Starting phenix.real_space_refine on Thu Feb 15 07:46:04 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wca_21604/02_2024/6wca_21604.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wca_21604/02_2024/6wca_21604.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.03 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wca_21604/02_2024/6wca_21604.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wca_21604/02_2024/6wca_21604.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wca_21604/02_2024/6wca_21604.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wca_21604/02_2024/6wca_21604.pdb" } resolution = 3.03 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= 1.000 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: 6 Type Number sf(0) Gaussians K 5 8.98 5 S 38 5.16 5 C 3758 2.51 5 N 940 2.21 5 O 994 1.98 5 H 5910 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 59": "OE1" <-> "OE2" Residue "A ASP 67": "OD1" <-> "OD2" Residue "A PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 135": "OD1" <-> "OD2" Residue "A PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A GLU 282": "OE1" <-> "OE2" Residue "A GLU 293": "OE1" <-> "OE2" Residue "A PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "A ASP 371": "OD1" <-> "OD2" Residue "A GLU 372": "OE1" <-> "OE2" Residue "A GLU 374": "OE1" <-> "OE2" Residue "A GLU 403": "OE1" <-> "OE2" Residue "A GLU 415": "OE1" <-> "OE2" Residue "A PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 59": "OE1" <-> "OE2" Residue "B ASP 67": "OD1" <-> "OD2" Residue "B PHE 85": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 135": "OD1" <-> "OD2" Residue "B PHE 143": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 160": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 162": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B GLU 282": "OE1" <-> "OE2" Residue "B GLU 293": "OE1" <-> "OE2" Residue "B PHE 310": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 314": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 317": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 331": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B TYR 359": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B PHE 365": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Residue "B ASP 371": "OD1" <-> "OD2" Residue "B GLU 372": "OE1" <-> "OE2" Residue "B GLU 374": "OE1" <-> "OE2" Residue "B GLU 403": "OE1" <-> "OE2" Residue "B GLU 415": "OE1" <-> "OE2" Residue "B PHE 434": "CD1" <-> "CD2" "CE1" <-> "CE2" "HD1" <-> "HD2" "HE1" <-> "HE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 11645 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5807 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5807 Number of conformers: 1 Conformer: "" Number of residues, atoms: 367, 5807 Classifications: {'peptide': 367} Link IDs: {'PTRANS': 16, 'TRANS': 350} Chain breaks: 1 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 3 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 3 Unusual residues: {' K': 3} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 2 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 2 Unusual residues: {' K': 2} Classifications: {'undetermined': 2} Link IDs: {None: 1} Chain: "A" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Chain: "B" Number of atoms: 13 Number of conformers: 1 Conformer: "" Number of residues, atoms: 13, 13 Classifications: {'water': 13} Link IDs: {None: 12} Time building chain proxies: 5.52, per 1000 atoms: 0.47 Number of scatterers: 11645 At special positions: 0 Unit cell: (107.712, 68.544, 77.248, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) K 5 19.00 S 38 16.00 O 994 8.00 N 940 7.00 C 3758 6.00 H 5910 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 Time building additional restraints: 10.57 Conformation dependent library (CDL) restraints added in 1.2 seconds 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1404 Finding SS restraints... Secondary structure from input PDB file: 40 helices and 0 sheets defined 88.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 52 through 57 Processing helix chain 'A' and resid 61 through 65 Processing helix chain 'A' and resid 67 through 103 removed outlier: 3.526A pdb=" N GLN A 71 " --> pdb=" O ASP A 67 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA A 75 " --> pdb=" O GLN A 71 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL A 101 " --> pdb=" O ARG A 97 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N GLY A 103 " --> pdb=" O PHE A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 122 removed outlier: 3.643A pdb=" N PHE A 122 " --> pdb=" O MET A 118 " (cutoff:3.500A) Processing helix chain 'A' and resid 122 through 133 removed outlier: 4.242A pdb=" N THR A 132 " --> pdb=" O SER A 128 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE A 133 " --> pdb=" O LEU A 129 " (cutoff:3.500A) Processing helix chain 'A' and resid 137 through 164 removed outlier: 3.545A pdb=" N PHE A 164 " --> pdb=" O TYR A 160 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 257 through 285 removed outlier: 3.852A pdb=" N VAL A 285 " --> pdb=" O CYS A 281 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 295 Processing helix chain 'A' and resid 298 through 305 removed outlier: 3.813A pdb=" N ALA A 302 " --> pdb=" O SER A 298 " (cutoff:3.500A) Processing helix chain 'A' and resid 306 through 333 removed outlier: 3.774A pdb=" N HIS A 333 " --> pdb=" O SER A 329 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 353 Processing helix chain 'A' and resid 354 through 359 Processing helix chain 'A' and resid 371 through 398 removed outlier: 4.046A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 5.047A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 476 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 52 through 57 Processing helix chain 'B' and resid 61 through 65 Processing helix chain 'B' and resid 67 through 103 removed outlier: 3.526A pdb=" N GLN B 71 " --> pdb=" O ASP B 67 " (cutoff:3.500A) removed outlier: 3.719A pdb=" N ALA B 75 " --> pdb=" O GLN B 71 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N VAL B 101 " --> pdb=" O ARG B 97 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N GLY B 103 " --> pdb=" O PHE B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 122 removed outlier: 3.642A pdb=" N PHE B 122 " --> pdb=" O MET B 118 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 removed outlier: 4.242A pdb=" N THR B 132 " --> pdb=" O SER B 128 " (cutoff:3.500A) removed outlier: 3.621A pdb=" N PHE B 133 " --> pdb=" O LEU B 129 " (cutoff:3.500A) Processing helix chain 'B' and resid 137 through 164 removed outlier: 3.545A pdb=" N PHE B 164 " --> pdb=" O TYR B 160 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 257 through 285 removed outlier: 3.852A pdb=" N VAL B 285 " --> pdb=" O CYS B 281 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 295 Processing helix chain 'B' and resid 298 through 305 removed outlier: 3.813A pdb=" N ALA B 302 " --> pdb=" O SER B 298 " (cutoff:3.500A) Processing helix chain 'B' and resid 306 through 333 removed outlier: 3.772A pdb=" N HIS B 333 " --> pdb=" O SER B 329 " (cutoff:3.500A) Processing helix chain 'B' and resid 338 through 353 Processing helix chain 'B' and resid 354 through 359 Processing helix chain 'B' and resid 371 through 398 removed outlier: 4.045A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.220A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 5.046A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 476 452 hydrogen bonds defined for protein. 1326 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: 4.26 Time building geometry restraints manager: 10.84 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.83 - 1.03: 5892 1.03 - 1.22: 18 1.22 - 1.42: 2386 1.42 - 1.62: 3394 1.62 - 1.81: 58 Bond restraints: 11748 Sorted by residual: bond pdb=" CA VAL B 455 " pdb=" CB VAL B 455 " ideal model delta sigma weight residual 1.539 1.530 0.009 5.40e-03 3.43e+04 2.71e+00 bond pdb=" CA VAL A 455 " pdb=" CB VAL A 455 " ideal model delta sigma weight residual 1.539 1.530 0.009 5.40e-03 3.43e+04 2.54e+00 bond pdb=" CB ASP B 371 " pdb=" HB3 ASP B 371 " ideal model delta sigma weight residual 0.970 1.001 -0.031 2.00e-02 2.50e+03 2.41e+00 bond pdb=" CB ASP B 371 " pdb=" HB2 ASP B 371 " ideal model delta sigma weight residual 0.970 0.939 0.031 2.00e-02 2.50e+03 2.35e+00 bond pdb=" CB ASP B 279 " pdb=" CG ASP B 279 " ideal model delta sigma weight residual 1.516 1.548 -0.032 2.50e-02 1.60e+03 1.62e+00 ... (remaining 11743 not shown) Histogram of bond angle deviations from ideal: 100.43 - 107.15: 300 107.15 - 113.86: 14013 113.86 - 120.57: 4191 120.57 - 127.28: 2728 127.28 - 134.00: 66 Bond angle restraints: 21298 Sorted by residual: angle pdb=" CA ARG A 294 " pdb=" CB ARG A 294 " pdb=" CG ARG A 294 " ideal model delta sigma weight residual 114.10 118.83 -4.73 2.00e+00 2.50e-01 5.59e+00 angle pdb=" CA ARG B 294 " pdb=" CB ARG B 294 " pdb=" CG ARG B 294 " ideal model delta sigma weight residual 114.10 118.80 -4.70 2.00e+00 2.50e-01 5.53e+00 angle pdb=" N SER B 441 " pdb=" CA SER B 441 " pdb=" CB SER B 441 " ideal model delta sigma weight residual 114.17 111.58 2.59 1.14e+00 7.69e-01 5.17e+00 angle pdb=" N SER A 441 " pdb=" CA SER A 441 " pdb=" CB SER A 441 " ideal model delta sigma weight residual 114.17 111.60 2.57 1.14e+00 7.69e-01 5.08e+00 angle pdb=" CG ASP A 371 " pdb=" CB ASP A 371 " pdb=" HB2 ASP A 371 " ideal model delta sigma weight residual 108.00 114.41 -6.41 3.00e+00 1.11e-01 4.57e+00 ... (remaining 21293 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.52: 4787 16.52 - 33.04: 548 33.04 - 49.56: 127 49.56 - 66.08: 58 66.08 - 82.60: 10 Dihedral angle restraints: 5530 sinusoidal: 2938 harmonic: 2592 Sorted by residual: dihedral pdb=" CA ASP A 283 " pdb=" C ASP A 283 " pdb=" N ASN A 284 " pdb=" CA ASN A 284 " ideal model delta harmonic sigma weight residual 180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASP B 283 " pdb=" C ASP B 283 " pdb=" N ASN B 284 " pdb=" CA ASN B 284 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA ASP A 287 " pdb=" C ASP A 287 " pdb=" N PRO A 288 " pdb=" CA PRO A 288 " ideal model delta harmonic sigma weight residual -180.00 -158.38 -21.62 0 5.00e+00 4.00e-02 1.87e+01 ... (remaining 5527 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.026: 636 0.026 - 0.052: 179 0.052 - 0.078: 108 0.078 - 0.104: 40 0.104 - 0.130: 15 Chirality restraints: 978 Sorted by residual: chirality pdb=" CA PRO B 288 " pdb=" N PRO B 288 " pdb=" C PRO B 288 " pdb=" CB PRO B 288 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.22e-01 chirality pdb=" CA PRO A 288 " pdb=" N PRO A 288 " pdb=" C PRO A 288 " pdb=" CB PRO A 288 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.06e-01 chirality pdb=" CA PRO B 62 " pdb=" N PRO B 62 " pdb=" C PRO B 62 " pdb=" CB PRO B 62 " both_signs ideal model delta sigma weight residual False 2.72 2.59 0.13 2.00e-01 2.50e+01 4.01e-01 ... (remaining 975 not shown) Planarity restraints: 1674 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " -0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO A 456 " 0.081 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.024 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C VAL B 455 " 0.031 5.00e-02 4.00e+02 4.68e-02 3.50e+00 pdb=" N PRO B 456 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO B 456 " 0.024 5.00e-02 4.00e+02 pdb=" CD PRO B 456 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LEU A 53 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 54 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 54 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 54 " 0.017 5.00e-02 4.00e+02 ... (remaining 1671 not shown) Histogram of nonbonded interaction distances: 1.59 - 2.30: 2189 2.30 - 3.01: 32664 3.01 - 3.72: 44616 3.72 - 4.43: 65194 4.43 - 5.14: 102460 Nonbonded interactions: 247123 Sorted by model distance: nonbonded pdb=" OD2 ASP B 279 " pdb=" H GLN B 361 " model vdw 1.592 1.850 nonbonded pdb=" OD2 ASP A 279 " pdb=" H GLN A 361 " model vdw 1.593 1.850 nonbonded pdb=" HG SER A 61 " pdb=" OE1 GLU A 63 " model vdw 1.596 1.850 nonbonded pdb=" HG SER B 61 " pdb=" OE1 GLU B 63 " model vdw 1.641 1.850 nonbonded pdb=" O PHE B 85 " pdb=" HG1 THR B 89 " model vdw 1.643 1.850 ... (remaining 247118 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 'A' and (resid 30 through 476 or resid 701 through 702)) selection = chain 'B' } 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: 0.100 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: 0.180 Extract box with map and model: 1.070 Check model and map are aligned: 0.180 Set scattering table: 0.100 Process input model: 42.320 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.050 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:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 47.290 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 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 0.034 5838 Z= 0.189 Angle : 0.607 5.130 7956 Z= 0.342 Chirality : 0.037 0.130 978 Planarity : 0.004 0.047 976 Dihedral : 15.592 82.599 2040 Min Nonbonded Distance : 2.102 Molprobity Statistics. All-atom Clashscore : 8.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.03 % Favored : 96.97 % Rotamer: Outliers : 1.94 % Allowed : 16.77 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.15 (0.30), residues: 726 helix: 0.49 (0.21), residues: 584 sheet: None (None), residues: 0 loop : -2.30 (0.50), residues: 142 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 394 HIS 0.003 0.001 HIS B 328 PHE 0.010 0.001 PHE A 99 TYR 0.016 0.002 TYR B 125 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 113 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 101 time to evaluate : 0.908 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 162 PHE cc_start: 0.8621 (m-80) cc_final: 0.8305 (m-80) REVERT: A 282 GLU cc_start: 0.5094 (mm-30) cc_final: 0.3769 (mm-30) REVERT: A 335 ARG cc_start: 0.7987 (mtp180) cc_final: 0.7736 (mtp-110) REVERT: B 142 LEU cc_start: 0.8401 (mt) cc_final: 0.8098 (tp) REVERT: B 162 PHE cc_start: 0.8685 (m-80) cc_final: 0.8353 (m-80) REVERT: B 282 GLU cc_start: 0.5079 (mm-30) cc_final: 0.3804 (mm-30) REVERT: B 335 ARG cc_start: 0.8035 (mtp180) cc_final: 0.7824 (mtp-110) outliers start: 12 outliers final: 8 residues processed: 113 average time/residue: 0.3796 time to fit residues: 56.2580 Evaluate side-chains 99 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 91 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 303 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 60 optimal weight: 0.2980 chunk 54 optimal weight: 0.9980 chunk 30 optimal weight: 3.9990 chunk 18 optimal weight: 6.9990 chunk 36 optimal weight: 0.9990 chunk 29 optimal weight: 0.9990 chunk 56 optimal weight: 7.9990 chunk 21 optimal weight: 4.9990 chunk 34 optimal weight: 8.9990 chunk 42 optimal weight: 2.9990 chunk 65 optimal weight: 5.9990 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 173 GLN A 368 GLN B 173 GLN B 368 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7565 moved from start: 0.1508 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 5838 Z= 0.187 Angle : 0.561 4.633 7956 Z= 0.290 Chirality : 0.037 0.140 978 Planarity : 0.004 0.045 976 Dihedral : 6.157 56.737 792 Min Nonbonded Distance : 1.900 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.75 % Favored : 97.25 % Rotamer: Outliers : 2.42 % Allowed : 16.45 % Favored : 81.13 % 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: 1.79 (0.32), residues: 726 helix: 1.85 (0.21), residues: 596 sheet: None (None), residues: 0 loop : -2.05 (0.52), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 394 HIS 0.003 0.001 HIS A 400 PHE 0.014 0.001 PHE B 99 TYR 0.013 0.002 TYR B 313 ARG 0.003 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 100 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 85 time to evaluate : 0.842 Fit side-chains REVERT: A 142 LEU cc_start: 0.8272 (mt) cc_final: 0.8032 (tp) REVERT: A 162 PHE cc_start: 0.8713 (m-80) cc_final: 0.8375 (m-80) REVERT: A 282 GLU cc_start: 0.5080 (mm-30) cc_final: 0.3854 (mm-30) REVERT: A 335 ARG cc_start: 0.8071 (mtp180) cc_final: 0.7858 (mtp-110) REVERT: B 142 LEU cc_start: 0.8449 (mt) cc_final: 0.8206 (tp) REVERT: B 162 PHE cc_start: 0.8759 (m-80) cc_final: 0.8409 (m-80) REVERT: B 282 GLU cc_start: 0.4989 (mm-30) cc_final: 0.3799 (mm-30) REVERT: B 335 ARG cc_start: 0.8099 (mtp180) cc_final: 0.7883 (mtp-110) outliers start: 15 outliers final: 13 residues processed: 100 average time/residue: 0.3776 time to fit residues: 49.6754 Evaluate side-chains 93 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 80 time to evaluate : 0.807 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 169 SER Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 36 optimal weight: 5.9990 chunk 20 optimal weight: 7.9990 chunk 54 optimal weight: 0.1980 chunk 44 optimal weight: 3.9990 chunk 18 optimal weight: 5.9990 chunk 65 optimal weight: 5.9990 chunk 70 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 64 optimal weight: 2.9990 chunk 22 optimal weight: 4.9990 chunk 52 optimal weight: 3.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 449 HIS A 452 GLN B 449 HIS B 452 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 5838 Z= 0.247 Angle : 0.562 4.700 7956 Z= 0.294 Chirality : 0.037 0.135 978 Planarity : 0.004 0.048 976 Dihedral : 5.976 59.460 791 Min Nonbonded Distance : 1.892 Molprobity Statistics. All-atom Clashscore : 5.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.93 % Favored : 98.07 % Rotamer: Outliers : 2.58 % Allowed : 16.13 % Favored : 81.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.30 (0.32), residues: 726 helix: 2.13 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.54 (0.53), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 394 HIS 0.006 0.001 HIS B 328 PHE 0.019 0.002 PHE A 99 TYR 0.010 0.002 TYR B 313 ARG 0.004 0.001 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 102 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.912 Fit side-chains REVERT: A 162 PHE cc_start: 0.8825 (m-80) cc_final: 0.8421 (m-80) REVERT: A 282 GLU cc_start: 0.5054 (mm-30) cc_final: 0.3863 (mm-30) REVERT: B 282 GLU cc_start: 0.4958 (mm-30) cc_final: 0.3830 (mm-30) outliers start: 16 outliers final: 14 residues processed: 102 average time/residue: 0.4249 time to fit residues: 56.2045 Evaluate side-chains 98 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 84 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 61 SER Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 64 optimal weight: 3.9990 chunk 49 optimal weight: 0.8980 chunk 33 optimal weight: 1.9990 chunk 7 optimal weight: 3.9990 chunk 31 optimal weight: 2.9990 chunk 43 optimal weight: 5.9990 chunk 65 optimal weight: 4.9990 chunk 69 optimal weight: 10.0000 chunk 34 optimal weight: 1.9990 chunk 62 optimal weight: 1.9990 chunk 18 optimal weight: 10.0000 overall best weight: 1.9788 ------------------------------------------------------------------------------- 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: 0.7642 moved from start: 0.2504 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 5838 Z= 0.198 Angle : 0.525 4.186 7956 Z= 0.270 Chirality : 0.036 0.125 978 Planarity : 0.004 0.047 976 Dihedral : 5.760 58.239 790 Min Nonbonded Distance : 1.914 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 3.06 % Allowed : 16.29 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.72 (0.32), residues: 726 helix: 2.43 (0.21), residues: 598 sheet: None (None), residues: 0 loop : -1.43 (0.52), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 394 HIS 0.003 0.001 HIS B 449 PHE 0.014 0.001 PHE B 99 TYR 0.014 0.002 TYR B 125 ARG 0.002 0.000 ARG A 474 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 87 time to evaluate : 0.852 Fit side-chains REVERT: A 162 PHE cc_start: 0.8831 (m-80) cc_final: 0.8427 (m-80) REVERT: A 282 GLU cc_start: 0.4951 (mm-30) cc_final: 0.3840 (mm-30) REVERT: B 43 LEU cc_start: 0.9048 (OUTLIER) cc_final: 0.8599 (tt) REVERT: B 282 GLU cc_start: 0.4899 (mm-30) cc_final: 0.3811 (mm-30) outliers start: 19 outliers final: 13 residues processed: 106 average time/residue: 0.3866 time to fit residues: 53.6725 Evaluate side-chains 97 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 83 time to evaluate : 0.826 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 5.9990 chunk 1 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 28 optimal weight: 4.9990 chunk 59 optimal weight: 3.9990 chunk 48 optimal weight: 3.9990 chunk 0 optimal weight: 4.9990 chunk 35 optimal weight: 5.9990 chunk 62 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 overall best weight: 2.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.2724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 5838 Z= 0.269 Angle : 0.550 4.389 7956 Z= 0.287 Chirality : 0.037 0.128 978 Planarity : 0.004 0.047 976 Dihedral : 5.504 56.715 789 Min Nonbonded Distance : 1.800 Molprobity Statistics. All-atom Clashscore : 6.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 3.39 % Allowed : 16.13 % Favored : 80.48 % 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: 2.60 (0.32), residues: 726 helix: 2.34 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.44 (0.52), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 394 HIS 0.006 0.001 HIS B 328 PHE 0.015 0.002 PHE A 99 TYR 0.010 0.002 TYR B 359 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 105 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.863 Fit side-chains REVERT: A 43 LEU cc_start: 0.9096 (OUTLIER) cc_final: 0.8630 (tt) REVERT: A 162 PHE cc_start: 0.8874 (m-80) cc_final: 0.8457 (m-80) REVERT: A 282 GLU cc_start: 0.4979 (mm-30) cc_final: 0.3899 (mm-30) REVERT: B 43 LEU cc_start: 0.9094 (OUTLIER) cc_final: 0.8619 (tt) REVERT: B 282 GLU cc_start: 0.4912 (mm-30) cc_final: 0.3876 (mm-30) outliers start: 21 outliers final: 15 residues processed: 104 average time/residue: 0.4133 time to fit residues: 55.5804 Evaluate side-chains 99 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 82 time to evaluate : 0.832 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 61 SER Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 122 PHE Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 23 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 40 optimal weight: 3.9990 chunk 17 optimal weight: 0.9980 chunk 69 optimal weight: 0.1980 chunk 57 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 5 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 67 optimal weight: 0.6980 overall best weight: 1.3784 ------------------------------------------------------------------------------- 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: 0.7645 moved from start: 0.2857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 5838 Z= 0.173 Angle : 0.508 4.530 7956 Z= 0.259 Chirality : 0.035 0.126 978 Planarity : 0.004 0.045 976 Dihedral : 5.353 54.553 789 Min Nonbonded Distance : 1.825 Molprobity Statistics. All-atom Clashscore : 5.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 17.10 % Favored : 80.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.32), residues: 726 helix: 2.63 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.30 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 394 HIS 0.003 0.001 HIS A 328 PHE 0.013 0.001 PHE A 99 TYR 0.014 0.002 TYR A 125 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 103 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 89 time to evaluate : 0.891 Fit side-chains revert: symmetry clash REVERT: A 162 PHE cc_start: 0.8853 (m-80) cc_final: 0.8448 (m-80) REVERT: A 282 GLU cc_start: 0.4785 (mm-30) cc_final: 0.3798 (mm-30) REVERT: B 43 LEU cc_start: 0.9086 (OUTLIER) cc_final: 0.8617 (tt) REVERT: B 282 GLU cc_start: 0.4743 (mm-30) cc_final: 0.3776 (mm-30) outliers start: 14 outliers final: 12 residues processed: 103 average time/residue: 0.3969 time to fit residues: 53.2176 Evaluate side-chains 100 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 7 optimal weight: 7.9990 chunk 39 optimal weight: 10.0000 chunk 50 optimal weight: 9.9990 chunk 58 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 69 optimal weight: 9.9990 chunk 43 optimal weight: 4.9990 chunk 42 optimal weight: 0.9990 chunk 32 optimal weight: 7.9990 chunk 27 optimal weight: 0.7980 chunk 41 optimal weight: 0.7980 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.3021 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 5838 Z= 0.230 Angle : 0.528 4.414 7956 Z= 0.274 Chirality : 0.036 0.130 978 Planarity : 0.004 0.046 976 Dihedral : 5.005 52.993 788 Min Nonbonded Distance : 1.814 Molprobity Statistics. All-atom Clashscore : 6.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.42 % Allowed : 17.58 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.93 (0.32), residues: 726 helix: 2.57 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.38 (0.54), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 394 HIS 0.006 0.001 HIS B 328 PHE 0.016 0.001 PHE A 99 TYR 0.015 0.002 TYR A 125 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 92 time to evaluate : 0.903 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9103 (OUTLIER) cc_final: 0.8618 (tt) REVERT: A 74 LEU cc_start: 0.7060 (OUTLIER) cc_final: 0.6739 (tp) REVERT: A 169 SER cc_start: 0.8455 (OUTLIER) cc_final: 0.7785 (p) REVERT: A 282 GLU cc_start: 0.4843 (mm-30) cc_final: 0.3858 (mm-30) REVERT: B 43 LEU cc_start: 0.9116 (OUTLIER) cc_final: 0.8640 (tt) REVERT: B 74 LEU cc_start: 0.7058 (OUTLIER) cc_final: 0.6753 (tp) REVERT: B 282 GLU cc_start: 0.4742 (mm-30) cc_final: 0.3798 (mm-30) outliers start: 15 outliers final: 10 residues processed: 107 average time/residue: 0.4088 time to fit residues: 56.9587 Evaluate side-chains 105 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 90 time to evaluate : 0.853 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 430 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 430 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 20 optimal weight: 8.9990 chunk 13 optimal weight: 0.6980 chunk 44 optimal weight: 4.9990 chunk 47 optimal weight: 0.5980 chunk 34 optimal weight: 0.6980 chunk 6 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 63 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 60 optimal weight: 2.9990 chunk 64 optimal weight: 1.9990 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 284 ASN ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7628 moved from start: 0.3078 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 5838 Z= 0.149 Angle : 0.498 5.900 7956 Z= 0.250 Chirality : 0.035 0.127 978 Planarity : 0.004 0.044 976 Dihedral : 4.837 50.861 788 Min Nonbonded Distance : 1.815 Molprobity Statistics. All-atom Clashscore : 5.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.26 % Allowed : 17.90 % Favored : 79.84 % 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: 3.34 (0.33), residues: 726 helix: 2.85 (0.22), residues: 600 sheet: None (None), residues: 0 loop : -1.23 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 394 HIS 0.003 0.001 HIS A 328 PHE 0.011 0.001 PHE B 99 TYR 0.018 0.002 TYR A 125 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 106 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.950 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9081 (OUTLIER) cc_final: 0.8594 (tt) REVERT: A 74 LEU cc_start: 0.6909 (OUTLIER) cc_final: 0.6548 (tp) REVERT: A 162 PHE cc_start: 0.8880 (m-80) cc_final: 0.8467 (m-80) REVERT: A 169 SER cc_start: 0.8410 (OUTLIER) cc_final: 0.7762 (p) REVERT: A 282 GLU cc_start: 0.4634 (mm-30) cc_final: 0.3745 (mm-30) REVERT: B 43 LEU cc_start: 0.9090 (OUTLIER) cc_final: 0.8619 (tt) REVERT: B 74 LEU cc_start: 0.6933 (OUTLIER) cc_final: 0.6596 (tp) REVERT: B 162 PHE cc_start: 0.8890 (m-80) cc_final: 0.8493 (m-80) REVERT: B 282 GLU cc_start: 0.4598 (mm-30) cc_final: 0.3718 (mm-30) outliers start: 14 outliers final: 8 residues processed: 106 average time/residue: 0.4099 time to fit residues: 56.2964 Evaluate side-chains 104 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.809 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 66 optimal weight: 3.9990 chunk 38 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 19 optimal weight: 10.0000 chunk 58 optimal weight: 0.8980 chunk 61 optimal weight: 9.9990 chunk 64 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 68 optimal weight: 7.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.8784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7650 moved from start: 0.3189 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 5838 Z= 0.198 Angle : 0.517 5.174 7956 Z= 0.262 Chirality : 0.035 0.129 978 Planarity : 0.004 0.044 976 Dihedral : 4.810 50.035 788 Min Nonbonded Distance : 1.822 Molprobity Statistics. All-atom Clashscore : 6.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.10 % Allowed : 18.23 % Favored : 79.68 % 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: 3.22 (0.32), residues: 726 helix: 2.77 (0.21), residues: 600 sheet: None (None), residues: 0 loop : -1.26 (0.55), residues: 126 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.015 0.001 PHE A 99 TYR 0.017 0.002 TYR B 125 ARG 0.002 0.000 ARG A 294 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.859 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9117 (OUTLIER) cc_final: 0.8652 (tt) REVERT: A 74 LEU cc_start: 0.6988 (OUTLIER) cc_final: 0.6643 (tp) REVERT: A 162 PHE cc_start: 0.8902 (m-80) cc_final: 0.8499 (m-80) REVERT: A 169 SER cc_start: 0.8437 (OUTLIER) cc_final: 0.7784 (p) REVERT: A 282 GLU cc_start: 0.4451 (mm-30) cc_final: 0.3548 (mm-30) REVERT: B 43 LEU cc_start: 0.9124 (OUTLIER) cc_final: 0.8669 (tt) REVERT: B 74 LEU cc_start: 0.6970 (OUTLIER) cc_final: 0.6638 (tp) REVERT: B 162 PHE cc_start: 0.8894 (m-80) cc_final: 0.8483 (m-80) REVERT: B 282 GLU cc_start: 0.4563 (mm-30) cc_final: 0.3752 (mm-30) outliers start: 13 outliers final: 8 residues processed: 107 average time/residue: 0.4101 time to fit residues: 56.9192 Evaluate side-chains 107 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 94 time to evaluate : 0.897 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 32 optimal weight: 7.9990 chunk 47 optimal weight: 6.9990 chunk 71 optimal weight: 4.9990 chunk 66 optimal weight: 0.0040 chunk 57 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 44 optimal weight: 5.9990 chunk 35 optimal weight: 3.9990 chunk 45 optimal weight: 0.6980 chunk 60 optimal weight: 2.9990 chunk 17 optimal weight: 0.9990 overall best weight: 1.5398 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.3269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.020 5838 Z= 0.175 Angle : 0.508 5.278 7956 Z= 0.256 Chirality : 0.035 0.128 978 Planarity : 0.004 0.044 976 Dihedral : 4.699 47.610 788 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.10 % Allowed : 18.23 % Favored : 79.68 % 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: 3.39 (0.32), residues: 726 helix: 2.86 (0.21), residues: 602 sheet: None (None), residues: 0 loop : -1.14 (0.56), residues: 124 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 394 HIS 0.004 0.001 HIS A 328 PHE 0.012 0.001 PHE B 99 TYR 0.007 0.002 TYR A 426 ARG 0.002 0.000 ARG A 294 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1452 Ramachandran restraints generated. 726 Oldfield, 0 Emsley, 726 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Residue TYR 125 is missing expected H atoms. Skipping. Residue TYR 125 is missing expected H atoms. Skipping. Evaluate side-chains 110 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.865 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 43 LEU cc_start: 0.9101 (OUTLIER) cc_final: 0.8639 (tt) REVERT: A 74 LEU cc_start: 0.6982 (OUTLIER) cc_final: 0.6607 (tp) REVERT: A 162 PHE cc_start: 0.8898 (m-80) cc_final: 0.8491 (m-80) REVERT: A 169 SER cc_start: 0.8433 (OUTLIER) cc_final: 0.7784 (p) REVERT: A 282 GLU cc_start: 0.4534 (mm-30) cc_final: 0.3674 (mm-30) REVERT: B 43 LEU cc_start: 0.9109 (OUTLIER) cc_final: 0.8647 (tt) REVERT: B 74 LEU cc_start: 0.6959 (OUTLIER) cc_final: 0.6597 (tp) REVERT: B 162 PHE cc_start: 0.8885 (m-80) cc_final: 0.8467 (m-80) REVERT: B 282 GLU cc_start: 0.4568 (mm-30) cc_final: 0.3711 (mm-30) outliers start: 13 outliers final: 8 residues processed: 110 average time/residue: 0.4681 time to fit residues: 64.6422 Evaluate side-chains 110 residues out of total 622 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.879 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 43 LEU Chi-restraints excluded: chain A residue 74 LEU Chi-restraints excluded: chain A residue 138 LEU Chi-restraints excluded: chain A residue 169 SER Chi-restraints excluded: chain A residue 303 LEU Chi-restraints excluded: chain A residue 387 SER Chi-restraints excluded: chain A residue 468 LEU Chi-restraints excluded: chain B residue 43 LEU Chi-restraints excluded: chain B residue 74 LEU Chi-restraints excluded: chain B residue 138 LEU Chi-restraints excluded: chain B residue 303 LEU Chi-restraints excluded: chain B residue 387 SER Chi-restraints excluded: chain B residue 468 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 72 random chunks: chunk 52 optimal weight: 3.9990 chunk 8 optimal weight: 6.9990 chunk 15 optimal weight: 4.9990 chunk 57 optimal weight: 3.9990 chunk 23 optimal weight: 0.8980 chunk 58 optimal weight: 4.9990 chunk 7 optimal weight: 4.9990 chunk 10 optimal weight: 0.8980 chunk 50 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 41 optimal weight: 2.9990 overall best weight: 1.9584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 452 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.163556 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.111005 restraints weight = 17797.530| |-----------------------------------------------------------------------------| r_work (start): 0.3184 rms_B_bonded: 2.15 r_work: 0.2997 rms_B_bonded: 2.96 restraints_weight: 0.5000 r_work: 0.2848 rms_B_bonded: 4.64 restraints_weight: 0.2500 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.3403 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 5838 Z= 0.203 Angle : 0.523 5.230 7956 Z= 0.265 Chirality : 0.035 0.131 978 Planarity : 0.005 0.074 976 Dihedral : 4.685 45.933 788 Min Nonbonded Distance : 1.819 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 2.58 % Allowed : 17.74 % Favored : 79.68 % 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: 3.27 (0.32), residues: 726 helix: 2.76 (0.21), residues: 604 sheet: None (None), residues: 0 loop : -1.16 (0.57), residues: 122 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 324 HIS 0.004 0.001 HIS A 328 PHE 0.014 0.001 PHE B 99 TYR 0.008 0.002 TYR B 426 ARG 0.010 0.000 ARG A 375 =============================================================================== Job complete usr+sys time: 2976.77 seconds wall clock time: 53 minutes 17.93 seconds (3197.93 seconds total)