Starting phenix.real_space_refine on Sat Apr 6 14:04:03 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/04_2024/6xms_22262_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/04_2024/6xms_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_22262/04_2024/6xms_22262.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/04_2024/6xms_22262.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/04_2024/6xms_22262_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6xms_22262/04_2024/6xms_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-dev-5288/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: 4.78, per 1000 atoms: 0.57 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: 3.01 Conformation dependent library (CDL) restraints added in 1.8 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: 2.16 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: 2.54 Time building geometry restraints manager: 3.30 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: 2.170 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: 7.140 Check model and map are aligned: 0.100 Set scattering table: 0.070 Process input model: 25.460 Find NCS groups from input model: 0.180 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:2.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.910 ------------------------------------------------------------------------------- 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 % Allowed : 5.35 % Favored : 94.65 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 PHE 0.022 0.002 PHE A1032 TYR 0.015 0.002 TYR A 625 ARG 0.004 0.001 ARG A 175 *********************** 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 : 0.979 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 44 average time/residue: 0.1953 time to fit residues: 13.1239 Evaluate side-chains 34 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 34 time to evaluate : 1.009 ------------------------------------------------------------------------------- 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 % Allowed : 9.03 % Favored : 90.30 % 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 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 415 HIS 0.004 0.001 HIS A 533 PHE 0.013 0.001 PHE A 402 TYR 0.011 0.001 TYR A 625 ARG 0.004 0.000 ARG A 588 *********************** 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 : 0.944 Fit side-chains REVERT: A 1136 MET cc_start: 0.8016 (tpt) cc_final: 0.7660 (tpp) REVERT: A 1198 MET cc_start: 0.8870 (tpt) cc_final: 0.8446 (tpt) outliers start: 6 outliers final: 2 residues processed: 49 average time/residue: 0.1788 time to fit residues: 13.9734 Evaluate side-chains 39 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 37 time to evaluate : 0.929 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 226 PHE Chi-restraints excluded: chain A residue 829 VAL 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: 5.9990 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: 1.4382 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.1284 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8568 Z= 0.220 Angle : 0.500 11.972 11635 Z= 0.262 Chirality : 0.039 0.145 1365 Planarity : 0.004 0.034 1467 Dihedral : 4.099 21.431 1152 Min Nonbonded Distance : 1.846 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 1.00 % Allowed : 10.93 % Favored : 88.07 % 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: -0.70 (0.25), residues: 1083 helix: 1.13 (0.25), residues: 466 sheet: -2.12 (0.43), residues: 127 loop : -1.59 (0.25), residues: 490 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 415 HIS 0.003 0.001 HIS A 706 PHE 0.012 0.001 PHE A 402 TYR 0.012 0.001 TYR A 625 ARG 0.004 0.000 ARG A 588 *********************** 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 47 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 38 time to evaluate : 0.961 Fit side-chains REVERT: A 497 LEU cc_start: 0.9007 (OUTLIER) cc_final: 0.8704 (pp) REVERT: A 1136 MET cc_start: 0.8208 (tpt) cc_final: 0.7845 (tpp) REVERT: A 1198 MET cc_start: 0.8843 (tpt) cc_final: 0.8433 (tpt) outliers start: 9 outliers final: 5 residues processed: 46 average time/residue: 0.1718 time to fit residues: 12.3820 Evaluate side-chains 42 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.992 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1030 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 8.9990 chunk 74 optimal weight: 2.9990 chunk 51 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 47 optimal weight: 5.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 2.9990 chunk 105 optimal weight: 0.9990 chunk 94 optimal weight: 1.9990 chunk 28 optimal weight: 4.9990 chunk 87 optimal weight: 0.6980 overall best weight: 1.3186 ------------------------------------------------------------------------------- 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: 0.8518 moved from start: 0.1465 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 8568 Z= 0.203 Angle : 0.494 12.546 11635 Z= 0.255 Chirality : 0.039 0.146 1365 Planarity : 0.004 0.032 1467 Dihedral : 4.018 21.002 1152 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.77 % Favored : 97.23 % Rotamer: Outliers : 1.56 % Allowed : 12.93 % Favored : 85.51 % 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: -0.35 (0.26), residues: 1083 helix: 1.51 (0.25), residues: 457 sheet: -1.99 (0.44), residues: 127 loop : -1.44 (0.25), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.002 0.001 HIS A 706 PHE 0.011 0.001 PHE A 402 TYR 0.011 0.001 TYR A 625 ARG 0.003 0.000 ARG A 588 *********************** 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 52 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 38 time to evaluate : 1.027 Fit side-chains REVERT: A 497 LEU cc_start: 0.8973 (OUTLIER) cc_final: 0.8690 (pp) REVERT: A 813 MET cc_start: 0.8183 (OUTLIER) cc_final: 0.7481 (ttt) REVERT: A 1136 MET cc_start: 0.8173 (tpt) cc_final: 0.7867 (tpp) outliers start: 14 outliers final: 8 residues processed: 49 average time/residue: 0.1825 time to fit residues: 14.1377 Evaluate side-chains 47 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 37 time to evaluate : 1.028 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1162 MET 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: 5.9990 chunk 78 optimal weight: 4.9990 chunk 43 optimal weight: 0.7980 chunk 89 optimal weight: 6.9990 chunk 72 optimal weight: 0.1980 chunk 0 optimal weight: 0.8980 chunk 53 optimal weight: 4.9990 chunk 94 optimal weight: 2.9990 chunk 26 optimal weight: 0.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- 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: 0.8501 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 8568 Z= 0.168 Angle : 0.478 13.444 11635 Z= 0.246 Chirality : 0.038 0.140 1365 Planarity : 0.004 0.031 1467 Dihedral : 3.878 20.472 1152 Min Nonbonded Distance : 1.878 Molprobity Statistics. All-atom Clashscore : 4.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.05 % Favored : 96.95 % Rotamer: Outliers : 1.45 % Allowed : 14.49 % Favored : 84.06 % 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: -0.17 (0.26), residues: 1083 helix: 1.61 (0.26), residues: 462 sheet: -2.01 (0.43), residues: 132 loop : -1.26 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.002 0.001 HIS A 706 PHE 0.010 0.001 PHE A 405 TYR 0.011 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 *********************** 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 51 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 38 time to evaluate : 0.942 Fit side-chains REVERT: A 497 LEU cc_start: 0.8985 (OUTLIER) cc_final: 0.8699 (pp) REVERT: A 1136 MET cc_start: 0.8115 (tpt) cc_final: 0.7835 (tpp) outliers start: 13 outliers final: 7 residues processed: 50 average time/residue: 0.1697 time to fit residues: 13.5649 Evaluate side-chains 44 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 36 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1162 MET 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: 1.9990 chunk 26 optimal weight: 0.0970 chunk 105 optimal weight: 0.6980 chunk 87 optimal weight: 1.9990 chunk 48 optimal weight: 7.9990 chunk 8 optimal weight: 6.9990 chunk 34 optimal weight: 4.9990 chunk 55 optimal weight: 10.0000 chunk 101 optimal weight: 1.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.8519 moved from start: 0.1695 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= 0.209 Angle : 0.490 13.706 11635 Z= 0.252 Chirality : 0.039 0.144 1365 Planarity : 0.004 0.032 1467 Dihedral : 3.898 20.259 1152 Min Nonbonded Distance : 1.840 Molprobity Statistics. All-atom Clashscore : 4.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.23 % Favored : 96.77 % Rotamer: Outliers : 1.78 % Allowed : 15.27 % Favored : 82.94 % 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: -0.12 (0.26), residues: 1083 helix: 1.68 (0.25), residues: 462 sheet: -1.96 (0.43), residues: 132 loop : -1.26 (0.26), residues: 489 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.002 0.001 HIS A 706 PHE 0.011 0.001 PHE A 405 TYR 0.011 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 *********************** 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 54 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 38 time to evaluate : 0.941 Fit side-chains REVERT: A 497 LEU cc_start: 0.8976 (OUTLIER) cc_final: 0.8687 (pp) REVERT: A 813 MET cc_start: 0.8205 (OUTLIER) cc_final: 0.7492 (ttt) REVERT: A 1136 MET cc_start: 0.8198 (tpt) cc_final: 0.7926 (tpp) outliers start: 16 outliers final: 11 residues processed: 51 average time/residue: 0.1741 time to fit residues: 13.9347 Evaluate side-chains 48 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 35 time to evaluate : 0.845 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1030 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1162 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 11 optimal weight: 0.6980 chunk 60 optimal weight: 0.1980 chunk 77 optimal weight: 2.9990 chunk 59 optimal weight: 3.9990 chunk 88 optimal weight: 0.7980 chunk 58 optimal weight: 2.9990 chunk 105 optimal weight: 1.9990 chunk 65 optimal weight: 5.9990 chunk 64 optimal weight: 0.8980 chunk 48 optimal weight: 0.9990 chunk 41 optimal weight: 4.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.8480 moved from start: 0.1901 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= 0.143 Angle : 0.466 14.297 11635 Z= 0.238 Chirality : 0.038 0.132 1365 Planarity : 0.004 0.034 1467 Dihedral : 3.738 19.587 1152 Min Nonbonded Distance : 1.880 Molprobity Statistics. All-atom Clashscore : 4.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 1.56 % Allowed : 15.94 % Favored : 82.50 % 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: 0.06 (0.26), residues: 1083 helix: 1.80 (0.26), residues: 463 sheet: -1.72 (0.44), residues: 127 loop : -1.20 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 415 HIS 0.002 0.000 HIS A 691 PHE 0.009 0.001 PHE A 405 TYR 0.009 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 *********************** 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 57 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 43 time to evaluate : 1.003 Fit side-chains REVERT: A 497 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8660 (pp) REVERT: A 813 MET cc_start: 0.8096 (OUTLIER) cc_final: 0.7344 (ttt) outliers start: 14 outliers final: 11 residues processed: 55 average time/residue: 0.1676 time to fit residues: 14.6678 Evaluate side-chains 52 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 39 time to evaluate : 1.026 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 813 MET Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1162 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 62 optimal weight: 8.9990 chunk 31 optimal weight: 0.0370 chunk 20 optimal weight: 4.9990 chunk 66 optimal weight: 1.9990 chunk 71 optimal weight: 0.0470 chunk 51 optimal weight: 0.0980 chunk 9 optimal weight: 0.8980 chunk 82 optimal weight: 0.9980 chunk 95 optimal weight: 0.6980 chunk 100 optimal weight: 6.9990 chunk 91 optimal weight: 6.9990 overall best weight: 0.3556 ------------------------------------------------------------------------------- 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: 0.8439 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8568 Z= 0.121 Angle : 0.458 14.862 11635 Z= 0.233 Chirality : 0.038 0.127 1365 Planarity : 0.004 0.032 1467 Dihedral : 3.554 19.162 1152 Min Nonbonded Distance : 1.933 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 1.34 % Allowed : 16.72 % Favored : 81.94 % 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: 0.23 (0.26), residues: 1083 helix: 1.93 (0.26), residues: 463 sheet: -1.52 (0.45), residues: 127 loop : -1.13 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 415 HIS 0.002 0.000 HIS A 691 PHE 0.009 0.001 PHE A1197 TYR 0.011 0.001 TYR A1137 ARG 0.002 0.000 ARG A1037 *********************** 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 54 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 42 time to evaluate : 1.010 Fit side-chains REVERT: A 409 PHE cc_start: 0.8961 (OUTLIER) cc_final: 0.8741 (m-80) REVERT: A 497 LEU cc_start: 0.8945 (OUTLIER) cc_final: 0.8669 (pp) REVERT: A 1198 MET cc_start: 0.8788 (tpt) cc_final: 0.8305 (tpt) outliers start: 12 outliers final: 7 residues processed: 52 average time/residue: 0.1715 time to fit residues: 14.1016 Evaluate side-chains 49 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 40 time to evaluate : 1.039 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 104 THR Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 622 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 829 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 97 optimal weight: 8.9990 chunk 100 optimal weight: 0.8980 chunk 58 optimal weight: 10.0000 chunk 42 optimal weight: 2.9990 chunk 76 optimal weight: 4.9990 chunk 30 optimal weight: 5.9990 chunk 88 optimal weight: 0.5980 chunk 92 optimal weight: 0.7980 chunk 64 optimal weight: 0.5980 chunk 103 optimal weight: 7.9990 chunk 63 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8464 moved from start: 0.2182 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= 0.154 Angle : 0.479 14.798 11635 Z= 0.241 Chirality : 0.038 0.174 1365 Planarity : 0.004 0.034 1467 Dihedral : 3.587 18.760 1152 Min Nonbonded Distance : 1.868 Molprobity Statistics. All-atom Clashscore : 5.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.14 % Favored : 96.86 % Rotamer: Outliers : 1.78 % Allowed : 16.39 % Favored : 81.83 % 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: 0.27 (0.26), residues: 1083 helix: 1.97 (0.26), residues: 463 sheet: -1.48 (0.45), residues: 127 loop : -1.12 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 415 HIS 0.002 0.000 HIS A 691 PHE 0.010 0.001 PHE A 405 TYR 0.009 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 *********************** 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 56 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 40 time to evaluate : 0.918 Fit side-chains REVERT: A 409 PHE cc_start: 0.8970 (OUTLIER) cc_final: 0.8767 (m-80) REVERT: A 497 LEU cc_start: 0.8965 (OUTLIER) cc_final: 0.8686 (pp) REVERT: A 1198 MET cc_start: 0.8767 (tpt) cc_final: 0.8316 (tpt) outliers start: 16 outliers final: 10 residues processed: 56 average time/residue: 0.1712 time to fit residues: 15.9369 Evaluate side-chains 51 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 0.848 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 497 LEU Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 49 optimal weight: 0.8980 chunk 71 optimal weight: 4.9990 chunk 108 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 8 optimal weight: 6.9990 chunk 66 optimal weight: 1.9990 chunk 53 optimal weight: 0.5980 chunk 68 optimal weight: 0.9990 chunk 92 optimal weight: 0.5980 chunk 26 optimal weight: 0.9980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A1133 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8463 moved from start: 0.2228 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.045 8568 Z= 0.157 Angle : 0.479 14.948 11635 Z= 0.241 Chirality : 0.038 0.185 1365 Planarity : 0.004 0.029 1467 Dihedral : 3.578 18.721 1152 Min Nonbonded Distance : 1.873 Molprobity Statistics. All-atom Clashscore : 5.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 1.34 % Allowed : 16.83 % Favored : 81.83 % 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: 0.32 (0.26), residues: 1083 helix: 1.97 (0.26), residues: 463 sheet: -1.38 (0.45), residues: 127 loop : -1.08 (0.26), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 415 HIS 0.002 0.000 HIS A 691 PHE 0.009 0.001 PHE A 405 TYR 0.009 0.001 TYR A1137 ARG 0.001 0.000 ARG A 588 ********************** 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 51 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 39 time to evaluate : 1.072 Fit side-chains REVERT: A 409 PHE cc_start: 0.8975 (OUTLIER) cc_final: 0.8754 (m-80) REVERT: A 1198 MET cc_start: 0.8750 (tpt) cc_final: 0.8303 (tpt) outliers start: 12 outliers final: 10 residues processed: 51 average time/residue: 0.1918 time to fit residues: 15.6765 Evaluate side-chains 49 residues out of total 944 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 38 time to evaluate : 0.964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 93 VAL Chi-restraints excluded: chain A residue 170 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 409 PHE Chi-restraints excluded: chain A residue 442 VAL Chi-restraints excluded: chain A residue 722 ASP Chi-restraints excluded: chain A residue 741 VAL Chi-restraints excluded: chain A residue 829 VAL Chi-restraints excluded: chain A residue 975 THR Chi-restraints excluded: chain A residue 1072 THR Chi-restraints excluded: chain A residue 1189 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 109 random chunks: chunk 79 optimal weight: 7.9990 chunk 12 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 86 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 88 optimal weight: 0.9980 chunk 10 optimal weight: 0.0980 chunk 15 optimal weight: 9.9990 chunk 76 optimal weight: 4.9990 chunk 4 optimal weight: 3.9990 chunk 62 optimal weight: 3.9990 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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 = 0.3303 r_free = 0.3303 target = 0.074494 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3014 r_free = 0.3014 target = 0.060992 restraints weight = 23769.259| |-----------------------------------------------------------------------------| r_work (start): 0.2995 rms_B_bonded: 2.96 r_work: 0.2878 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2878 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8675 moved from start: 0.2077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 8568 Z= 0.218 Angle : 0.508 14.699 11635 Z= 0.258 Chirality : 0.039 0.173 1365 Planarity : 0.004 0.028 1467 Dihedral : 3.747 19.452 1152 Min Nonbonded Distance : 1.828 Molprobity Statistics. All-atom Clashscore : 4.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 1.11 % Allowed : 16.72 % Favored : 82.16 % 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: 0.30 (0.26), residues: 1083 helix: 2.05 (0.26), residues: 456 sheet: -1.45 (0.45), residues: 127 loop : -1.13 (0.26), residues: 500 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 415 HIS 0.002 0.001 HIS A 706 PHE 0.012 0.001 PHE A 405 TYR 0.011 0.001 TYR A 625 ARG 0.002 0.000 ARG A 588 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.55 seconds wall clock time: 30 minutes 58.22 seconds (1858.22 seconds total)