Starting phenix.real_space_refine (version: 1.21rc1) on Thu Aug 10 16:28:08 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/08_2023/6xms_22262_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/08_2023/6xms_22262.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/08_2023/6xms_22262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/08_2023/6xms_22262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/08_2023/6xms_22262_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/08_2023/6xms_22262_updated.pdb" } resolution = 3.4 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= 0.001 sd= 0.043 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: 7 Type Number sf(0) Gaussians Al 1 5.89 5 Mg 1 5.21 5 S 38 5.16 5 C 5434 2.51 5 N 1374 2.21 5 O 1537 1.98 5 F 4 1.80 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A ARG 13": "NH1" <-> "NH2" Residue "A TYR 87": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 175": "NH1" <-> "NH2" Residue "A GLU 179": "OE1" <-> "OE2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A GLU 271": "OE1" <-> "OE2" Residue "A ARG 282": "NH1" <-> "NH2" Residue "A GLU 285": "OE1" <-> "OE2" Residue "A ARG 322": "NH1" <-> "NH2" Residue "A ARG 383": "NH1" <-> "NH2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A GLU 510": "OE1" <-> "OE2" Residue "A ARG 513": "NH1" <-> "NH2" Residue "A GLU 523": "OE1" <-> "OE2" Residue "A ARG 579": "NH1" <-> "NH2" Residue "A ARG 588": "NH1" <-> "NH2" Residue "A ARG 611": "NH1" <-> "NH2" Residue "A ARG 656": "NH1" <-> "NH2" Residue "A ARG 692": "NH1" <-> "NH2" Residue "A ARG 723": "NH1" <-> "NH2" Residue "A ARG 735": "NH1" <-> "NH2" Residue "A ARG 760": "NH1" <-> "NH2" Residue "A ARG 791": "NH1" <-> "NH2" Residue "A GLU 839": "OE1" <-> "OE2" Residue "A GLU 1042": "OE1" <-> "OE2" Residue "A GLU 1079": "OE1" <-> "OE2" Residue "A ARG 1086": "NH1" <-> "NH2" Residue "A GLU 1087": "OE1" <-> "OE2" Residue "A GLU 1093": "OE1" <-> "OE2" Residue "A ARG 1127": "NH1" <-> "NH2" Residue "A GLU 1157": "OE1" <-> "OE2" Residue "A GLU 1190": "OE1" <-> "OE2" Residue "A PHE 1197": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/modules/chem_data/mon_lib" Total number of atoms: 8389 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 8389 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1093, 8389 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 1091, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 47} Link IDs: {'PTRANS': 48, 'TRANS': 1042, None: 2} Not linked: pdbres="LYS A1211 " pdbres=" MG A1301 " Not linked: pdbres=" MG A1301 " pdbres="ALF A1302 " Chain breaks: 3 Unresolved non-hydrogen bonds: 185 Unresolved non-hydrogen angles: 226 Unresolved non-hydrogen dihedrals: 149 Unresolved non-hydrogen chiralities: 4 Planarities with less than four sites: {'GLN:plan1': 4, 'TYR:plan': 1, 'ASN:plan1': 3, 'ASP:plan': 8, 'PHE:plan': 1, 'GLU:plan': 11, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 136 Time building chain proxies: 4.71, per 1000 atoms: 0.56 Number of scatterers: 8389 At special positions: 0 Unit cell: (82.8, 95.4, 135.9, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 38 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1537 8.00 N 1374 7.00 C 5434 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: 3.13 Conformation dependent library (CDL) restraints added in 1.4 seconds 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2052 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 10 sheets defined 42.3% alpha, 10.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.09 Creating SS restraints... Processing helix chain 'A' and resid 23 through 25 No H-bonds generated for 'chain 'A' and resid 23 through 25' Processing helix chain 'A' and resid 33 through 43 Processing helix chain 'A' and resid 58 through 76 Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 80 through 85 Processing helix chain 'A' and resid 157 through 162 Processing helix chain 'A' and resid 171 through 177 Processing helix chain 'A' and resid 189 through 196 removed outlier: 4.073A pdb=" N GLU A 195 " --> pdb=" O GLU A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 200 through 214 Processing helix chain 'A' and resid 218 through 249 removed outlier: 3.977A pdb=" N ALA A 242 " --> pdb=" O GLN A 238 " (cutoff:3.500A) removed outlier: 3.777A pdb=" N LEU A 243 " --> pdb=" O ARG A 239 " (cutoff:3.500A) removed outlier: 4.356A pdb=" N THR A 248 " --> pdb=" O LYS A 244 " (cutoff:3.500A) removed outlier: 4.750A pdb=" N MET A 249 " --> pdb=" O GLU A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 305 through 308 No H-bonds generated for 'chain 'A' and resid 305 through 308' Processing helix chain 'A' and resid 333 through 337 removed outlier: 4.437A pdb=" N ILE A 336 " --> pdb=" O VAL A 333 " (cutoff:3.500A) removed outlier: 3.840A pdb=" N ALA A 337 " --> pdb=" O ASP A 334 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 333 through 337' Processing helix chain 'A' and resid 373 through 375 No H-bonds generated for 'chain 'A' and resid 373 through 375' Processing helix chain 'A' and resid 377 through 386 removed outlier: 3.643A pdb=" N LEU A 381 " --> pdb=" O SER A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 397 through 423 removed outlier: 4.002A pdb=" N TYR A 416 " --> pdb=" O ILE A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 442 Processing helix chain 'A' and resid 450 through 465 removed outlier: 4.176A pdb=" N PHE A 465 " --> pdb=" O ALA A 461 " (cutoff:3.500A) Processing helix chain 'A' and resid 472 through 474 No H-bonds generated for 'chain 'A' and resid 472 through 474' Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 523 through 531 Processing helix chain 'A' and resid 547 through 556 Processing helix chain 'A' and resid 607 through 611 Processing helix chain 'A' and resid 621 through 629 removed outlier: 3.862A pdb=" N TYR A 625 " --> pdb=" O TYR A 621 " (cutoff:3.500A) removed outlier: 3.927A pdb=" N LYS A 626 " --> pdb=" O ASP A 622 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 659 No H-bonds generated for 'chain 'A' and resid 656 through 659' Processing helix chain 'A' and resid 679 through 688 Processing helix chain 'A' and resid 701 through 711 Processing helix chain 'A' and resid 754 through 761 removed outlier: 4.633A pdb=" N ASP A 759 " --> pdb=" O SER A 755 " (cutoff:3.500A) removed outlier: 5.535A pdb=" N ARG A 760 " --> pdb=" O LYS A 756 " (cutoff:3.500A) Processing helix chain 'A' and resid 767 through 772 Processing helix chain 'A' and resid 779 through 782 No H-bonds generated for 'chain 'A' and resid 779 through 782' Processing helix chain 'A' and resid 794 through 806 removed outlier: 4.268A pdb=" N GLU A 798 " --> pdb=" O PRO A 794 " (cutoff:3.500A) removed outlier: 3.559A pdb=" N PHE A 799 " --> pdb=" O SER A 795 " (cutoff:3.500A) Processing helix chain 'A' and resid 818 through 826 removed outlier: 4.001A pdb=" N VAL A 821 " --> pdb=" O THR A 818 " (cutoff:3.500A) removed outlier: 5.468A pdb=" N GLY A 822 " --> pdb=" O ASN A 819 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N ALA A 823 " --> pdb=" O ASP A 820 " (cutoff:3.500A) Processing helix chain 'A' and resid 838 through 850 Processing helix chain 'A' and resid 955 through 957 No H-bonds generated for 'chain 'A' and resid 955 through 957' Processing helix chain 'A' and resid 971 through 1011 removed outlier: 3.792A pdb=" N MET A1011 " --> pdb=" O ILE A1008 " (cutoff:3.500A) Processing helix chain 'A' and resid 1019 through 1035 removed outlier: 3.925A pdb=" N CYS A1031 " --> pdb=" O LEU A1027 " (cutoff:3.500A) removed outlier: 3.624A pdb=" N SER A1034 " --> pdb=" O VAL A1030 " (cutoff:3.500A) Processing helix chain 'A' and resid 1056 through 1083 Processing helix chain 'A' and resid 1100 through 1119 removed outlier: 3.621A pdb=" N VAL A1114 " --> pdb=" O LEU A1110 " (cutoff:3.500A) Processing helix chain 'A' and resid 1134 through 1151 removed outlier: 4.113A pdb=" N GLY A1139 " --> pdb=" O GLY A1135 " (cutoff:3.500A) Processing helix chain 'A' and resid 1156 through 1161 Processing helix chain 'A' and resid 1169 through 1197 removed outlier: 4.180A pdb=" N ILE A1173 " --> pdb=" O ASP A1169 " (cutoff:3.500A) removed outlier: 3.712A pdb=" N LYS A1174 " --> pdb=" O ASP A1170 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N PHE A1184 " --> pdb=" O LEU A1180 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 6 through 8 Processing sheet with id= B, first strand: chain 'A' and resid 111 through 113 removed outlier: 3.817A pdb=" N HIS A 98 " --> pdb=" O LEU A 18 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N THR A 16 " --> pdb=" O LEU A 100 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'A' and resid 256 through 260 removed outlier: 3.549A pdb=" N LEU A 267 " --> pdb=" O ILE A 256 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 277 through 280 removed outlier: 6.994A pdb=" N ASP A 292 " --> pdb=" O THR A 370 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 467 through 469 Processing sheet with id= F, first strand: chain 'A' and resid 692 through 695 removed outlier: 6.934A pdb=" N VAL A 829 " --> pdb=" O MET A 813 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 497 through 501 removed outlier: 3.503A pdb=" N VAL A 498 " --> pdb=" O HIS A 672 " (cutoff:3.500A) removed outlier: 7.337A pdb=" N ILE A 670 " --> pdb=" O GLU A 500 " (cutoff:3.500A) removed outlier: 6.506A pdb=" N LEU A 638 " --> pdb=" O ASN A 666 " (cutoff:3.500A) removed outlier: 4.520A pdb=" N PHE A 668 " --> pdb=" O LEU A 636 " (cutoff:3.500A) removed outlier: 6.306A pdb=" N LEU A 636 " --> pdb=" O PHE A 668 " (cutoff:3.500A) removed outlier: 4.785A pdb=" N ILE A 670 " --> pdb=" O ARG A 634 " (cutoff:3.500A) removed outlier: 6.211A pdb=" N ARG A 634 " --> pdb=" O ILE A 670 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 605 " --> pdb=" O ALA A 637 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N LYS A 641 " --> pdb=" O ALA A 601 " (cutoff:3.500A) removed outlier: 3.794A pdb=" N PHE A 600 " --> pdb=" O ALA A 593 " (cutoff:3.500A) removed outlier: 3.580A pdb=" N ARG A 578 " --> pdb=" O ILE A 592 " (cutoff:3.500A) removed outlier: 7.090A pdb=" N SER A 594 " --> pdb=" O ILE A 576 " (cutoff:3.500A) removed outlier: 6.014A pdb=" N ILE A 576 " --> pdb=" O SER A 594 " (cutoff:3.500A) Processing sheet with id= H, first strand: chain 'A' and resid 719 through 723 removed outlier: 3.543A pdb=" N PHE A 745 " --> pdb=" O LEU A 732 " (cutoff:3.500A) Processing sheet with id= I, first strand: chain 'A' and resid 764 through 766 removed outlier: 6.296A pdb=" N VAL A 788 " --> pdb=" O VAL A 765 " (cutoff:3.500A) No H-bonds generated for sheet with id= I Processing sheet with id= J, first strand: chain 'A' and resid 299 through 303 removed outlier: 3.532A pdb=" N SER A 299 " --> pdb=" O THR A 349 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLN A 347 " --> pdb=" O ILE A 301 " (cutoff:3.500A) removed outlier: 6.776A pdb=" N ASN A 303 " --> pdb=" O ALA A 345 " (cutoff:3.500A) removed outlier: 6.089A pdb=" N ALA A 345 " --> pdb=" O ASN A 303 " (cutoff:3.500A) 339 hydrogen bonds defined for protein. 882 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.90 Time building geometry restraints manager: 3.33 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: 2661 1.34 - 1.46: 1456 1.46 - 1.57: 4384 1.57 - 1.69: 0 1.69 - 1.81: 67 Bond restraints: 8568 Sorted by residual: bond pdb=" F1 ALF A1302 " pdb="AL ALF A1302 " ideal model delta sigma weight residual 1.684 1.781 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" F2 ALF A1302 " pdb="AL ALF A1302 " ideal model delta sigma weight residual 1.685 1.779 -0.094 2.00e-02 2.50e+03 2.22e+01 bond pdb=" F3 ALF A1302 " pdb="AL ALF A1302 " ideal model delta sigma weight residual 1.685 1.779 -0.094 2.00e-02 2.50e+03 2.21e+01 bond pdb=" F4 ALF A1302 " pdb="AL ALF A1302 " ideal model delta sigma weight residual 1.686 1.780 -0.094 2.00e-02 2.50e+03 2.19e+01 bond pdb=" CA TYR A 567 " pdb=" CB TYR A 567 " ideal model delta sigma weight residual 1.539 1.521 0.018 1.36e-02 5.41e+03 1.74e+00 ... (remaining 8563 not shown) Histogram of bond angle deviations from ideal: 89.59 - 107.44: 299 107.44 - 125.29: 11219 125.29 - 143.14: 115 143.14 - 160.99: 0 160.99 - 178.84: 2 Bond angle restraints: 11635 Sorted by residual: angle pdb=" F1 ALF A1302 " pdb="AL ALF A1302 " pdb=" F2 ALF A1302 " ideal model delta sigma weight residual 108.68 178.84 -70.16 3.00e+00 1.11e-01 5.47e+02 angle pdb=" F3 ALF A1302 " pdb="AL ALF A1302 " pdb=" F4 ALF A1302 " ideal model delta sigma weight residual 109.63 178.62 -68.99 3.00e+00 1.11e-01 5.29e+02 angle pdb=" F2 ALF A1302 " pdb="AL ALF A1302 " pdb=" F4 ALF A1302 " ideal model delta sigma weight residual 110.21 89.59 20.62 3.00e+00 1.11e-01 4.72e+01 angle pdb=" F2 ALF A1302 " pdb="AL ALF A1302 " pdb=" F3 ALF A1302 " ideal model delta sigma weight residual 109.59 89.66 19.93 3.00e+00 1.11e-01 4.41e+01 angle pdb=" F1 ALF A1302 " pdb="AL ALF A1302 " pdb=" F3 ALF A1302 " ideal model delta sigma weight residual 109.69 90.17 19.52 3.00e+00 1.11e-01 4.23e+01 ... (remaining 11630 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.91: 4596 15.91 - 31.81: 426 31.81 - 47.72: 82 47.72 - 63.63: 10 63.63 - 79.54: 3 Dihedral angle restraints: 5117 sinusoidal: 1948 harmonic: 3169 Sorted by residual: dihedral pdb=" CA ARG A 760 " pdb=" C ARG A 760 " pdb=" N TYR A 761 " pdb=" CA TYR A 761 " ideal model delta harmonic sigma weight residual -180.00 -156.01 -23.99 0 5.00e+00 4.00e-02 2.30e+01 dihedral pdb=" CA ASP A 762 " pdb=" C ASP A 762 " pdb=" N ILE A 763 " pdb=" CA ILE A 763 " ideal model delta harmonic sigma weight residual -180.00 -162.00 -18.00 0 5.00e+00 4.00e-02 1.30e+01 dihedral pdb=" CA VAL A 737 " pdb=" C VAL A 737 " pdb=" N GLU A 738 " pdb=" CA GLU A 738 " ideal model delta harmonic sigma weight residual 180.00 162.00 18.00 0 5.00e+00 4.00e-02 1.30e+01 ... (remaining 5114 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 773 0.031 - 0.063: 407 0.063 - 0.094: 125 0.094 - 0.126: 52 0.126 - 0.157: 8 Chirality restraints: 1365 Sorted by residual: chirality pdb=" CA TYR A 761 " pdb=" N TYR A 761 " pdb=" C TYR A 761 " pdb=" CB TYR A 761 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.19e-01 chirality pdb=" CA ILE A 368 " pdb=" N ILE A 368 " pdb=" C ILE A 368 " pdb=" CB ILE A 368 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.62e-01 chirality pdb=" CA ILE A 743 " pdb=" N ILE A 743 " pdb=" C ILE A 743 " pdb=" CB ILE A 743 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.39e-01 ... (remaining 1362 not shown) Planarity restraints: 1467 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C MET A 74 " 0.031 5.00e-02 4.00e+02 4.61e-02 3.40e+00 pdb=" N PRO A 75 " -0.080 5.00e-02 4.00e+02 pdb=" CA PRO A 75 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 75 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 273 " -0.028 5.00e-02 4.00e+02 4.19e-02 2.81e+00 pdb=" N PRO A 274 " 0.073 5.00e-02 4.00e+02 pdb=" CA PRO A 274 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 274 " -0.023 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A1039 " 0.024 5.00e-02 4.00e+02 3.65e-02 2.13e+00 pdb=" N PRO A1040 " -0.063 5.00e-02 4.00e+02 pdb=" CA PRO A1040 " 0.019 5.00e-02 4.00e+02 pdb=" CD PRO A1040 " 0.020 5.00e-02 4.00e+02 ... (remaining 1464 not shown) Histogram of nonbonded interaction distances: 1.86 - 2.47: 32 2.47 - 3.08: 5842 3.08 - 3.68: 11499 3.68 - 4.29: 16417 4.29 - 4.90: 28094 Nonbonded interactions: 61884 Sorted by model distance: nonbonded pdb="MG MG A1301 " pdb=" F1 ALF A1302 " model vdw 1.862 2.120 nonbonded pdb=" OD1 ASP A 816 " pdb="MG MG A1301 " model vdw 2.019 2.170 nonbonded pdb=" OD2 ASP A 746 " pdb=" OG SER A 748 " model vdw 2.150 2.440 nonbonded pdb=" OD2 ASP A 487 " pdb="MG MG A1301 " model vdw 2.165 2.170 nonbonded pdb=" OD2 ASP A 487 " pdb=" F1 ALF A1302 " model vdw 2.200 2.390 ... (remaining 61879 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=1.00 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: 1.760 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: 7.450 Check model and map are aligned: 0.130 Set scattering table: 0.070 Process input model: 25.250 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:2.860 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.830 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.097 8568 Z= 0.405 Angle : 1.183 70.161 11635 Z= 0.489 Chirality : 0.043 0.157 1365 Planarity : 0.004 0.046 1467 Dihedral : 12.682 79.535 3065 Min Nonbonded Distance : 1.862 Molprobity Statistics. All-atom Clashscore : 6.08 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.62 % Favored : 95.38 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.39 (0.22), residues: 1083 helix: -0.40 (0.22), residues: 468 sheet: -2.87 (0.39), residues: 134 loop : -2.38 (0.23), residues: 481 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 44 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 1.147 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.2031 time to fit residues: 13.6532 Evaluate side-chains 34 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 0.974 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.3586 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 92 optimal weight: 0.8980 chunk 82 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 55 optimal weight: 20.0000 chunk 44 optimal weight: 0.8980 chunk 85 optimal weight: 0.9980 chunk 33 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 63 optimal weight: 7.9990 chunk 98 optimal weight: 0.9980 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 161 GLN A 533 HIS ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 776 HIS A 785 HIS A 987 ASN A1089 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8490 moved from start: 0.1056 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8568 Z= 0.175 Angle : 0.507 11.310 11635 Z= 0.268 Chirality : 0.040 0.164 1365 Planarity : 0.005 0.037 1467 Dihedral : 4.266 21.335 1152 Min Nonbonded Distance : 1.969 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.67 % 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: -1.15 (0.24), residues: 1083 helix: 0.72 (0.24), residues: 468 sheet: -2.28 (0.42), residues: 127 loop : -1.82 (0.24), residues: 488 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 44 time to evaluate : 0.978 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.1812 time to fit residues: 13.8440 Evaluate side-chains 39 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.979 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0874 time to fit residues: 1.6532 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 55 optimal weight: 10.0000 chunk 30 optimal weight: 20.0000 chunk 82 optimal weight: 5.9990 chunk 67 optimal weight: 5.9990 chunk 27 optimal weight: 0.5980 chunk 99 optimal weight: 3.9990 chunk 107 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 33 optimal weight: 0.9980 chunk 79 optimal weight: 6.9990 overall best weight: 1.2382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 700 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A1133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8568 Z= 0.198 Angle : 0.490 11.953 11635 Z= 0.257 Chirality : 0.039 0.143 1365 Planarity : 0.004 0.034 1467 Dihedral : 4.053 21.247 1152 Min Nonbonded Distance : 1.851 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.51 % Favored : 96.49 % Rotamer Outliers : 1.00 % 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: -0.68 (0.25), residues: 1083 helix: 1.15 (0.25), residues: 466 sheet: -2.09 (0.43), residues: 127 loop : -1.58 (0.25), residues: 490 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 39 time to evaluate : 1.089 Fit side-chains outliers start: 9 outliers final: 4 residues processed: 47 average time/residue: 0.1930 time to fit residues: 14.4868 Evaluate side-chains 40 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0855 time to fit residues: 2.0319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 7.9990 chunk 74 optimal weight: 3.9990 chunk 51 optimal weight: 0.3980 chunk 10 optimal weight: 0.7980 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 6.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.1984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8507 moved from start: 0.1484 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.038 8568 Z= 0.191 Angle : 0.497 12.802 11635 Z= 0.255 Chirality : 0.039 0.145 1365 Planarity : 0.004 0.035 1467 Dihedral : 3.986 20.816 1152 Min Nonbonded Distance : 1.887 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer Outliers : 0.89 % 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: -0.33 (0.26), residues: 1083 helix: 1.53 (0.26), residues: 457 sheet: -1.97 (0.44), residues: 127 loop : -1.42 (0.25), residues: 499 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 39 time to evaluate : 0.944 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 46 average time/residue: 0.1758 time to fit residues: 12.8664 Evaluate side-chains 41 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 37 time to evaluate : 0.950 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0851 time to fit residues: 1.9349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 59 optimal weight: 4.9990 chunk 1 optimal weight: 3.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.9980 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.7980 chunk 0 optimal weight: 0.6980 chunk 53 optimal weight: 0.8980 chunk 94 optimal weight: 3.9990 chunk 26 optimal weight: 0.0980 chunk 35 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8473 moved from start: 0.1741 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.035 8568 Z= 0.138 Angle : 0.470 13.455 11635 Z= 0.241 Chirality : 0.038 0.133 1365 Planarity : 0.004 0.036 1467 Dihedral : 3.793 20.054 1152 Min Nonbonded Distance : 1.921 Molprobity Statistics. All-atom Clashscore : 4.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer Outliers : 0.67 % 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: -0.14 (0.26), residues: 1083 helix: 1.63 (0.26), residues: 462 sheet: -1.94 (0.43), residues: 132 loop : -1.24 (0.26), residues: 489 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 42 time to evaluate : 0.992 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 47 average time/residue: 0.1774 time to fit residues: 13.2164 Evaluate side-chains 41 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0785 time to fit residues: 1.6382 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 94 optimal weight: 2.9990 chunk 20 optimal weight: 4.9990 chunk 61 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 105 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 5.9990 chunk 34 optimal weight: 0.6980 chunk 55 optimal weight: 20.0000 chunk 101 optimal weight: 0.5980 overall best weight: 0.8384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8479 moved from start: 0.1834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 8568 Z= 0.155 Angle : 0.469 13.897 11635 Z= 0.239 Chirality : 0.038 0.127 1365 Planarity : 0.004 0.034 1467 Dihedral : 3.729 20.206 1152 Min Nonbonded Distance : 1.882 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 0.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.26), residues: 1083 helix: 1.72 (0.26), residues: 462 sheet: -1.79 (0.43), residues: 132 loop : -1.17 (0.26), residues: 489 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 48 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 43 time to evaluate : 1.040 Fit side-chains outliers start: 5 outliers final: 1 residues processed: 48 average time/residue: 0.1812 time to fit residues: 13.6737 Evaluate side-chains 40 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 1.001 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0809 time to fit residues: 1.4909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 3.9990 chunk 60 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 1.9990 chunk 88 optimal weight: 1.9990 chunk 58 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 2.9990 chunk 48 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8533 moved from start: 0.1766 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.048 8568 Z= 0.260 Angle : 0.521 13.977 11635 Z= 0.267 Chirality : 0.040 0.147 1365 Planarity : 0.004 0.036 1467 Dihedral : 3.924 20.659 1152 Min Nonbonded Distance : 1.820 Molprobity Statistics. All-atom Clashscore : 5.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer Outliers : 0.33 % 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: -0.04 (0.26), residues: 1083 helix: 1.70 (0.25), residues: 462 sheet: -1.88 (0.43), residues: 132 loop : -1.19 (0.26), residues: 489 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 38 time to evaluate : 1.023 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.1926 time to fit residues: 12.4955 Evaluate side-chains 40 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.973 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0800 time to fit residues: 1.6220 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 1.9990 chunk 31 optimal weight: 0.0270 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 51 optimal weight: 0.9980 chunk 9 optimal weight: 0.4980 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 0.9990 chunk 100 optimal weight: 5.9990 chunk 91 optimal weight: 0.9990 overall best weight: 0.7040 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8486 moved from start: 0.1957 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 8568 Z= 0.144 Angle : 0.477 14.508 11635 Z= 0.243 Chirality : 0.038 0.133 1365 Planarity : 0.004 0.034 1467 Dihedral : 3.766 20.089 1152 Min Nonbonded Distance : 1.871 Molprobity Statistics. All-atom Clashscore : 5.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer Outliers : 0.00 % 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: 0.14 (0.26), residues: 1083 helix: 1.86 (0.26), residues: 461 sheet: -1.76 (0.43), residues: 132 loop : -1.09 (0.26), residues: 490 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 41 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 41 time to evaluate : 0.942 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 41 average time/residue: 0.2043 time to fit residues: 12.8644 Evaluate side-chains 40 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 40 time to evaluate : 1.003 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 1.2585 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 6.9990 chunk 100 optimal weight: 0.5980 chunk 58 optimal weight: 9.9990 chunk 42 optimal weight: 0.0570 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 0.8980 chunk 92 optimal weight: 0.6980 chunk 64 optimal weight: 6.9990 chunk 103 optimal weight: 8.9990 chunk 63 optimal weight: 6.9990 overall best weight: 1.4500 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1917 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.045 8568 Z= 0.223 Angle : 0.505 14.555 11635 Z= 0.257 Chirality : 0.039 0.146 1365 Planarity : 0.004 0.035 1467 Dihedral : 3.846 20.356 1152 Min Nonbonded Distance : 1.827 Molprobity Statistics. All-atom Clashscore : 5.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer Outliers : 0.22 % 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: 0.11 (0.26), residues: 1083 helix: 1.86 (0.26), residues: 461 sheet: -1.77 (0.43), residues: 132 loop : -1.14 (0.26), residues: 490 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.990 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 39 average time/residue: 0.1938 time to fit residues: 11.9101 Evaluate side-chains 38 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.981 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0766 time to fit residues: 1.4672 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 108 optimal weight: 3.9990 chunk 99 optimal weight: 0.7980 chunk 86 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 66 optimal weight: 2.9990 chunk 53 optimal weight: 7.9990 chunk 68 optimal weight: 3.9990 chunk 92 optimal weight: 1.9990 chunk 26 optimal weight: 0.0270 overall best weight: 1.5644 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8528 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 8568 Z= 0.233 Angle : 0.513 14.665 11635 Z= 0.261 Chirality : 0.039 0.147 1365 Planarity : 0.004 0.035 1467 Dihedral : 3.933 20.719 1152 Min Nonbonded Distance : 1.813 Molprobity Statistics. All-atom Clashscore : 4.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer Outliers : 0.22 % 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: 0.12 (0.26), residues: 1083 helix: 1.91 (0.25), residues: 455 sheet: -1.77 (0.42), residues: 132 loop : -1.15 (0.26), residues: 496 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2166 Ramachandran restraints generated. 1083 Oldfield, 0 Emsley, 1083 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.921 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 39 average time/residue: 0.1850 time to fit residues: 11.4187 Evaluate side-chains 39 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.918 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0929 time to fit residues: 1.6509 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 6.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.9980 chunk 86 optimal weight: 3.9990 chunk 36 optimal weight: 5.9990 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 76 optimal weight: 3.9990 chunk 4 optimal weight: 5.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3268 r_free = 0.3268 target = 0.073489 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2977 r_free = 0.2977 target = 0.060047 restraints weight = 24373.190| |-----------------------------------------------------------------------------| r_work (start): 0.2972 rms_B_bonded: 2.98 r_work: 0.2855 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2855 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 8568 Z= 0.287 Angle : 0.550 14.492 11635 Z= 0.279 Chirality : 0.040 0.155 1365 Planarity : 0.004 0.034 1467 Dihedral : 4.068 21.152 1152 Min Nonbonded Distance : 1.797 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.71 % Favored : 95.29 % Rotamer Outliers : 0.11 % 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: 0.02 (0.26), residues: 1083 helix: 1.85 (0.25), residues: 456 sheet: -1.87 (0.41), residues: 139 loop : -1.19 (0.26), residues: 488 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1640.13 seconds wall clock time: 30 minutes 41.86 seconds (1841.86 seconds total)