Starting phenix.real_space_refine on Wed Feb 14 18:35:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7v_8642/02_2024/5v7v_8642_neut_trim.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7v_8642/02_2024/5v7v_8642.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7v_8642/02_2024/5v7v_8642.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7v_8642/02_2024/5v7v_8642.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7v_8642/02_2024/5v7v_8642_neut_trim.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/5v7v_8642/02_2024/5v7v_8642_neut_trim.pdb" } resolution = 3.9 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 ------------------------------------------------------------------------------- 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= 0.008 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: 5 Type Number sf(0) Gaussians S 20 5.16 5 C 3260 2.51 5 N 852 2.21 5 O 976 1.98 5 H 4811 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 59": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ARG 87": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 180": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 338": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 414": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 525": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Residue "A ARG 589": "NH1" <-> "NH2" "HH11" <-> "HH21" "HH12" <-> "HH22" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9919 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 9799 Number of conformers: 1 Conformer: "" Number of residues, atoms: 613, 9799 Classifications: {'peptide': 613} Link IDs: {'PTRANS': 21, 'TRANS': 591} Chain breaks: 1 Unresolved non-hydrogen bonds: 7 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 7 Chain: "B" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "C" Number of atoms: 39 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 39 Unusual residues: {'BMA': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Chain: "A" Number of atoms: 42 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 42 Unusual residues: {'NAG': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 5.12, per 1000 atoms: 0.52 Number of scatterers: 9919 At special positions: 0 Unit cell: (81, 94.5, 109.35, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 20 16.00 O 976 8.00 N 852 7.00 C 3260 6.00 H 4811 1.00 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " " NAG B 2 " - " BMA B 3 " " NAG C 1 " - " NAG C 2 " " NAG C 2 " - " BMA C 3 " NAG-ASN " NAG A 908 " - " ASN A 429 " " NAG A 909 " - " ASN A 611 " " NAG B 1 " - " ASN A 123 " " NAG C 1 " - " ASN A 142 " Time building additional restraints: 8.59 Conformation dependent library (CDL) restraints added in 1.1 seconds 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1170 Finding SS restraints... Secondary structure from input PDB file: 30 helices and 0 sheets defined 71.6% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.70 Creating SS restraints... Processing helix chain 'A' and resid 26 through 38 removed outlier: 3.790A pdb=" N ALA A 30 " --> pdb=" O PRO A 26 " (cutoff:3.500A) removed outlier: 4.064A pdb=" N HIS A 32 " --> pdb=" O PRO A 28 " (cutoff:3.500A) removed outlier: 3.591A pdb=" N LEU A 33 " --> pdb=" O GLU A 29 " (cutoff:3.500A) removed outlier: 4.096A pdb=" N ALA A 38 " --> pdb=" O LEU A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 42 through 50 removed outlier: 3.817A pdb=" N GLU A 46 " --> pdb=" O ASP A 42 " (cutoff:3.500A) removed outlier: 4.353A pdb=" N MET A 49 " --> pdb=" O LYS A 45 " (cutoff:3.500A) removed outlier: 4.284A pdb=" N GLU A 50 " --> pdb=" O GLU A 46 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 80 removed outlier: 3.687A pdb=" N GLU A 71 " --> pdb=" O PRO A 67 " (cutoff:3.500A) removed outlier: 3.943A pdb=" N LYS A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 100 removed outlier: 3.588A pdb=" N TYR A 90 " --> pdb=" O GLN A 86 " (cutoff:3.500A) removed outlier: 4.027A pdb=" N LEU A 92 " --> pdb=" O HIS A 88 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N LEU A 93 " --> pdb=" O ILE A 89 " (cutoff:3.500A) removed outlier: 4.116A pdb=" N VAL A 94 " --> pdb=" O TYR A 90 " (cutoff:3.500A) Processing helix chain 'A' and resid 103 through 114 removed outlier: 3.528A pdb=" N TYR A 107 " --> pdb=" O SER A 103 " (cutoff:3.500A) Processing helix chain 'A' and resid 123 through 137 removed outlier: 3.577A pdb=" N GLU A 132 " --> pdb=" O HIS A 128 " (cutoff:3.500A) removed outlier: 3.817A pdb=" N LYS A 133 " --> pdb=" O LYS A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 156 removed outlier: 3.617A pdb=" N ILE A 146 " --> pdb=" O ASN A 142 " (cutoff:3.500A) removed outlier: 4.545A pdb=" N ASP A 148 " --> pdb=" O SER A 144 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY A 156 " --> pdb=" O MET A 152 " (cutoff:3.500A) Processing helix chain 'A' and resid 170 through 185 removed outlier: 3.634A pdb=" N ALA A 174 " --> pdb=" O ASP A 170 " (cutoff:3.500A) removed outlier: 4.056A pdb=" N TYR A 177 " --> pdb=" O LYS A 173 " (cutoff:3.500A) Processing helix chain 'A' and resid 186 through 200 removed outlier: 3.710A pdb=" N LYS A 190 " --> pdb=" O ASN A 186 " (cutoff:3.500A) Processing helix chain 'A' and resid 206 through 225 removed outlier: 3.750A pdb=" N SER A 210 " --> pdb=" O ASN A 206 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N TYR A 225 " --> pdb=" O LEU A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 233 removed outlier: 3.655A pdb=" N VAL A 233 " --> pdb=" O GLU A 229 " (cutoff:3.500A) Processing helix chain 'A' and resid 318 through 331 removed outlier: 3.864A pdb=" N ILE A 322 " --> pdb=" O ARG A 318 " (cutoff:3.500A) removed outlier: 3.918A pdb=" N ASP A 329 " --> pdb=" O ALA A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 340 through 355 removed outlier: 3.581A pdb=" N GLN A 355 " --> pdb=" O TYR A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 383 removed outlier: 3.818A pdb=" N TYR A 368 " --> pdb=" O LEU A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 406 removed outlier: 3.582A pdb=" N ALA A 394 " --> pdb=" O ASN A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 412 through 426 removed outlier: 3.987A pdb=" N GLN A 424 " --> pdb=" O GLY A 420 " (cutoff:3.500A) Processing helix chain 'A' and resid 429 through 440 Processing helix chain 'A' and resid 448 through 461 removed outlier: 3.821A pdb=" N LYS A 456 " --> pdb=" O PHE A 452 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N LEU A 457 " --> pdb=" O GLN A 453 " (cutoff:3.500A) Processing helix chain 'A' and resid 468 through 478 removed outlier: 3.761A pdb=" N LEU A 472 " --> pdb=" O ASP A 468 " (cutoff:3.500A) removed outlier: 4.218A pdb=" N LEU A 478 " --> pdb=" O GLU A 474 " (cutoff:3.500A) Processing helix chain 'A' and resid 482 through 495 removed outlier: 4.235A pdb=" N TYR A 486 " --> pdb=" O ILE A 482 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N GLU A 487 " --> pdb=" O PRO A 483 " (cutoff:3.500A) removed outlier: 3.919A pdb=" N ILE A 492 " --> pdb=" O PHE A 488 " (cutoff:3.500A) Processing helix chain 'A' and resid 502 through 517 removed outlier: 3.787A pdb=" N ALA A 506 " --> pdb=" O VAL A 502 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N LYS A 515 " --> pdb=" O THR A 511 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N GLU A 517 " --> pdb=" O VAL A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.601A pdb=" N ALA A 529 " --> pdb=" O ARG A 525 " (cutoff:3.500A) removed outlier: 3.746A pdb=" N ASN A 533 " --> pdb=" O ALA A 529 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 547 removed outlier: 4.322A pdb=" N ALA A 539 " --> pdb=" O ARG A 535 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 563 Processing helix chain 'A' and resid 576 through 592 removed outlier: 3.510A pdb=" N LYS A 580 " --> pdb=" O THR A 576 " (cutoff:3.500A) removed outlier: 3.949A pdb=" N SER A 585 " --> pdb=" O THR A 581 " (cutoff:3.500A) Processing helix chain 'A' and resid 595 through 609 removed outlier: 4.145A pdb=" N GLY A 599 " --> pdb=" O ASN A 595 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N VAL A 600 " --> pdb=" O ILE A 596 " (cutoff:3.500A) removed outlier: 4.385A pdb=" N GLN A 608 " --> pdb=" O ASP A 604 " (cutoff:3.500A) removed outlier: 3.534A pdb=" N MET A 609 " --> pdb=" O ILE A 605 " (cutoff:3.500A) Processing helix chain 'A' and resid 611 through 624 removed outlier: 3.601A pdb=" N LEU A 624 " --> pdb=" O GLN A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 640 Processing helix chain 'A' and resid 648 through 663 removed outlier: 3.628A pdb=" N LYS A 652 " --> pdb=" O PHE A 648 " (cutoff:3.500A) removed outlier: 3.590A pdb=" N ARG A 653 " --> pdb=" O HIS A 649 " (cutoff:3.500A) removed outlier: 4.505A pdb=" N SER A 659 " --> pdb=" O TYR A 655 " (cutoff:3.500A) Processing helix chain 'A' and resid 665 through 684 removed outlier: 3.691A pdb=" N SER A 669 " --> pdb=" O PHE A 665 " (cutoff:3.500A) removed outlier: 4.259A pdb=" N LYS A 670 " --> pdb=" O TYR A 666 " (cutoff:3.500A) removed outlier: 3.687A pdb=" N SER A 680 " --> pdb=" O LEU A 676 " (cutoff:3.500A) 262 hydrogen bonds defined for protein. 786 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 3.06 Time building geometry restraints manager: 8.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.82 - 1.02: 4807 1.02 - 1.22: 5 1.22 - 1.41: 2259 1.41 - 1.61: 2938 1.61 - 1.81: 38 Bond restraints: 10047 Sorted by residual: bond pdb=" CA ASN A 101 " pdb=" C ASN A 101 " ideal model delta sigma weight residual 1.523 1.637 -0.114 1.34e-02 5.57e+03 7.21e+01 bond pdb=" CA TRP A 115 " pdb=" C TRP A 115 " ideal model delta sigma weight residual 1.522 1.630 -0.108 1.32e-02 5.74e+03 6.68e+01 bond pdb=" CA PHE A 120 " pdb=" C PHE A 120 " ideal model delta sigma weight residual 1.519 1.587 -0.068 9.50e-03 1.11e+04 5.10e+01 bond pdb=" CZ ARG A 646 " pdb=" NH2 ARG A 646 " ideal model delta sigma weight residual 1.330 1.420 -0.090 1.30e-02 5.92e+03 4.77e+01 bond pdb=" CZ ARG A 646 " pdb=" NH1 ARG A 646 " ideal model delta sigma weight residual 1.323 1.416 -0.093 1.40e-02 5.10e+03 4.44e+01 ... (remaining 10042 not shown) Histogram of bond angle deviations from ideal: 93.44 - 101.57: 30 101.57 - 109.69: 6973 109.69 - 117.81: 5918 117.81 - 125.93: 4923 125.93 - 134.05: 140 Bond angle restraints: 17984 Sorted by residual: angle pdb=" N SER A 116 " pdb=" CA SER A 116 " pdb=" C SER A 116 " ideal model delta sigma weight residual 111.74 95.84 15.90 1.35e+00 5.49e-01 1.39e+02 angle pdb=" N ASN A 102 " pdb=" CA ASN A 102 " pdb=" CB ASN A 102 " ideal model delta sigma weight residual 109.82 126.49 -16.67 1.52e+00 4.33e-01 1.20e+02 angle pdb=" N TRP A 115 " pdb=" CA TRP A 115 " pdb=" C TRP A 115 " ideal model delta sigma weight residual 113.50 126.40 -12.90 1.23e+00 6.61e-01 1.10e+02 angle pdb=" CA TRP A 115 " pdb=" C TRP A 115 " pdb=" O TRP A 115 " ideal model delta sigma weight residual 119.14 129.75 -10.61 1.10e+00 8.26e-01 9.31e+01 angle pdb=" CA TRP A 115 " pdb=" C TRP A 115 " pdb=" N SER A 116 " ideal model delta sigma weight residual 118.31 107.46 10.85 1.40e+00 5.10e-01 6.01e+01 ... (remaining 17979 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 21.99: 4512 21.99 - 43.98: 313 43.98 - 65.96: 62 65.96 - 87.95: 24 87.95 - 109.94: 8 Dihedral angle restraints: 4919 sinusoidal: 2668 harmonic: 2251 Sorted by residual: dihedral pdb=" N ASN A 102 " pdb=" C ASN A 102 " pdb=" CA ASN A 102 " pdb=" CB ASN A 102 " ideal model delta harmonic sigma weight residual 122.80 141.39 -18.59 0 2.50e+00 1.60e-01 5.53e+01 dihedral pdb=" CA PHE A 569 " pdb=" C PHE A 569 " pdb=" N GLU A 570 " pdb=" CA GLU A 570 " ideal model delta harmonic sigma weight residual -180.00 -150.98 -29.02 0 5.00e+00 4.00e-02 3.37e+01 dihedral pdb=" CA ASN A 516 " pdb=" C ASN A 516 " pdb=" N GLU A 517 " pdb=" CA GLU A 517 " ideal model delta harmonic sigma weight residual 180.00 151.22 28.78 0 5.00e+00 4.00e-02 3.31e+01 ... (remaining 4916 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.095: 689 0.095 - 0.191: 76 0.191 - 0.286: 9 0.286 - 0.381: 1 0.381 - 0.476: 2 Chirality restraints: 777 Sorted by residual: chirality pdb=" C1 BMA B 3 " pdb=" O4 NAG B 2 " pdb=" C2 BMA B 3 " pdb=" O5 BMA B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.47 0.07 2.00e-02 2.50e+03 1.18e+01 chirality pdb=" C1 BMA C 3 " pdb=" O4 NAG C 2 " pdb=" C2 BMA C 3 " pdb=" O5 BMA C 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.35 -0.05 2.00e-02 2.50e+03 7.20e+00 chirality pdb=" CA TRP A 115 " pdb=" N TRP A 115 " pdb=" C TRP A 115 " pdb=" CB TRP A 115 " both_signs ideal model delta sigma weight residual False 2.51 2.03 0.48 2.00e-01 2.50e+01 5.67e+00 ... (remaining 774 not shown) Planarity restraints: 1494 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB ASN A 102 " -0.132 2.00e-02 2.50e+03 4.83e-01 3.51e+03 pdb=" CG ASN A 102 " 0.006 2.00e-02 2.50e+03 pdb=" OD1 ASN A 102 " 0.133 2.00e-02 2.50e+03 pdb=" ND2 ASN A 102 " -0.000 2.00e-02 2.50e+03 pdb="HD21 ASN A 102 " 0.824 2.00e-02 2.50e+03 pdb="HD22 ASN A 102 " -0.830 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 99 " 0.033 2.00e-02 2.50e+03 4.29e-01 2.76e+03 pdb=" CD GLN A 99 " -0.006 2.00e-02 2.50e+03 pdb=" OE1 GLN A 99 " -0.031 2.00e-02 2.50e+03 pdb=" NE2 GLN A 99 " -0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 99 " 0.745 2.00e-02 2.50e+03 pdb="HE22 GLN A 99 " -0.741 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CG GLN A 95 " 0.123 2.00e-02 2.50e+03 4.20e-01 2.64e+03 pdb=" CD GLN A 95 " -0.008 2.00e-02 2.50e+03 pdb=" OE1 GLN A 95 " -0.121 2.00e-02 2.50e+03 pdb=" NE2 GLN A 95 " 0.000 2.00e-02 2.50e+03 pdb="HE21 GLN A 95 " -0.713 2.00e-02 2.50e+03 pdb="HE22 GLN A 95 " 0.719 2.00e-02 2.50e+03 ... (remaining 1491 not shown) Histogram of nonbonded interaction distances: 1.10 - 1.80: 38 1.80 - 2.50: 7443 2.50 - 3.20: 29283 3.20 - 3.90: 36037 3.90 - 4.60: 55896 Nonbonded interactions: 128697 Sorted by model distance: nonbonded pdb=" HB2 SER A 40 " pdb="HE22 GLN A 117 " model vdw 1.096 2.270 nonbonded pdb=" HD2 TYR A 612 " pdb=" HB3 LEU A 642 " model vdw 1.139 2.270 nonbonded pdb="HD22 ASN A 102 " pdb=" HG3 GLU A 104 " model vdw 1.200 2.270 nonbonded pdb="HD13 ILE A 37 " pdb=" HD1 TYR A 118 " model vdw 1.217 2.270 nonbonded pdb=" HB2 SER A 40 " pdb=" NE2 GLN A 117 " model vdw 1.238 2.770 ... (remaining 128692 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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 group one per residue 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: 0.320 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: 0.140 Extract box with map and model: 2.080 Check model and map are aligned: 0.130 Set scattering table: 0.100 Process input model: 35.290 Find NCS groups from input model: 0.180 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.580 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.860 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6958 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 : 0.011 0.114 5236 Z= 0.719 Angle : 1.216 16.672 7097 Z= 0.737 Chirality : 0.067 0.476 777 Planarity : 0.007 0.069 900 Dihedral : 15.676 109.939 2053 Min Nonbonded Distance : 1.713 Molprobity Statistics. All-atom Clashscore : 18.52 Ramachandran Plot: Outliers : 0.16 % Allowed : 11.17 % Favored : 88.67 % Rotamer: Outliers : 0.00 % Allowed : 10.96 % Favored : 89.04 % Cbeta Deviations : 0.17 % 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: -4.92 (0.26), residues: 609 helix: -2.93 (0.19), residues: 393 sheet: None (None), residues: 0 loop : -3.66 (0.38), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP A 541 HIS 0.009 0.002 HIS A 113 PHE 0.022 0.003 PHE A 59 TYR 0.032 0.003 TYR A 655 ARG 0.013 0.002 ARG A 574 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 171 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 171 time to evaluate : 0.765 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.3729 (p90) cc_final: 0.3044 (p90) REVERT: A 65 TYR cc_start: 0.8512 (t80) cc_final: 0.8218 (t80) REVERT: A 87 ARG cc_start: 0.8880 (mtp85) cc_final: 0.8581 (mtp85) REVERT: A 91 GLU cc_start: 0.8486 (tt0) cc_final: 0.7896 (tp30) REVERT: A 122 HIS cc_start: 0.8578 (p90) cc_final: 0.7864 (p90) REVERT: A 329 ASP cc_start: 0.8063 (t70) cc_final: 0.7682 (t70) REVERT: A 595 ASN cc_start: 0.7219 (t0) cc_final: 0.6814 (t0) REVERT: A 604 ASP cc_start: 0.8875 (m-30) cc_final: 0.8560 (m-30) REVERT: A 620 GLN cc_start: 0.9046 (tm-30) cc_final: 0.8712 (tm-30) REVERT: A 637 MET cc_start: 0.7251 (tpt) cc_final: 0.6711 (tpt) outliers start: 0 outliers final: 0 residues processed: 171 average time/residue: 0.4482 time to fit residues: 92.9648 Evaluate side-chains 116 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 51 optimal weight: 1.9990 chunk 46 optimal weight: 0.9980 chunk 25 optimal weight: 3.9990 chunk 15 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 24 optimal weight: 1.9990 chunk 47 optimal weight: 0.6980 chunk 18 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 0.6980 chunk 55 optimal weight: 0.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 206 ASN A 355 GLN ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 593 GLN A 677 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6967 moved from start: 0.3126 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 5236 Z= 0.218 Angle : 0.737 8.056 7097 Z= 0.392 Chirality : 0.039 0.161 777 Planarity : 0.006 0.069 900 Dihedral : 11.775 67.278 871 Min Nonbonded Distance : 2.065 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.17 % Favored : 88.83 % Rotamer: Outliers : 1.70 % Allowed : 15.88 % Favored : 82.42 % 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: -3.54 (0.29), residues: 609 helix: -1.73 (0.21), residues: 413 sheet: None (None), residues: 0 loop : -3.49 (0.41), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 78 HIS 0.003 0.001 HIS A 139 PHE 0.014 0.002 PHE A 488 TYR 0.014 0.002 TYR A 560 ARG 0.005 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 132 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 123 time to evaluate : 0.752 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.3682 (p90) cc_final: 0.3013 (p90) REVERT: A 87 ARG cc_start: 0.8768 (mtp85) cc_final: 0.8267 (mtp85) REVERT: A 91 GLU cc_start: 0.8564 (tt0) cc_final: 0.7997 (tp30) REVERT: A 100 PHE cc_start: 0.7865 (m-80) cc_final: 0.7374 (m-10) REVERT: A 122 HIS cc_start: 0.8640 (p90) cc_final: 0.8004 (p90) REVERT: A 179 GLN cc_start: 0.9016 (mt0) cc_final: 0.8561 (mt0) REVERT: A 396 GLU cc_start: 0.8407 (mp0) cc_final: 0.8145 (mp0) REVERT: A 451 GLU cc_start: 0.9361 (mp0) cc_final: 0.8953 (mp0) REVERT: A 595 ASN cc_start: 0.7340 (t0) cc_final: 0.7029 (t0) REVERT: A 604 ASP cc_start: 0.8607 (m-30) cc_final: 0.8239 (m-30) REVERT: A 620 GLN cc_start: 0.8878 (tm-30) cc_final: 0.8444 (tm-30) REVERT: A 637 MET cc_start: 0.7286 (tpt) cc_final: 0.6906 (tpt) outliers start: 9 outliers final: 5 residues processed: 128 average time/residue: 0.3125 time to fit residues: 52.6854 Evaluate side-chains 116 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 111 time to evaluate : 0.835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 645 ASN Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 30 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 59 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 18 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 overall best weight: 2.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 202 ASN ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 564 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7031 moved from start: 0.3932 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 5236 Z= 0.310 Angle : 0.694 6.812 7097 Z= 0.377 Chirality : 0.040 0.158 777 Planarity : 0.006 0.066 900 Dihedral : 8.284 50.617 871 Min Nonbonded Distance : 1.986 Molprobity Statistics. All-atom Clashscore : 14.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 3.21 % Allowed : 15.88 % Favored : 80.91 % 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: -2.71 (0.31), residues: 609 helix: -1.04 (0.23), residues: 410 sheet: None (None), residues: 0 loop : -3.29 (0.43), residues: 199 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 27 HIS 0.004 0.001 HIS A 113 PHE 0.016 0.002 PHE A 607 TYR 0.017 0.002 TYR A 563 ARG 0.003 0.001 ARG A 227 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 127 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 110 time to evaluate : 0.852 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 56 PHE cc_start: 0.4010 (p90) cc_final: 0.3247 (p90) REVERT: A 87 ARG cc_start: 0.8848 (mtp85) cc_final: 0.8504 (mtp180) REVERT: A 90 TYR cc_start: 0.8521 (t80) cc_final: 0.8290 (t80) REVERT: A 91 GLU cc_start: 0.8592 (tt0) cc_final: 0.8031 (tp30) REVERT: A 158 CYS cc_start: 0.6255 (m) cc_final: 0.5737 (m) REVERT: A 241 ASN cc_start: 0.8933 (p0) cc_final: 0.8702 (p0) REVERT: A 320 ILE cc_start: 0.8929 (pp) cc_final: 0.8725 (tt) REVERT: A 395 GLU cc_start: 0.8968 (tm-30) cc_final: 0.8737 (tm-30) REVERT: A 441 MET cc_start: 0.8173 (tmm) cc_final: 0.7690 (tmm) REVERT: A 451 GLU cc_start: 0.9194 (mp0) cc_final: 0.8770 (mp0) REVERT: A 485 ILE cc_start: 0.8183 (mm) cc_final: 0.7962 (mt) REVERT: A 604 ASP cc_start: 0.8688 (m-30) cc_final: 0.8335 (m-30) REVERT: A 620 GLN cc_start: 0.8970 (tm-30) cc_final: 0.8610 (tm-30) REVERT: A 637 MET cc_start: 0.7651 (tpt) cc_final: 0.7337 (tpt) outliers start: 17 outliers final: 13 residues processed: 119 average time/residue: 0.3447 time to fit residues: 53.7529 Evaluate side-chains 118 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.801 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 41 optimal weight: 0.9980 chunk 28 optimal weight: 0.2980 chunk 6 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 37 optimal weight: 4.9990 chunk 55 optimal weight: 3.9990 chunk 58 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 52 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 49 optimal weight: 0.6980 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 102 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7014 moved from start: 0.4381 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 5236 Z= 0.191 Angle : 0.608 7.971 7097 Z= 0.325 Chirality : 0.037 0.203 777 Planarity : 0.005 0.058 900 Dihedral : 7.314 52.747 871 Min Nonbonded Distance : 2.050 Molprobity Statistics. All-atom Clashscore : 11.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.20 % Favored : 90.80 % Rotamer: Outliers : 1.89 % Allowed : 17.96 % Favored : 80.15 % 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: -2.04 (0.33), residues: 609 helix: -0.47 (0.24), residues: 414 sheet: None (None), residues: 0 loop : -3.23 (0.44), residues: 195 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 27 HIS 0.004 0.001 HIS A 128 PHE 0.020 0.002 PHE A 120 TYR 0.010 0.001 TYR A 619 ARG 0.003 0.000 ARG A 31 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 115 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 105 time to evaluate : 0.827 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8873 (mpp) cc_final: 0.8488 (mtm) REVERT: A 78 TRP cc_start: 0.8733 (t60) cc_final: 0.8448 (t60) REVERT: A 87 ARG cc_start: 0.8747 (mtp85) cc_final: 0.8359 (mtp180) REVERT: A 90 TYR cc_start: 0.8533 (t80) cc_final: 0.8221 (t80) REVERT: A 91 GLU cc_start: 0.8511 (tt0) cc_final: 0.8080 (tp30) REVERT: A 158 CYS cc_start: 0.6020 (m) cc_final: 0.5491 (m) REVERT: A 241 ASN cc_start: 0.9068 (p0) cc_final: 0.8825 (p0) REVERT: A 320 ILE cc_start: 0.8854 (pp) cc_final: 0.8622 (tt) REVERT: A 396 GLU cc_start: 0.8626 (mp0) cc_final: 0.8324 (tp30) REVERT: A 451 GLU cc_start: 0.9147 (mp0) cc_final: 0.8787 (mp0) REVERT: A 485 ILE cc_start: 0.8204 (mm) cc_final: 0.7991 (mt) REVERT: A 604 ASP cc_start: 0.8637 (m-30) cc_final: 0.8292 (m-30) REVERT: A 620 GLN cc_start: 0.8944 (tm-30) cc_final: 0.8568 (tm-30) outliers start: 10 outliers final: 8 residues processed: 110 average time/residue: 0.3141 time to fit residues: 45.9900 Evaluate side-chains 113 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 105 time to evaluate : 0.780 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 607 PHE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 0.5980 chunk 24 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 40 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 chunk 52 optimal weight: 2.9990 chunk 14 optimal weight: 6.9990 chunk 19 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 overall best weight: 1.4984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 424 GLN A 564 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7030 moved from start: 0.4731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 5236 Z= 0.216 Angle : 0.615 9.771 7097 Z= 0.326 Chirality : 0.038 0.207 777 Planarity : 0.005 0.058 900 Dihedral : 6.859 54.715 871 Min Nonbonded Distance : 1.999 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.33 % Favored : 88.67 % Rotamer: Outliers : 3.21 % Allowed : 17.96 % Favored : 78.83 % 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: -1.76 (0.34), residues: 609 helix: -0.20 (0.25), residues: 413 sheet: None (None), residues: 0 loop : -3.26 (0.44), residues: 196 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP A 681 HIS 0.005 0.001 HIS A 113 PHE 0.014 0.002 PHE A 120 TYR 0.010 0.001 TYR A 563 ARG 0.002 0.000 ARG A 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.763 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8792 (mpp) cc_final: 0.8443 (mtm) REVERT: A 87 ARG cc_start: 0.8585 (mtp85) cc_final: 0.8245 (mtp180) REVERT: A 91 GLU cc_start: 0.8406 (tt0) cc_final: 0.7980 (tp30) REVERT: A 158 CYS cc_start: 0.6123 (m) cc_final: 0.5486 (m) REVERT: A 241 ASN cc_start: 0.9140 (p0) cc_final: 0.8920 (p0) REVERT: A 320 ILE cc_start: 0.8909 (pp) cc_final: 0.8683 (tt) REVERT: A 393 MET cc_start: 0.8972 (ttp) cc_final: 0.8770 (tpp) REVERT: A 441 MET cc_start: 0.8304 (tmm) cc_final: 0.7740 (tmm) REVERT: A 604 ASP cc_start: 0.8601 (m-30) cc_final: 0.8289 (m-30) REVERT: A 620 GLN cc_start: 0.8951 (tm-30) cc_final: 0.8565 (tm-30) outliers start: 17 outliers final: 13 residues processed: 111 average time/residue: 0.3254 time to fit residues: 47.4795 Evaluate side-chains 118 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 105 time to evaluate : 0.748 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 219 GLU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 3.9990 chunk 14 optimal weight: 6.9990 chunk 59 optimal weight: 4.9990 chunk 48 optimal weight: 2.9990 chunk 27 optimal weight: 4.9990 chunk 4 optimal weight: 1.9990 chunk 19 optimal weight: 3.9990 chunk 30 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 6 optimal weight: 2.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 101 ASN A 424 GLN A 564 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 moved from start: 0.5197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.053 5236 Z= 0.374 Angle : 0.686 9.774 7097 Z= 0.379 Chirality : 0.040 0.210 777 Planarity : 0.005 0.064 900 Dihedral : 7.232 51.468 871 Min Nonbonded Distance : 1.928 Molprobity Statistics. All-atom Clashscore : 16.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.81 % Favored : 87.19 % Rotamer: Outliers : 3.97 % Allowed : 17.77 % Favored : 78.26 % 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: -2.10 (0.33), residues: 609 helix: -0.49 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -3.37 (0.45), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 230 HIS 0.010 0.002 HIS A 113 PHE 0.016 0.002 PHE A 607 TYR 0.020 0.002 TYR A 563 ARG 0.004 0.001 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 128 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 107 time to evaluate : 0.734 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8824 (mpp) cc_final: 0.8581 (mpp) REVERT: A 158 CYS cc_start: 0.6634 (m) cc_final: 0.6092 (m) REVERT: A 241 ASN cc_start: 0.9096 (p0) cc_final: 0.8878 (p0) REVERT: A 441 MET cc_start: 0.8623 (tmm) cc_final: 0.8192 (tmm) REVERT: A 451 GLU cc_start: 0.9111 (mp0) cc_final: 0.8800 (mp0) REVERT: A 491 MET cc_start: 0.7730 (mtt) cc_final: 0.7319 (mtm) REVERT: A 517 GLU cc_start: 0.8475 (tm-30) cc_final: 0.8257 (tm-30) REVERT: A 604 ASP cc_start: 0.8650 (m-30) cc_final: 0.8321 (m-30) REVERT: A 620 GLN cc_start: 0.9013 (tm-30) cc_final: 0.8646 (tm-30) outliers start: 21 outliers final: 18 residues processed: 118 average time/residue: 0.3193 time to fit residues: 49.5332 Evaluate side-chains 119 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 101 time to evaluate : 0.755 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 199 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 508 LEU Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 33 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 49 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 58 optimal weight: 4.9990 chunk 36 optimal weight: 1.9990 chunk 35 optimal weight: 0.6980 chunk 27 optimal weight: 3.9990 chunk 23 optimal weight: 4.9990 chunk 17 optimal weight: 0.9980 chunk 11 optimal weight: 5.9990 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7048 moved from start: 0.5436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 5236 Z= 0.196 Angle : 0.600 9.138 7097 Z= 0.322 Chirality : 0.037 0.182 777 Planarity : 0.005 0.065 900 Dihedral : 6.843 50.638 871 Min Nonbonded Distance : 2.011 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.00 % Favored : 89.00 % Rotamer: Outliers : 3.21 % Allowed : 18.53 % Favored : 78.26 % 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: -1.64 (0.34), residues: 609 helix: -0.12 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -3.25 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 230 HIS 0.004 0.001 HIS A 128 PHE 0.015 0.002 PHE A 207 TYR 0.010 0.001 TYR A 655 ARG 0.003 0.000 ARG A 406 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 123 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 106 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8916 (mpp) cc_final: 0.8653 (mpp) REVERT: A 158 CYS cc_start: 0.6494 (m) cc_final: 0.6045 (m) REVERT: A 219 GLU cc_start: 0.8441 (mm-30) cc_final: 0.8236 (mm-30) REVERT: A 241 ASN cc_start: 0.9188 (p0) cc_final: 0.8958 (p0) REVERT: A 491 MET cc_start: 0.7737 (mtt) cc_final: 0.7357 (mtm) REVERT: A 604 ASP cc_start: 0.8597 (m-30) cc_final: 0.8285 (m-30) REVERT: A 620 GLN cc_start: 0.9027 (tm-30) cc_final: 0.8642 (tm-30) outliers start: 17 outliers final: 16 residues processed: 114 average time/residue: 0.2847 time to fit residues: 44.3296 Evaluate side-chains 119 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 103 time to evaluate : 0.785 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 4.9990 chunk 40 optimal weight: 3.9990 chunk 29 optimal weight: 3.9990 chunk 5 optimal weight: 0.9990 chunk 46 optimal weight: 3.9990 chunk 53 optimal weight: 4.9990 chunk 56 optimal weight: 3.9990 chunk 51 optimal weight: 2.9990 chunk 54 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 424 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7072 moved from start: 0.5635 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 5236 Z= 0.274 Angle : 0.624 8.921 7097 Z= 0.340 Chirality : 0.038 0.167 777 Planarity : 0.005 0.067 900 Dihedral : 6.806 48.603 871 Min Nonbonded Distance : 1.974 Molprobity Statistics. All-atom Clashscore : 16.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.64 % Favored : 87.36 % Rotamer: Outliers : 3.21 % Allowed : 18.53 % Favored : 78.26 % 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: -1.61 (0.34), residues: 609 helix: -0.07 (0.24), residues: 418 sheet: None (None), residues: 0 loop : -3.32 (0.46), residues: 191 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 237 HIS 0.004 0.001 HIS A 143 PHE 0.014 0.002 PHE A 607 TYR 0.014 0.001 TYR A 368 ARG 0.003 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 121 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 104 time to evaluate : 0.853 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8914 (mpp) cc_final: 0.8632 (mpp) REVERT: A 158 CYS cc_start: 0.6616 (m) cc_final: 0.6110 (m) REVERT: A 219 GLU cc_start: 0.8512 (mm-30) cc_final: 0.8156 (mp0) REVERT: A 491 MET cc_start: 0.7778 (mtt) cc_final: 0.7423 (mtm) REVERT: A 604 ASP cc_start: 0.8533 (m-30) cc_final: 0.8194 (m-30) REVERT: A 620 GLN cc_start: 0.9066 (tm-30) cc_final: 0.8742 (tm-30) outliers start: 17 outliers final: 17 residues processed: 114 average time/residue: 0.2790 time to fit residues: 43.5254 Evaluate side-chains 116 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 99 time to evaluate : 0.737 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 76 SER Chi-restraints excluded: chain A residue 77 ILE Chi-restraints excluded: chain A residue 100 PHE Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 228 ASP Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 23 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 49 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 54 optimal weight: 4.9990 chunk 35 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 overall best weight: 1.3184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7044 moved from start: 0.5765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 5236 Z= 0.196 Angle : 0.596 8.366 7097 Z= 0.318 Chirality : 0.037 0.170 777 Planarity : 0.004 0.064 900 Dihedral : 6.610 47.695 871 Min Nonbonded Distance : 2.030 Molprobity Statistics. All-atom Clashscore : 15.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.18 % Favored : 89.82 % Rotamer: Outliers : 3.21 % Allowed : 19.66 % Favored : 77.13 % 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: -1.27 (0.35), residues: 609 helix: 0.24 (0.25), residues: 416 sheet: None (None), residues: 0 loop : -3.29 (0.46), residues: 193 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 681 HIS 0.003 0.001 HIS A 378 PHE 0.013 0.002 PHE A 207 TYR 0.016 0.001 TYR A 666 ARG 0.002 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 102 time to evaluate : 0.806 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8985 (mpp) cc_final: 0.8714 (mpp) REVERT: A 158 CYS cc_start: 0.6508 (m) cc_final: 0.5852 (m) REVERT: A 176 LEU cc_start: 0.9172 (tp) cc_final: 0.8811 (mm) REVERT: A 177 TYR cc_start: 0.8655 (m-10) cc_final: 0.8354 (m-10) REVERT: A 219 GLU cc_start: 0.8495 (mm-30) cc_final: 0.8147 (mp0) REVERT: A 256 LEU cc_start: 0.6980 (OUTLIER) cc_final: 0.6300 (pt) REVERT: A 441 MET cc_start: 0.8595 (tmm) cc_final: 0.8004 (tmm) REVERT: A 491 MET cc_start: 0.7752 (mtt) cc_final: 0.7390 (mtm) REVERT: A 604 ASP cc_start: 0.8496 (m-30) cc_final: 0.8175 (m-30) REVERT: A 620 GLN cc_start: 0.9033 (tm-30) cc_final: 0.8674 (tm-30) outliers start: 17 outliers final: 15 residues processed: 111 average time/residue: 0.2679 time to fit residues: 40.6379 Evaluate side-chains 116 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 100 time to evaluate : 0.779 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 109 LEU Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 256 LEU Chi-restraints excluded: chain A residue 319 ILE Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 447 ASN Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 552 GLU Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 55 optimal weight: 1.9990 chunk 48 optimal weight: 0.4980 chunk 5 optimal weight: 0.9980 chunk 37 optimal weight: 0.1980 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 14 optimal weight: 5.9990 chunk 44 optimal weight: 1.9990 chunk 7 optimal weight: 6.9990 chunk 13 optimal weight: 4.9990 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7029 moved from start: 0.5931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 5236 Z= 0.175 Angle : 0.581 7.512 7097 Z= 0.306 Chirality : 0.036 0.144 777 Planarity : 0.004 0.062 900 Dihedral : 6.355 47.413 871 Min Nonbonded Distance : 2.037 Molprobity Statistics. All-atom Clashscore : 14.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.51 % Favored : 89.49 % Rotamer: Outliers : 2.46 % Allowed : 20.23 % Favored : 77.32 % 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: -1.07 (0.35), residues: 609 helix: 0.44 (0.25), residues: 419 sheet: None (None), residues: 0 loop : -3.41 (0.44), residues: 190 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 681 HIS 0.003 0.001 HIS A 378 PHE 0.011 0.001 PHE A 207 TYR 0.010 0.001 TYR A 666 ARG 0.002 0.000 ARG A 227 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1218 Ramachandran restraints generated. 609 Oldfield, 0 Emsley, 609 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue ALA 30 is missing expected H atoms. Skipping. Residue LYS 39 is missing expected H atoms. Skipping. Residue MET 496 is missing expected H atoms. Skipping. Evaluate side-chains 119 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 106 time to evaluate : 0.742 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 MET cc_start: 0.8975 (mpp) cc_final: 0.8746 (mpp) REVERT: A 158 CYS cc_start: 0.6148 (m) cc_final: 0.5900 (m) REVERT: A 177 TYR cc_start: 0.8628 (m-10) cc_final: 0.8395 (m-10) REVERT: A 355 GLN cc_start: 0.7045 (tp-100) cc_final: 0.6791 (tp-100) REVERT: A 441 MET cc_start: 0.8561 (tmm) cc_final: 0.7963 (tmm) REVERT: A 491 MET cc_start: 0.7743 (mtt) cc_final: 0.7395 (mtm) REVERT: A 604 ASP cc_start: 0.8490 (m-30) cc_final: 0.8202 (m-30) REVERT: A 620 GLN cc_start: 0.9032 (tm-30) cc_final: 0.8669 (tm-30) REVERT: A 666 TYR cc_start: 0.6936 (t80) cc_final: 0.6234 (t80) outliers start: 13 outliers final: 12 residues processed: 113 average time/residue: 0.2836 time to fit residues: 43.7561 Evaluate side-chains 115 residues out of total 531 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 103 time to evaluate : 0.908 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 144 SER Chi-restraints excluded: chain A residue 149 LEU Chi-restraints excluded: chain A residue 234 PHE Chi-restraints excluded: chain A residue 251 LEU Chi-restraints excluded: chain A residue 349 LEU Chi-restraints excluded: chain A residue 396 GLU Chi-restraints excluded: chain A residue 398 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 538 VAL Chi-restraints excluded: chain A residue 544 SER Chi-restraints excluded: chain A residue 607 PHE Chi-restraints excluded: chain A residue 648 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 61 random chunks: chunk 48 optimal weight: 2.9990 chunk 20 optimal weight: 0.8980 chunk 49 optimal weight: 0.7980 chunk 6 optimal weight: 2.9990 chunk 8 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 chunk 2 optimal weight: 0.6980 chunk 35 optimal weight: 0.9980 chunk 55 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 41 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 564 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3489 r_free = 0.3489 target = 0.112280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3189 r_free = 0.3189 target = 0.093960 restraints weight = 34477.205| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.097673 restraints weight = 15323.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.100133 restraints weight = 9184.561| |-----------------------------------------------------------------------------| r_work (final): 0.3287 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8005 moved from start: 0.5967 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 5236 Z= 0.169 Angle : 0.578 6.460 7097 Z= 0.306 Chirality : 0.036 0.157 777 Planarity : 0.004 0.062 900 Dihedral : 6.250 48.061 871 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 15.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 2.84 % Allowed : 20.42 % Favored : 76.75 % 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: -1.02 (0.35), residues: 609 helix: 0.49 (0.26), residues: 421 sheet: None (None), residues: 0 loop : -3.46 (0.43), residues: 188 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 632 HIS 0.003 0.001 HIS A 143 PHE 0.012 0.001 PHE A 207 TYR 0.016 0.001 TYR A 368 ARG 0.002 0.000 ARG A 227 =============================================================================== Job complete usr+sys time: 2545.77 seconds wall clock time: 45 minutes 55.88 seconds (2755.88 seconds total)