_final: 0.7538 (tttp) REVERT: A 924 ILE cc_start: 0.8365 (mp) cc_final: 0.8132 (mt) outliers start: 6 outliers final: 3 residues processed: 166 average time/residue: 0.2595 time to fit residues: 56.1694 Evaluate side-chains 92 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 89 time to evaluate : 0.903 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 1170 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 3.9990 chunk 77 optimal weight: 7.9990 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 8.9990 chunk 52 optimal weight: 7.9990 chunk 41 optimal weight: 0.9980 chunk 79 optimal weight: 5.9990 chunk 30 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 3.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 ASN A 264 GLN A 421 HIS A 456 ASN A 529 HIS A 585 GLN A 622 GLN A 633 GLN A 639 GLN A 737 ASN A 760 GLN A 772 GLN A 799 ASN ** A 854 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 855 GLN A 937 GLN A 959 GLN A1082 GLN A1089 ASN A1148 GLN A1160 GLN Total number of N/Q/H flips: 20 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7969 moved from start: 0.3344 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.060 8546 Z= 0.364 Angle : 0.681 15.554 11570 Z= 0.355 Chirality : 0.048 0.165 1186 Planarity : 0.005 0.043 1528 Dihedral : 5.048 31.077 1159 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.22 % Favored : 88.78 % Rotamer: Outliers : 3.04 % Allowed : 11.70 % Favored : 85.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.24), residues: 1025 helix: -1.12 (1.45), residues: 13 sheet: -0.35 (0.34), residues: 237 loop : -2.29 (0.20), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP A 856 HIS 0.009 0.002 HIS A 556 PHE 0.029 0.002 PHE A1075 TYR 0.023 0.002 TYR A1094 ARG 0.004 0.001 ARG A 770 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 105 time to evaluate : 0.986 Fit side-chains REVERT: A 228 GLU cc_start: 0.7673 (mm-30) cc_final: 0.7337 (mm-30) REVERT: A 487 LEU cc_start: 0.8559 (mm) cc_final: 0.8236 (mm) REVERT: A 508 LEU cc_start: 0.8751 (mt) cc_final: 0.8531 (mp) REVERT: A 658 GLN cc_start: 0.8129 (mm-40) cc_final: 0.7866 (tp40) REVERT: A 783 ARG cc_start: 0.7783 (ptt90) cc_final: 0.7562 (ttp-110) REVERT: A 918 LYS cc_start: 0.8035 (tttt) cc_final: 0.7743 (ttmm) outliers start: 27 outliers final: 16 residues processed: 123 average time/residue: 0.1935 time to fit residues: 33.6494 Evaluate side-chains 100 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 84 time to evaluate : 0.971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 625 THR Chi-restraints excluded: chain A residue 768 THR Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1004 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 0.4980 chunk 28 optimal weight: 4.9990 chunk 77 optimal weight: 7.9990 chunk 63 optimal weight: 0.8980 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.4980 chunk 100 optimal weight: 4.9990 chunk 82 optimal weight: 4.9990 chunk 31 optimal weight: 0.9990 chunk 74 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 854 GLN A 868 GLN A 937 GLN A1121 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.3398 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8546 Z= 0.189 Angle : 0.574 14.401 11570 Z= 0.295 Chirality : 0.044 0.163 1186 Planarity : 0.003 0.041 1528 Dihedral : 4.706 30.745 1158 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.07 % Favored : 90.93 % Rotamer: Outliers : 2.36 % Allowed : 14.85 % Favored : 82.79 % 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: -2.17 (0.25), residues: 1025 helix: -0.51 (1.52), residues: 13 sheet: -0.12 (0.35), residues: 236 loop : -2.07 (0.20), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 177 HIS 0.004 0.001 HIS A 650 PHE 0.011 0.001 PHE A 229 TYR 0.014 0.001 TYR A1094 ARG 0.003 0.000 ARG A 931 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 117 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 96 time to evaluate : 1.062 Fit side-chains REVERT: A 226 GLU cc_start: 0.6016 (OUTLIER) cc_final: 0.5691 (pt0) REVERT: A 487 LEU cc_start: 0.8614 (mm) cc_final: 0.8297 (mm) REVERT: A 783 ARG cc_start: 0.7746 (ptt90) cc_final: 0.7531 (ttp-110) REVERT: A 918 LYS cc_start: 0.7890 (tttt) cc_final: 0.7605 (ttmm) outliers start: 21 outliers final: 13 residues processed: 114 average time/residue: 0.1853 time to fit residues: 30.6056 Evaluate side-chains 97 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.962 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1132 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 10 optimal weight: 3.9990 chunk 44 optimal weight: 0.7980 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 82 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7980 moved from start: 0.3760 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 8546 Z= 0.228 Angle : 0.594 15.131 11570 Z= 0.305 Chirality : 0.045 0.159 1186 Planarity : 0.003 0.043 1528 Dihedral : 4.880 32.961 1158 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.61 % Favored : 88.39 % Rotamer: Outliers : 2.70 % Allowed : 15.75 % Favored : 81.55 % 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: -2.09 (0.25), residues: 1025 helix: -0.28 (1.55), residues: 13 sheet: 0.03 (0.35), residues: 235 loop : -2.05 (0.20), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 513 HIS 0.004 0.001 HIS A 766 PHE 0.016 0.001 PHE A1075 TYR 0.017 0.001 TYR A1094 ARG 0.003 0.000 ARG A 659 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 85 time to evaluate : 1.089 Fit side-chains REVERT: A 918 LYS cc_start: 0.7827 (tttt) cc_final: 0.7548 (ttmm) outliers start: 24 outliers final: 16 residues processed: 105 average time/residue: 0.1741 time to fit residues: 27.6760 Evaluate side-chains 94 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 78 time to evaluate : 1.015 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 5.9990 chunk 40 optimal weight: 2.9990 chunk 84 optimal weight: 3.9990 chunk 68 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 50 optimal weight: 3.9990 chunk 88 optimal weight: 5.9990 chunk 24 optimal weight: 10.0000 chunk 33 optimal weight: 2.9990 chunk 19 optimal weight: 7.9990 overall best weight: 3.7990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 234 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.4499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.083 8546 Z= 0.519 Angle : 0.782 16.828 11570 Z= 0.406 Chirality : 0.051 0.185 1186 Planarity : 0.005 0.050 1528 Dihedral : 5.954 35.618 1158 Min Nonbonded Distance : 2.157 Molprobity Statistics. All-atom Clashscore : 9.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.98 % Favored : 87.02 % Rotamer: Outliers : 3.82 % Allowed : 17.21 % Favored : 78.97 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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 (0.24), residues: 1025 helix: -0.62 (1.38), residues: 12 sheet: -0.49 (0.34), residues: 254 loop : -2.18 (0.20), residues: 759 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP A 513 HIS 0.009 0.002 HIS A 766 PHE 0.026 0.002 PHE A1075 TYR 0.020 0.002 TYR A1094 ARG 0.004 0.001 ARG A 952 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 82 time to evaluate : 0.985 Fit side-chains REVERT: A 149 GLU cc_start: 0.5904 (pm20) cc_final: 0.5367 (pm20) REVERT: A 226 GLU cc_start: 0.6330 (OUTLIER) cc_final: 0.6005 (pt0) REVERT: A 240 GLN cc_start: 0.7988 (OUTLIER) cc_final: 0.7725 (tp40) REVERT: A 918 LYS cc_start: 0.7894 (tttt) cc_final: 0.7609 (ttmm) REVERT: A 943 ARG cc_start: 0.8192 (tmm-80) cc_final: 0.7490 (ttp-170) outliers start: 34 outliers final: 22 residues processed: 109 average time/residue: 0.1944 time to fit residues: 30.3832 Evaluate side-chains 99 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 75 time to evaluate : 1.072 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 226 GLU Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 307 VAL Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 629 VAL Chi-restraints excluded: chain A residue 658 GLN Chi-restraints excluded: chain A residue 662 THR Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 776 GLU Chi-restraints excluded: chain A residue 798 PHE Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 958 SER Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1084 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 2.9990 chunk 24 optimal weight: 7.9990 chunk 98 optimal weight: 0.6980 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 0.5980 chunk 8 optimal weight: 10.0000 chunk 32 optimal weight: 0.8980 chunk 51 optimal weight: 2.9990 chunk 95 optimal weight: 0.9980 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7975 moved from start: 0.4127 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8546 Z= 0.158 Angle : 0.584 14.362 11570 Z= 0.299 Chirality : 0.044 0.158 1186 Planarity : 0.003 0.048 1528 Dihedral : 4.971 32.895 1158 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.85 % Favored : 90.15 % Rotamer: Outliers : 2.02 % Allowed : 19.46 % Favored : 78.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.06 (0.25), residues: 1025 helix: 0.09 (1.59), residues: 13 sheet: 0.15 (0.36), residues: 223 loop : -2.04 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 513 HIS 0.004 0.001 HIS A 198 PHE 0.011 0.001 PHE A 954 TYR 0.013 0.001 TYR A1094 ARG 0.003 0.000 ARG A 783 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 1.075 Fit side-chains REVERT: A 943 ARG cc_start: 0.8092 (tmm-80) cc_final: 0.7412 (ttp-170) outliers start: 18 outliers final: 16 residues processed: 106 average time/residue: 0.2047 time to fit residues: 30.8704 Evaluate side-chains 97 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 81 time to evaluate : 1.157 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Chi-restraints excluded: chain A residue 1105 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 5.9990 chunk 55 optimal weight: 4.9990 chunk 83 optimal weight: 4.9990 chunk 98 optimal weight: 0.0000 chunk 61 optimal weight: 5.9990 chunk 59 optimal weight: 0.9980 chunk 45 optimal weight: 6.9990 chunk 60 optimal weight: 0.9980 chunk 39 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 overall best weight: 0.7984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 198 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7963 moved from start: 0.4081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.032 8546 Z= 0.151 Angle : 0.570 14.097 11570 Z= 0.293 Chirality : 0.044 0.155 1186 Planarity : 0.003 0.044 1528 Dihedral : 4.748 34.064 1158 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 6.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.54 % Favored : 89.46 % Rotamer: Outliers : 2.70 % Allowed : 19.01 % Favored : 78.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.88 (0.25), residues: 1025 helix: 0.26 (1.63), residues: 13 sheet: 0.33 (0.37), residues: 223 loop : -1.92 (0.20), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 513 HIS 0.007 0.001 HIS A 234 PHE 0.010 0.001 PHE A1075 TYR 0.013 0.001 TYR A1094 ARG 0.002 0.000 ARG A 840 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 88 time to evaluate : 1.076 Fit side-chains REVERT: A 240 GLN cc_start: 0.7727 (OUTLIER) cc_final: 0.7347 (tm-30) REVERT: A 390 PHE cc_start: 0.6715 (OUTLIER) cc_final: 0.6331 (m-80) REVERT: A 943 ARG cc_start: 0.8082 (tmm-80) cc_final: 0.7412 (ttp-170) outliers start: 24 outliers final: 17 residues processed: 107 average time/residue: 0.1889 time to fit residues: 29.1200 Evaluate side-chains 99 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 6.9990 chunk 62 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 48 optimal weight: 4.9990 chunk 9 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 chunk 89 optimal weight: 2.9990 chunk 94 optimal weight: 4.9990 chunk 85 optimal weight: 4.9990 chunk 91 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 3.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8096 moved from start: 0.4671 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.078 8546 Z= 0.471 Angle : 0.752 16.745 11570 Z= 0.389 Chirality : 0.050 0.188 1186 Planarity : 0.005 0.051 1528 Dihedral : 5.834 34.870 1158 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 8.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.27 % Favored : 86.73 % Rotamer: Outliers : 2.92 % Allowed : 19.91 % Favored : 77.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -2.22 (0.25), residues: 1025 helix: -0.54 (1.43), residues: 13 sheet: -0.26 (0.35), residues: 243 loop : -2.08 (0.20), residues: 769 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 513 HIS 0.008 0.002 HIS A 766 PHE 0.024 0.002 PHE A1075 TYR 0.020 0.002 TYR A1094 ARG 0.005 0.001 ARG A 952 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 76 time to evaluate : 0.949 Fit side-chains REVERT: A 240 GLN cc_start: 0.7996 (OUTLIER) cc_final: 0.7758 (tp40) REVERT: A 943 ARG cc_start: 0.8151 (tmm-80) cc_final: 0.7520 (ttp-170) REVERT: A 1002 GLU cc_start: 0.8079 (OUTLIER) cc_final: 0.7813 (pm20) outliers start: 26 outliers final: 22 residues processed: 98 average time/residue: 0.1850 time to fit residues: 26.1241 Evaluate side-chains 100 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 76 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 165 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 214 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 263 ASP Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 506 ASN Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 704 ILE Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 967 SER Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 4.9990 chunk 71 optimal weight: 0.6980 chunk 28 optimal weight: 1.9990 chunk 82 optimal weight: 0.9980 chunk 86 optimal weight: 0.9980 chunk 91 optimal weight: 0.7980 chunk 60 optimal weight: 0.0870 chunk 96 optimal weight: 3.9990 chunk 59 optimal weight: 0.7980 chunk 45 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN ** A 234 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 479 GLN A 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7967 moved from start: 0.4299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8546 Z= 0.143 Angle : 0.582 14.434 11570 Z= 0.300 Chirality : 0.044 0.158 1186 Planarity : 0.003 0.047 1528 Dihedral : 4.984 33.020 1158 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.37 % Favored : 90.63 % Rotamer: Outliers : 2.02 % Allowed : 20.92 % Favored : 77.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % 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: -1.94 (0.25), residues: 1025 helix: 0.18 (1.56), residues: 13 sheet: 0.21 (0.37), residues: 222 loop : -1.94 (0.20), residues: 790 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 513 HIS 0.006 0.001 HIS A 234 PHE 0.010 0.001 PHE A 798 TYR 0.014 0.001 TYR A 591 ARG 0.002 0.000 ARG A 931 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 86 time to evaluate : 0.993 Fit side-chains REVERT: A 240 GLN cc_start: 0.7805 (OUTLIER) cc_final: 0.7600 (tp40) REVERT: A 388 ARG cc_start: 0.8168 (tpt170) cc_final: 0.7949 (tpt170) REVERT: A 658 GLN cc_start: 0.7907 (mt0) cc_final: 0.7670 (mp10) REVERT: A 943 ARG cc_start: 0.8082 (tmm-80) cc_final: 0.7438 (ttp-170) REVERT: A 1002 GLU cc_start: 0.8040 (OUTLIER) cc_final: 0.7832 (pm20) outliers start: 18 outliers final: 15 residues processed: 101 average time/residue: 0.1927 time to fit residues: 27.9671 Evaluate side-chains 98 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 81 time to evaluate : 1.022 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 725 HIS Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 0.7980 chunk 93 optimal weight: 0.8980 chunk 80 optimal weight: 2.9990 chunk 8 optimal weight: 9.9990 chunk 62 optimal weight: 5.9990 chunk 49 optimal weight: 20.0000 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 0.9990 chunk 24 optimal weight: 10.0000 chunk 74 optimal weight: 3.9990 chunk 11 optimal weight: 3.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 234 HIS A 479 GLN A 481 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8038 moved from start: 0.4454 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 8546 Z= 0.282 Angle : 0.648 15.728 11570 Z= 0.333 Chirality : 0.046 0.174 1186 Planarity : 0.004 0.048 1528 Dihedral : 5.267 34.562 1158 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.80 % Favored : 88.20 % Rotamer: Outliers : 2.14 % Allowed : 20.92 % Favored : 76.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.97 (0.25), residues: 1025 helix: -0.07 (1.54), residues: 13 sheet: 0.03 (0.36), residues: 234 loop : -1.93 (0.21), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 513 HIS 0.005 0.001 HIS A 198 PHE 0.017 0.002 PHE A1075 TYR 0.017 0.001 TYR A1094 ARG 0.003 0.000 ARG A 952 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2050 Ramachandran restraints generated. 1025 Oldfield, 0 Emsley, 1025 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 79 time to evaluate : 1.083 Fit side-chains REVERT: A 240 GLN cc_start: 0.7931 (OUTLIER) cc_final: 0.7663 (tp40) REVERT: A 943 ARG cc_start: 0.8094 (tmm-80) cc_final: 0.7459 (ttp-170) REVERT: A 1002 GLU cc_start: 0.8076 (OUTLIER) cc_final: 0.7852 (pm20) REVERT: A 1143 MET cc_start: 0.7262 (mtp) cc_final: 0.7044 (mtp) outliers start: 19 outliers final: 16 residues processed: 97 average time/residue: 0.1915 time to fit residues: 26.7323 Evaluate side-chains 95 residues out of total 889 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 THR Chi-restraints excluded: chain A residue 167 ASN Chi-restraints excluded: chain A residue 169 VAL Chi-restraints excluded: chain A residue 234 HIS Chi-restraints excluded: chain A residue 240 GLN Chi-restraints excluded: chain A residue 362 ILE Chi-restraints excluded: chain A residue 372 THR Chi-restraints excluded: chain A residue 470 ILE Chi-restraints excluded: chain A residue 487 LEU Chi-restraints excluded: chain A residue 491 VAL Chi-restraints excluded: chain A residue 493 THR Chi-restraints excluded: chain A residue 606 VAL Chi-restraints excluded: chain A residue 804 THR Chi-restraints excluded: chain A residue 997 GLU Chi-restraints excluded: chain A residue 1002 GLU Chi-restraints excluded: chain A residue 1017 THR Chi-restraints excluded: chain A residue 1037 VAL Chi-restraints excluded: chain A residue 1066 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.2980 chunk 81 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 83 optimal weight: 0.0670 chunk 10 optimal weight: 1.9990 chunk 14 optimal weight: 0.7980 chunk 71 optimal weight: 0.9990 chunk 4 optimal weight: 0.0060 chunk 58 optimal weight: 2.9990 chunk 92 optimal weight: 3.9990 chunk 54 optimal weight: 0.7980 overall best weight: 0.3934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 ASN A 234 HIS A 479 GLN A 481 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.151857 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3600 r_free = 0.3600 target = 0.132542 restraints weight = 10905.505| |-----------------------------------------------------------------------------| r_work (start): 0.3612 rms_B_bonded: 2.22 r_work: 0.3505 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.3365 rms_B_bonded: 4.75 restraints_weight: 0.2500 r_work (final): 0.3365 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.4145 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8546 Z= 0.127 Angle : 0.565 13.852 11570 Z= 0.290 Chirality : 0.043 0.157 1186 Planarity : 0.003 0.044 1528 Dihedral : 4.708 33.372 1158 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.27 % Favored : 90.73 % Rotamer: Outliers : 2.14 % Allowed : 21.15 % Favored : 76.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.80 (0.25), residues: 1025 helix: 0.44 (1.64), residues: 13 sheet: 0.35 (0.37), residues: 223 loop : -1.86 (0.21), residues: 789 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 438 HIS 0.005 0.001 HIS A 234 PHE 0.010 0.001 PHE A 954 TYR 0.013 0.001 TYR A 591 ARG 0.002 0.000 ARG A 931 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2108.69 seconds wall clock time: 38 minutes 55.39 seconds (2335.39 seconds total)