Starting phenix.real_space_refine on Mon Mar 11 09:33:54 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7w_32350/03_2024/7w7w_32350_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7w_32350/03_2024/7w7w_32350.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7w_32350/03_2024/7w7w_32350.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7w_32350/03_2024/7w7w_32350.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7w_32350/03_2024/7w7w_32350_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7w7w_32350/03_2024/7w7w_32350_updated.pdb" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.011 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 58 5.16 5 C 5011 2.51 5 N 1315 2.21 5 O 1480 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 GLU 11": "OE1" <-> "OE2" Residue "A GLU 20": "OE1" <-> "OE2" Residue "A GLU 40": "OE1" <-> "OE2" Residue "A PHE 78": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 367": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 373": "OE1" <-> "OE2" Residue "A GLU 381": "OE1" <-> "OE2" Residue "A GLU 394": "OE1" <-> "OE2" Residue "A GLU 412": "OE1" <-> "OE2" Residue "A GLU 442": "OE1" <-> "OE2" Residue "A PHE 487": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 586": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 587": "OE1" <-> "OE2" Residue "A PHE 592": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 626": "OD1" <-> "OD2" Residue "A PHE 657": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 736": "OD1" <-> "OD2" Residue "A PHE 759": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 866": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 7870 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 7870 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1020, 7870 Unusual residues: {' MG': 1, 'ALF': 1} Classifications: {'peptide': 1018, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 46, 'TRANS': 971, None: 2} Not linked: pdbres="SER A1042 " pdbres="ALF A2001 " Not linked: pdbres="ALF A2001 " pdbres=" MG A2002 " Chain breaks: 1 Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 7 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'PHE:plan': 1} Unresolved non-hydrogen planarities: 5 Time building chain proxies: 4.91, per 1000 atoms: 0.62 Number of scatterers: 7870 At special positions: 0 Unit cell: (99.935, 92.345, 136.62, 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 58 16.00 Al 1 13.00 Mg 1 11.99 F 4 9.00 O 1480 8.00 N 1315 7.00 C 5011 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS A 875 " - pdb=" SG CYS A 887 " distance=2.03 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=1, symmetry=0 Number of additional bonds: simple=1, symmetry=0 Coordination: Other bonds: Time building additional restraints: 3.25 Conformation dependent library (CDL) restraints added in 1.5 seconds 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1908 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 38 helices and 7 sheets defined 47.2% alpha, 10.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.14 Creating SS restraints... Processing helix chain 'A' and resid 9 through 16 removed outlier: 3.617A pdb=" N PHE A 16 " --> pdb=" O VAL A 12 " (cutoff:3.500A) Processing helix chain 'A' and resid 26 through 36 removed outlier: 3.833A pdb=" N LYS A 30 " --> pdb=" O LEU A 26 " (cutoff:3.500A) Processing helix chain 'A' and resid 49 through 58 Processing helix chain 'A' and resid 60 through 78 removed outlier: 3.615A pdb=" N PHE A 78 " --> pdb=" O VAL A 74 " (cutoff:3.500A) Processing helix chain 'A' and resid 85 through 109 removed outlier: 4.412A pdb=" N GLU A 90 " --> pdb=" O ALA A 87 " (cutoff:3.500A) Proline residue: A 91 - end of helix Processing helix chain 'A' and resid 142 through 144 No H-bonds generated for 'chain 'A' and resid 142 through 144' Processing helix chain 'A' and resid 178 through 181 No H-bonds generated for 'chain 'A' and resid 178 through 181' Processing helix chain 'A' and resid 227 through 229 No H-bonds generated for 'chain 'A' and resid 227 through 229' Processing helix chain 'A' and resid 231 through 241 Processing helix chain 'A' and resid 248 through 278 removed outlier: 3.778A pdb=" N GLY A 277 " --> pdb=" O ILE A 273 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 306 removed outlier: 4.071A pdb=" N ALA A 292 " --> pdb=" O TRP A 288 " (cutoff:3.500A) removed outlier: 5.252A pdb=" N ILE A 293 " --> pdb=" O ILE A 289 " (cutoff:3.500A) removed outlier: 3.663A pdb=" N TYR A 294 " --> pdb=" O ARG A 290 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 328 removed outlier: 4.661A pdb=" N ALA A 313 " --> pdb=" O GLU A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 342 removed outlier: 4.005A pdb=" N THR A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) removed outlier: 3.701A pdb=" N LEU A 342 " --> pdb=" O SER A 338 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 337 through 342' Processing helix chain 'A' and resid 408 through 419 Processing helix chain 'A' and resid 440 through 451 Processing helix chain 'A' and resid 464 through 467 No H-bonds generated for 'chain 'A' and resid 464 through 467' Processing helix chain 'A' and resid 470 through 478 removed outlier: 3.624A pdb=" N LEU A 478 " --> pdb=" O VAL A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 517 through 522 Processing helix chain 'A' and resid 538 through 552 Processing helix chain 'A' and resid 581 through 586 removed outlier: 3.827A pdb=" N LYS A 585 " --> pdb=" O ALA A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 606 through 615 Processing helix chain 'A' and resid 628 through 638 Processing helix chain 'A' and resid 654 through 658 Processing helix chain 'A' and resid 662 through 671 removed outlier: 3.958A pdb=" N CYS A 669 " --> pdb=" O GLN A 665 " (cutoff:3.500A) Processing helix chain 'A' and resid 680 through 693 removed outlier: 3.658A pdb=" N PHE A 693 " --> pdb=" O PHE A 689 " (cutoff:3.500A) Processing helix chain 'A' and resid 707 through 712 Processing helix chain 'A' and resid 724 through 728 Processing helix chain 'A' and resid 740 through 780 Processing helix chain 'A' and resid 788 through 808 removed outlier: 3.810A pdb=" N THR A 798 " --> pdb=" O VAL A 794 " (cutoff:3.500A) removed outlier: 4.588A pdb=" N ASP A 799 " --> pdb=" O ASN A 795 " (cutoff:3.500A) Proline residue: A 802 - end of helix Processing helix chain 'A' and resid 830 through 856 removed outlier: 3.530A pdb=" N PHE A 855 " --> pdb=" O ALA A 851 " (cutoff:3.500A) Processing helix chain 'A' and resid 867 through 869 No H-bonds generated for 'chain 'A' and resid 867 through 869' Processing helix chain 'A' and resid 887 through 891 removed outlier: 3.843A pdb=" N PHE A 890 " --> pdb=" O CYS A 887 " (cutoff:3.500A) removed outlier: 3.531A pdb=" N GLU A 891 " --> pdb=" O ALA A 888 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 887 through 891' Processing helix chain 'A' and resid 893 through 913 Processing helix chain 'A' and resid 926 through 928 No H-bonds generated for 'chain 'A' and resid 926 through 928' Processing helix chain 'A' and resid 930 through 948 Processing helix chain 'A' and resid 952 through 955 No H-bonds generated for 'chain 'A' and resid 952 through 955' Processing helix chain 'A' and resid 963 through 988 Proline residue: A 975 - end of helix removed outlier: 4.044A pdb=" N LEU A 978 " --> pdb=" O LEU A 974 " (cutoff:3.500A) Processing helix chain 'A' and resid 1016 through 1030 removed outlier: 3.626A pdb=" N ILE A1022 " --> pdb=" O PHE A1018 " (cutoff:3.500A) removed outlier: 3.568A pdb=" N MET A1023 " --> pdb=" O VAL A1019 " (cutoff:3.500A) Proline residue: A1024 - end of helix removed outlier: 3.536A pdb=" N ILE A1027 " --> pdb=" O MET A1023 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N TRP A1028 " --> pdb=" O PRO A1024 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 150 through 153 removed outlier: 6.900A pdb=" N ASP A 162 " --> pdb=" O VAL A 224 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 174 through 176 Processing sheet with id= C, first strand: chain 'A' and resid 331 through 333 removed outlier: 3.565A pdb=" N ILE A 715 " --> pdb=" O THR A 697 " (cutoff:3.500A) removed outlier: 6.709A pdb=" N VAL A 347 " --> pdb=" O ALA A 698 " (cutoff:3.500A) removed outlier: 7.830A pdb=" N THR A 700 " --> pdb=" O VAL A 347 " (cutoff:3.500A) removed outlier: 6.511A pdb=" N CYS A 349 " --> pdb=" O THR A 700 " (cutoff:3.500A) removed outlier: 6.130A pdb=" N ARG A 619 " --> pdb=" O ILE A 348 " (cutoff:3.500A) removed outlier: 7.513A pdb=" N SER A 350 " --> pdb=" O ARG A 619 " (cutoff:3.500A) removed outlier: 6.811A pdb=" N ILE A 621 " --> pdb=" O SER A 350 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'A' and resid 394 through 396 removed outlier: 3.954A pdb=" N GLU A 394 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.782A pdb=" N ARG A 371 " --> pdb=" O SER A 378 " (cutoff:3.500A) removed outlier: 6.163A pdb=" N ASN A 380 " --> pdb=" O LEU A 369 " (cutoff:3.500A) removed outlier: 5.925A pdb=" N LEU A 369 " --> pdb=" O ASN A 380 " (cutoff:3.500A) removed outlier: 6.933A pdb=" N PHE A 382 " --> pdb=" O PHE A 367 " (cutoff:3.500A) removed outlier: 5.443A pdb=" N PHE A 367 " --> pdb=" O PHE A 382 " (cutoff:3.500A) removed outlier: 6.525A pdb=" N ILE A 384 " --> pdb=" O ARG A 365 " (cutoff:3.500A) removed outlier: 5.754A pdb=" N ARG A 365 " --> pdb=" O ILE A 384 " (cutoff:3.500A) removed outlier: 6.766A pdb=" N GLY A 597 " --> pdb=" O CYS A 364 " (cutoff:3.500A) removed outlier: 4.538A pdb=" N MET A 366 " --> pdb=" O CYS A 595 " (cutoff:3.500A) removed outlier: 6.832A pdb=" N CYS A 595 " --> pdb=" O MET A 366 " (cutoff:3.500A) removed outlier: 3.797A pdb=" N GLY A 594 " --> pdb=" O LEU A 563 " (cutoff:3.500A) removed outlier: 3.762A pdb=" N PHE A 483 " --> pdb=" O TYR A 497 " (cutoff:3.500A) removed outlier: 6.772A pdb=" N THR A 499 " --> pdb=" O LYS A 481 " (cutoff:3.500A) removed outlier: 5.569A pdb=" N LYS A 481 " --> pdb=" O THR A 499 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'A' and resid 425 through 427 removed outlier: 3.562A pdb=" N ASP A 426 " --> pdb=" O GLU A 435 " (cutoff:3.500A) Processing sheet with id= F, first strand: chain 'A' and resid 532 through 535 removed outlier: 7.148A pdb=" N LEU A 590 " --> pdb=" O THR A 525 " (cutoff:3.500A) removed outlier: 5.620A pdb=" N ILE A 527 " --> pdb=" O LEU A 590 " (cutoff:3.500A) removed outlier: 5.918A pdb=" N PHE A 592 " --> pdb=" O ILE A 527 " (cutoff:3.500A) removed outlier: 5.966A pdb=" N VAL A 529 " --> pdb=" O PHE A 592 " (cutoff:3.500A) Processing sheet with id= G, first strand: chain 'A' and resid 651 through 653 removed outlier: 6.492A pdb=" N CYS A 674 " --> pdb=" O PHE A 652 " (cutoff:3.500A) No H-bonds generated for sheet with id= G 350 hydrogen bonds defined for protein. 978 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: 2.65 Time building geometry restraints manager: 3.50 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: 2561 1.34 - 1.46: 1086 1.46 - 1.58: 4276 1.58 - 1.69: 0 1.69 - 1.81: 94 Bond restraints: 8017 Sorted by residual: bond pdb=" F1 ALF A2001 " pdb="AL ALF A2001 " ideal model delta sigma weight residual 1.684 1.783 -0.099 2.00e-02 2.50e+03 2.46e+01 bond pdb=" F2 ALF A2001 " pdb="AL ALF A2001 " ideal model delta sigma weight residual 1.685 1.784 -0.099 2.00e-02 2.50e+03 2.44e+01 bond pdb=" F3 ALF A2001 " pdb="AL ALF A2001 " ideal model delta sigma weight residual 1.685 1.782 -0.097 2.00e-02 2.50e+03 2.38e+01 bond pdb=" F4 ALF A2001 " pdb="AL ALF A2001 " ideal model delta sigma weight residual 1.686 1.783 -0.097 2.00e-02 2.50e+03 2.37e+01 bond pdb=" N LEU A 796 " pdb=" CA LEU A 796 " ideal model delta sigma weight residual 1.468 1.455 0.014 1.24e-02 6.50e+03 1.20e+00 ... (remaining 8012 not shown) Histogram of bond angle deviations from ideal: 89.78 - 107.81: 309 107.81 - 125.84: 10446 125.84 - 143.87: 125 143.87 - 161.90: 0 161.90 - 179.93: 2 Bond angle restraints: 10882 Sorted by residual: angle pdb=" F1 ALF A2001 " pdb="AL ALF A2001 " pdb=" F2 ALF A2001 " ideal model delta sigma weight residual 108.68 179.68 -71.00 3.00e+00 1.11e-01 5.60e+02 angle pdb=" F3 ALF A2001 " pdb="AL ALF A2001 " pdb=" F4 ALF A2001 " ideal model delta sigma weight residual 109.63 179.93 -70.30 3.00e+00 1.11e-01 5.49e+02 angle pdb=" F2 ALF A2001 " pdb="AL ALF A2001 " pdb=" F4 ALF A2001 " ideal model delta sigma weight residual 110.21 90.17 20.04 3.00e+00 1.11e-01 4.46e+01 angle pdb=" F2 ALF A2001 " pdb="AL ALF A2001 " pdb=" F3 ALF A2001 " ideal model delta sigma weight residual 109.59 89.78 19.81 3.00e+00 1.11e-01 4.36e+01 angle pdb=" F1 ALF A2001 " pdb="AL ALF A2001 " pdb=" F3 ALF A2001 " ideal model delta sigma weight residual 109.69 89.90 19.79 3.00e+00 1.11e-01 4.35e+01 ... (remaining 10877 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 18.01: 4394 18.01 - 36.03: 402 36.03 - 54.04: 54 54.04 - 72.06: 9 72.06 - 90.07: 3 Dihedral angle restraints: 4862 sinusoidal: 1919 harmonic: 2943 Sorted by residual: dihedral pdb=" CB CYS A 875 " pdb=" SG CYS A 875 " pdb=" SG CYS A 887 " pdb=" CB CYS A 887 " ideal model delta sinusoidal sigma weight residual -86.00 -176.07 90.07 1 1.00e+01 1.00e-02 9.61e+01 dihedral pdb=" CA ASP A 157 " pdb=" CB ASP A 157 " pdb=" CG ASP A 157 " pdb=" OD1 ASP A 157 " ideal model delta sinusoidal sigma weight residual -30.00 -84.22 54.22 1 2.00e+01 2.50e-03 9.97e+00 dihedral pdb=" CA ILE A 116 " pdb=" C ILE A 116 " pdb=" N GLU A 117 " pdb=" CA GLU A 117 " ideal model delta harmonic sigma weight residual 180.00 -164.40 -15.60 0 5.00e+00 4.00e-02 9.74e+00 ... (remaining 4859 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.037: 880 0.037 - 0.073: 276 0.073 - 0.110: 103 0.110 - 0.147: 15 0.147 - 0.183: 2 Chirality restraints: 1276 Sorted by residual: chirality pdb=" CB ILE A 715 " pdb=" CA ILE A 715 " pdb=" CG1 ILE A 715 " pdb=" CG2 ILE A 715 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.18 2.00e-01 2.50e+01 8.41e-01 chirality pdb=" CA PHE A 759 " pdb=" N PHE A 759 " pdb=" C PHE A 759 " pdb=" CB PHE A 759 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.15 2.00e-01 2.50e+01 5.97e-01 chirality pdb=" CA ILE A 623 " pdb=" N ILE A 623 " pdb=" C ILE A 623 " pdb=" CB ILE A 623 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.13 2.00e-01 2.50e+01 4.36e-01 ... (remaining 1273 not shown) Planarity restraints: 1387 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 534 " -0.036 5.00e-02 4.00e+02 5.51e-02 4.85e+00 pdb=" N PRO A 535 " 0.095 5.00e-02 4.00e+02 pdb=" CA PRO A 535 " -0.029 5.00e-02 4.00e+02 pdb=" CD PRO A 535 " -0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 796 " 0.009 2.00e-02 2.50e+03 1.82e-02 3.32e+00 pdb=" C LEU A 796 " -0.032 2.00e-02 2.50e+03 pdb=" O LEU A 796 " 0.012 2.00e-02 2.50e+03 pdb=" N VAL A 797 " 0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 959 " 0.027 5.00e-02 4.00e+02 4.09e-02 2.68e+00 pdb=" N PRO A 960 " -0.071 5.00e-02 4.00e+02 pdb=" CA PRO A 960 " 0.021 5.00e-02 4.00e+02 pdb=" CD PRO A 960 " 0.023 5.00e-02 4.00e+02 ... (remaining 1384 not shown) Histogram of nonbonded interaction distances: 2.05 - 2.62: 58 2.62 - 3.19: 7204 3.19 - 3.76: 12493 3.76 - 4.33: 16680 4.33 - 4.90: 27879 Nonbonded interactions: 64314 Sorted by model distance: nonbonded pdb=" OD2 ASP A 351 " pdb="MG MG A2002 " model vdw 2.051 2.170 nonbonded pdb=" F3 ALF A2001 " pdb="MG MG A2002 " model vdw 2.055 2.120 nonbonded pdb=" OD1 ASP A 702 " pdb="MG MG A2002 " model vdw 2.064 2.170 nonbonded pdb=" O THR A 353 " pdb="MG MG A2002 " model vdw 2.071 2.170 nonbonded pdb=" NH2 ARG A 131 " pdb=" OE1 GLU A 152 " model vdw 2.167 2.520 ... (remaining 64309 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: 0.240 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: 1.570 Check model and map are aligned: 0.130 Set scattering table: 0.080 Process input model: 26.540 Find NCS groups from input model: 0.220 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:2.620 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 31.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7070 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 : 0.003 0.099 8017 Z= 0.205 Angle : 1.162 71.002 10882 Z= 0.455 Chirality : 0.041 0.183 1276 Planarity : 0.004 0.055 1387 Dihedral : 13.443 75.289 2951 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 8.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 0.23 % Favored : 99.77 % 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: 0.82 (0.26), residues: 1014 helix: 1.66 (0.24), residues: 489 sheet: -0.03 (0.50), residues: 105 loop : -0.62 (0.29), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 831 HIS 0.002 0.001 HIS A 943 PHE 0.019 0.001 PHE A 759 TYR 0.025 0.001 TYR A 586 ARG 0.005 0.000 ARG A 467 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 123 time to evaluate : 0.907 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.6826 (ptt) cc_final: 0.6150 (ptt) REVERT: A 557 THR cc_start: 0.7993 (p) cc_final: 0.7663 (p) REVERT: A 784 GLU cc_start: 0.5533 (mm-30) cc_final: 0.4672 (mm-30) REVERT: A 1023 MET cc_start: 0.1857 (mmt) cc_final: 0.1158 (mmt) outliers start: 0 outliers final: 0 residues processed: 123 average time/residue: 0.2053 time to fit residues: 34.6668 Evaluate side-chains 98 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 98 time to evaluate : 1.633 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 86 optimal weight: 9.9990 chunk 77 optimal weight: 5.9990 chunk 42 optimal weight: 5.9990 chunk 26 optimal weight: 4.9990 chunk 52 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 79 optimal weight: 0.9990 chunk 30 optimal weight: 1.9990 chunk 48 optimal weight: 4.9990 chunk 59 optimal weight: 1.9990 chunk 92 optimal weight: 0.0870 overall best weight: 2.0166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 114 ASN A 738 ASN A 879 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7199 moved from start: 0.1094 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 8017 Z= 0.267 Angle : 0.849 32.034 10882 Z= 0.365 Chirality : 0.044 0.213 1276 Planarity : 0.005 0.043 1387 Dihedral : 4.325 17.025 1078 Min Nonbonded Distance : 1.843 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 0.92 % Allowed : 8.62 % Favored : 90.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.26), residues: 1014 helix: 1.18 (0.23), residues: 487 sheet: -0.15 (0.50), residues: 95 loop : -0.73 (0.29), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.004 0.001 HIS A 278 PHE 0.031 0.002 PHE A 759 TYR 0.014 0.002 TYR A 434 ARG 0.005 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 110 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 102 time to evaluate : 0.903 Fit side-chains REVERT: A 452 MET cc_start: 0.6900 (ptt) cc_final: 0.6456 (ptt) REVERT: A 557 THR cc_start: 0.7991 (p) cc_final: 0.7679 (p) REVERT: A 784 GLU cc_start: 0.5777 (mm-30) cc_final: 0.4886 (mm-30) REVERT: A 1023 MET cc_start: 0.1938 (mmt) cc_final: 0.1085 (mmt) outliers start: 8 outliers final: 7 residues processed: 108 average time/residue: 0.1985 time to fit residues: 29.7964 Evaluate side-chains 102 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 95 time to evaluate : 0.900 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 106 VAL Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 738 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 51 optimal weight: 5.9990 chunk 28 optimal weight: 9.9990 chunk 77 optimal weight: 4.9990 chunk 63 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 92 optimal weight: 0.0370 chunk 100 optimal weight: 0.2980 chunk 82 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 74 optimal weight: 0.9980 chunk 91 optimal weight: 2.9990 overall best weight: 0.6260 ------------------------------------------------------------------------------- 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: 0.7138 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8017 Z= 0.147 Angle : 0.798 30.190 10882 Z= 0.331 Chirality : 0.041 0.162 1276 Planarity : 0.004 0.042 1387 Dihedral : 4.010 16.403 1078 Min Nonbonded Distance : 1.978 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Rotamer: Outliers : 1.49 % Allowed : 10.46 % Favored : 88.05 % 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: 0.53 (0.26), residues: 1014 helix: 1.45 (0.24), residues: 480 sheet: -0.20 (0.51), residues: 96 loop : -0.72 (0.29), residues: 438 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.030 0.001 PHE A 759 TYR 0.009 0.001 TYR A 842 ARG 0.002 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 100 time to evaluate : 0.806 Fit side-chains revert: symmetry clash REVERT: A 452 MET cc_start: 0.6646 (ptt) cc_final: 0.6208 (ptt) REVERT: A 536 MET cc_start: 0.7097 (tpt) cc_final: 0.6759 (tpt) REVERT: A 557 THR cc_start: 0.7943 (p) cc_final: 0.7637 (p) REVERT: A 715 ILE cc_start: 0.8339 (OUTLIER) cc_final: 0.7732 (tp) REVERT: A 784 GLU cc_start: 0.5719 (mm-30) cc_final: 0.4831 (mm-30) REVERT: A 792 LEU cc_start: 0.7965 (OUTLIER) cc_final: 0.7673 (mm) REVERT: A 1023 MET cc_start: 0.1816 (mmt) cc_final: 0.1105 (mmt) outliers start: 13 outliers final: 9 residues processed: 107 average time/residue: 0.1896 time to fit residues: 28.3375 Evaluate side-chains 109 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 792 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 9.9990 chunk 10 optimal weight: 6.9990 chunk 44 optimal weight: 5.9990 chunk 62 optimal weight: 0.6980 chunk 93 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 88 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 55 optimal weight: 0.9980 overall best weight: 1.3784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 56 GLN A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7184 moved from start: 0.1377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 8017 Z= 0.203 Angle : 0.809 30.548 10882 Z= 0.338 Chirality : 0.042 0.168 1276 Planarity : 0.004 0.044 1387 Dihedral : 4.068 16.874 1078 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 8.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.07 % Allowed : 12.41 % Favored : 85.52 % 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: 0.41 (0.26), residues: 1014 helix: 1.27 (0.24), residues: 485 sheet: -0.41 (0.49), residues: 103 loop : -0.67 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.028 0.001 PHE A 759 TYR 0.010 0.001 TYR A 762 ARG 0.003 0.000 ARG A 164 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 124 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 106 time to evaluate : 0.992 Fit side-chains REVERT: A 107 TRP cc_start: 0.6808 (t60) cc_final: 0.6593 (t60) REVERT: A 452 MET cc_start: 0.6672 (ptt) cc_final: 0.6222 (ptt) REVERT: A 536 MET cc_start: 0.7119 (tpt) cc_final: 0.6820 (tpt) REVERT: A 557 THR cc_start: 0.7967 (p) cc_final: 0.7656 (p) REVERT: A 575 MET cc_start: 0.5663 (OUTLIER) cc_final: 0.4319 (mmm) REVERT: A 715 ILE cc_start: 0.8300 (OUTLIER) cc_final: 0.7633 (tp) REVERT: A 784 GLU cc_start: 0.5680 (mm-30) cc_final: 0.4705 (mm-30) REVERT: A 1023 MET cc_start: 0.1856 (mmt) cc_final: 0.1067 (mmt) outliers start: 18 outliers final: 14 residues processed: 115 average time/residue: 0.1851 time to fit residues: 30.0161 Evaluate side-chains 117 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 101 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 1 optimal weight: 4.9990 chunk 73 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 84 optimal weight: 1.9990 chunk 68 optimal weight: 0.8980 chunk 0 optimal weight: 8.9990 chunk 50 optimal weight: 0.0870 chunk 88 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 33 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 overall best weight: 1.1964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7180 moved from start: 0.1489 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 8017 Z= 0.184 Angle : 0.803 30.594 10882 Z= 0.333 Chirality : 0.042 0.168 1276 Planarity : 0.004 0.043 1387 Dihedral : 4.029 16.682 1078 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.64 % Allowed : 12.53 % Favored : 84.83 % 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: 0.42 (0.26), residues: 1014 helix: 1.31 (0.24), residues: 485 sheet: -0.42 (0.49), residues: 103 loop : -0.69 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.028 0.001 PHE A 759 TYR 0.009 0.001 TYR A 122 ARG 0.003 0.000 ARG A 246 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 106 time to evaluate : 0.910 Fit side-chains REVERT: A 107 TRP cc_start: 0.6818 (t60) cc_final: 0.6546 (t60) REVERT: A 452 MET cc_start: 0.6808 (ptt) cc_final: 0.6394 (ptt) REVERT: A 536 MET cc_start: 0.7106 (tpt) cc_final: 0.6850 (tpt) REVERT: A 557 THR cc_start: 0.7963 (p) cc_final: 0.7707 (p) REVERT: A 575 MET cc_start: 0.5708 (OUTLIER) cc_final: 0.4528 (mmm) REVERT: A 715 ILE cc_start: 0.8295 (OUTLIER) cc_final: 0.7638 (tp) REVERT: A 784 GLU cc_start: 0.5715 (mm-30) cc_final: 0.4708 (mm-30) REVERT: A 1023 MET cc_start: 0.1604 (mmt) cc_final: 0.0911 (mmt) outliers start: 23 outliers final: 16 residues processed: 119 average time/residue: 0.1880 time to fit residues: 31.2646 Evaluate side-chains 121 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 103 time to evaluate : 0.901 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 57 optimal weight: 6.9990 chunk 24 optimal weight: 10.0000 chunk 98 optimal weight: 4.9990 chunk 81 optimal weight: 0.5980 chunk 45 optimal weight: 7.9990 chunk 8 optimal weight: 0.0980 chunk 32 optimal weight: 6.9990 chunk 51 optimal weight: 8.9990 chunk 95 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 56 optimal weight: 0.6980 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1594 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8017 Z= 0.193 Angle : 0.807 30.476 10882 Z= 0.338 Chirality : 0.041 0.169 1276 Planarity : 0.004 0.043 1387 Dihedral : 4.028 16.807 1078 Min Nonbonded Distance : 1.966 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 2.41 % Allowed : 13.79 % Favored : 83.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.26), residues: 1014 helix: 1.30 (0.24), residues: 485 sheet: -0.43 (0.49), residues: 103 loop : -0.69 (0.30), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.002 0.001 HIS A 278 PHE 0.028 0.001 PHE A 759 TYR 0.009 0.001 TYR A 762 ARG 0.003 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 1.005 Fit side-chains revert: symmetry clash REVERT: A 59 ASP cc_start: 0.6404 (t0) cc_final: 0.5966 (t0) REVERT: A 373 GLU cc_start: 0.5313 (OUTLIER) cc_final: 0.4843 (mm-30) REVERT: A 452 MET cc_start: 0.6926 (ptt) cc_final: 0.6566 (ptt) REVERT: A 536 MET cc_start: 0.7096 (tpt) cc_final: 0.6855 (tpt) REVERT: A 557 THR cc_start: 0.7997 (p) cc_final: 0.7694 (p) REVERT: A 573 GLU cc_start: 0.6486 (pt0) cc_final: 0.6050 (pt0) REVERT: A 575 MET cc_start: 0.6020 (OUTLIER) cc_final: 0.5031 (mmm) REVERT: A 715 ILE cc_start: 0.8307 (OUTLIER) cc_final: 0.7653 (tp) REVERT: A 784 GLU cc_start: 0.5736 (mm-30) cc_final: 0.4726 (mm-30) REVERT: A 1023 MET cc_start: 0.1748 (mmt) cc_final: 0.1016 (mmt) outliers start: 21 outliers final: 16 residues processed: 116 average time/residue: 0.1917 time to fit residues: 31.4088 Evaluate side-chains 124 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.937 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 72 optimal weight: 2.9990 chunk 55 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 61 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 8.9990 chunk 60 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 58 optimal weight: 0.9990 chunk 29 optimal weight: 0.9980 overall best weight: 1.1384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 566 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7178 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 8017 Z= 0.180 Angle : 0.803 30.244 10882 Z= 0.334 Chirality : 0.041 0.168 1276 Planarity : 0.004 0.043 1387 Dihedral : 3.984 16.577 1078 Min Nonbonded Distance : 1.961 Molprobity Statistics. All-atom Clashscore : 7.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.53 % Allowed : 14.60 % Favored : 82.87 % 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: 0.40 (0.26), residues: 1014 helix: 1.30 (0.24), residues: 484 sheet: -0.34 (0.49), residues: 103 loop : -0.72 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.028 0.001 PHE A 759 TYR 0.009 0.001 TYR A 122 ARG 0.004 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 131 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 109 time to evaluate : 0.923 Fit side-chains REVERT: A 59 ASP cc_start: 0.6402 (t0) cc_final: 0.5959 (t0) REVERT: A 373 GLU cc_start: 0.5265 (OUTLIER) cc_final: 0.4868 (mm-30) REVERT: A 452 MET cc_start: 0.6919 (ptt) cc_final: 0.6561 (ptt) REVERT: A 536 MET cc_start: 0.7079 (tpt) cc_final: 0.6847 (tpt) REVERT: A 557 THR cc_start: 0.7987 (p) cc_final: 0.7683 (p) REVERT: A 573 GLU cc_start: 0.6495 (pt0) cc_final: 0.5850 (pt0) REVERT: A 575 MET cc_start: 0.5801 (OUTLIER) cc_final: 0.4927 (mmm) REVERT: A 715 ILE cc_start: 0.8298 (OUTLIER) cc_final: 0.7649 (tp) REVERT: A 784 GLU cc_start: 0.5687 (mm-30) cc_final: 0.4677 (mm-30) REVERT: A 1023 MET cc_start: 0.1862 (mmt) cc_final: 0.1215 (mmt) outliers start: 22 outliers final: 17 residues processed: 119 average time/residue: 0.1816 time to fit residues: 30.5470 Evaluate side-chains 127 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 494 MET Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 19 optimal weight: 0.5980 chunk 62 optimal weight: 0.5980 chunk 66 optimal weight: 0.9980 chunk 48 optimal weight: 5.9990 chunk 9 optimal weight: 0.6980 chunk 77 optimal weight: 3.9990 chunk 89 optimal weight: 0.0970 chunk 94 optimal weight: 0.8980 chunk 85 optimal weight: 3.9990 chunk 91 optimal weight: 0.9980 chunk 55 optimal weight: 6.9990 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 396 HIS A 738 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7148 moved from start: 0.1744 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 8017 Z= 0.143 Angle : 0.795 29.584 10882 Z= 0.328 Chirality : 0.040 0.163 1276 Planarity : 0.004 0.043 1387 Dihedral : 3.866 16.436 1078 Min Nonbonded Distance : 1.985 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.94 % Favored : 96.06 % Rotamer: Outliers : 2.64 % Allowed : 15.06 % Favored : 82.30 % 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: 0.56 (0.27), residues: 1014 helix: 1.43 (0.24), residues: 484 sheet: -0.18 (0.50), residues: 103 loop : -0.68 (0.29), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 854 HIS 0.002 0.000 HIS A 566 PHE 0.028 0.001 PHE A 759 TYR 0.008 0.001 TYR A 586 ARG 0.004 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 107 time to evaluate : 1.002 Fit side-chains REVERT: A 373 GLU cc_start: 0.5307 (OUTLIER) cc_final: 0.4988 (mm-30) REVERT: A 452 MET cc_start: 0.6738 (ptt) cc_final: 0.6354 (ptt) REVERT: A 536 MET cc_start: 0.7031 (tpt) cc_final: 0.6813 (tpt) REVERT: A 557 THR cc_start: 0.7960 (p) cc_final: 0.7650 (p) REVERT: A 573 GLU cc_start: 0.6409 (pt0) cc_final: 0.5782 (pt0) REVERT: A 575 MET cc_start: 0.5751 (OUTLIER) cc_final: 0.4856 (mmm) REVERT: A 715 ILE cc_start: 0.8258 (OUTLIER) cc_final: 0.7631 (tp) REVERT: A 784 GLU cc_start: 0.5684 (mm-30) cc_final: 0.4658 (mm-30) REVERT: A 1023 MET cc_start: 0.1840 (mmt) cc_final: 0.1206 (mmt) outliers start: 23 outliers final: 17 residues processed: 118 average time/residue: 0.1838 time to fit residues: 30.8027 Evaluate side-chains 127 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 107 time to evaluate : 0.896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 128 LYS Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 593 VAL Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 39 optimal weight: 8.9990 chunk 71 optimal weight: 3.9990 chunk 28 optimal weight: 0.6980 chunk 82 optimal weight: 0.4980 chunk 86 optimal weight: 7.9990 chunk 91 optimal weight: 6.9990 chunk 60 optimal weight: 1.9990 chunk 96 optimal weight: 4.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 6.9990 chunk 67 optimal weight: 4.9990 overall best weight: 2.0386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7228 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.076 8017 Z= 0.262 Angle : 0.845 30.707 10882 Z= 0.359 Chirality : 0.043 0.177 1276 Planarity : 0.005 0.045 1387 Dihedral : 4.187 17.171 1078 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 9.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.41 % Allowed : 16.09 % Favored : 81.49 % 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: 0.22 (0.26), residues: 1014 helix: 1.11 (0.24), residues: 488 sheet: -0.50 (0.50), residues: 105 loop : -0.78 (0.29), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 36 HIS 0.004 0.001 HIS A 566 PHE 0.027 0.002 PHE A 759 TYR 0.013 0.002 TYR A 762 ARG 0.003 0.000 ARG A 549 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 111 time to evaluate : 0.841 Fit side-chains REVERT: A 373 GLU cc_start: 0.5342 (OUTLIER) cc_final: 0.5025 (mm-30) REVERT: A 452 MET cc_start: 0.6993 (ptt) cc_final: 0.6653 (ptt) REVERT: A 467 ARG cc_start: 0.6376 (tmt170) cc_final: 0.6000 (tpt90) REVERT: A 557 THR cc_start: 0.8011 (p) cc_final: 0.7701 (p) REVERT: A 573 GLU cc_start: 0.6357 (pt0) cc_final: 0.5813 (pt0) REVERT: A 575 MET cc_start: 0.6130 (OUTLIER) cc_final: 0.5061 (mmm) REVERT: A 715 ILE cc_start: 0.8382 (OUTLIER) cc_final: 0.7711 (tp) REVERT: A 784 GLU cc_start: 0.5722 (mm-30) cc_final: 0.4711 (mm-30) REVERT: A 1023 MET cc_start: 0.1577 (mmt) cc_final: 0.0605 (mtp) outliers start: 21 outliers final: 16 residues processed: 124 average time/residue: 0.1963 time to fit residues: 33.9439 Evaluate side-chains 124 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 105 time to evaluate : 0.876 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 101 optimal weight: 3.9990 chunk 93 optimal weight: 1.9990 chunk 80 optimal weight: 4.9990 chunk 8 optimal weight: 0.7980 chunk 62 optimal weight: 0.1980 chunk 49 optimal weight: 7.9990 chunk 64 optimal weight: 6.9990 chunk 86 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 74 optimal weight: 6.9990 chunk 11 optimal weight: 0.0670 overall best weight: 1.0122 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 738 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7186 moved from start: 0.1927 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 8017 Z= 0.175 Angle : 0.817 29.898 10882 Z= 0.340 Chirality : 0.041 0.168 1276 Planarity : 0.004 0.044 1387 Dihedral : 4.012 16.614 1078 Min Nonbonded Distance : 1.959 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.85 % Favored : 96.15 % Rotamer: Outliers : 2.41 % Allowed : 16.21 % Favored : 81.38 % 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: 0.34 (0.26), residues: 1014 helix: 1.23 (0.24), residues: 487 sheet: -0.40 (0.50), residues: 103 loop : -0.75 (0.29), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.028 0.001 PHE A 759 TYR 0.009 0.001 TYR A 122 ARG 0.004 0.000 ARG A 549 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2028 Ramachandran restraints generated. 1014 Oldfield, 0 Emsley, 1014 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 105 time to evaluate : 0.857 Fit side-chains REVERT: A 373 GLU cc_start: 0.5293 (OUTLIER) cc_final: 0.5015 (mm-30) REVERT: A 452 MET cc_start: 0.6981 (ptt) cc_final: 0.6628 (ptt) REVERT: A 467 ARG cc_start: 0.6316 (tmt170) cc_final: 0.6008 (tpt90) REVERT: A 557 THR cc_start: 0.7959 (p) cc_final: 0.7641 (p) REVERT: A 573 GLU cc_start: 0.6318 (pt0) cc_final: 0.5813 (pt0) REVERT: A 575 MET cc_start: 0.6093 (OUTLIER) cc_final: 0.5164 (mmm) REVERT: A 715 ILE cc_start: 0.8309 (OUTLIER) cc_final: 0.7663 (tp) REVERT: A 784 GLU cc_start: 0.5719 (mm-30) cc_final: 0.4708 (mm-30) REVERT: A 1023 MET cc_start: 0.1561 (mmt) cc_final: 0.0593 (mtp) outliers start: 21 outliers final: 16 residues processed: 119 average time/residue: 0.1798 time to fit residues: 30.3088 Evaluate side-chains 123 residues out of total 872 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 104 time to evaluate : 0.891 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 LEU Chi-restraints excluded: chain A residue 99 VAL Chi-restraints excluded: chain A residue 104 VAL Chi-restraints excluded: chain A residue 119 LEU Chi-restraints excluded: chain A residue 140 ILE Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 373 GLU Chi-restraints excluded: chain A residue 376 THR Chi-restraints excluded: chain A residue 448 LEU Chi-restraints excluded: chain A residue 508 MET Chi-restraints excluded: chain A residue 553 SER Chi-restraints excluded: chain A residue 575 MET Chi-restraints excluded: chain A residue 591 THR Chi-restraints excluded: chain A residue 659 GLU Chi-restraints excluded: chain A residue 715 ILE Chi-restraints excluded: chain A residue 738 ASN Chi-restraints excluded: chain A residue 771 VAL Chi-restraints excluded: chain A residue 916 SER Chi-restraints excluded: chain A residue 969 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 102 random chunks: chunk 22 optimal weight: 0.0670 chunk 81 optimal weight: 0.5980 chunk 33 optimal weight: 7.9990 chunk 83 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 14 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 4 optimal weight: 6.9990 chunk 58 optimal weight: 4.9990 chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.8520 ------------------------------------------------------------------------------- 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 = 0.4000 r_free = 0.4000 target = 0.178430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3628 r_free = 0.3628 target = 0.143344 restraints weight = 8700.126| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.78 r_work: 0.3528 rms_B_bonded: 2.51 restraints_weight: 0.5000 r_work: 0.3389 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.3389 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7335 moved from start: 0.1912 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.035 8017 Z= 0.162 Angle : 0.811 29.796 10882 Z= 0.335 Chirality : 0.041 0.166 1276 Planarity : 0.004 0.044 1387 Dihedral : 3.935 16.595 1078 Min Nonbonded Distance : 1.970 Molprobity Statistics. All-atom Clashscore : 8.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.41 % Allowed : 16.21 % Favored : 81.38 % 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: 0.44 (0.26), residues: 1014 helix: 1.30 (0.24), residues: 485 sheet: -0.32 (0.50), residues: 103 loop : -0.67 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 854 HIS 0.003 0.001 HIS A 566 PHE 0.027 0.001 PHE A 759 TYR 0.017 0.001 TYR A 295 ARG 0.004 0.000 ARG A 549 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1908.34 seconds wall clock time: 35 minutes 11.25 seconds (2111.25 seconds total)