Starting phenix.real_space_refine on Wed Feb 14 15:24:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/02_2024/6jpf_6822.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/02_2024/6jpf_6822.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/02_2024/6jpf_6822.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/02_2024/6jpf_6822.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/02_2024/6jpf_6822.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6jpf_6822/02_2024/6jpf_6822.pdb" } resolution = 3.52 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 sd= 0.071 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: 4 Type Number sf(0) Gaussians S 42 5.16 5 C 6368 2.51 5 N 1572 2.21 5 O 1606 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 36": "NH1" <-> "NH2" Residue "A ARG 45": "NH1" <-> "NH2" Residue "A PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 358": "NH1" <-> "NH2" Residue "A PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 33": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 36": "NH1" <-> "NH2" Residue "B ARG 45": "NH1" <-> "NH2" Residue "B PHE 224": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 358": "NH1" <-> "NH2" Residue "B PHE 384": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 472": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 9588 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4794 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 577} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Chain: "B" Number of atoms: 4794 Number of conformers: 1 Conformer: "" Number of residues, atoms: 610, 4794 Classifications: {'peptide': 610} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 32, 'TRANS': 577} Chain breaks: 6 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 158 Unresolved non-hydrogen angles: 191 Unresolved non-hydrogen dihedrals: 132 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'GLN:plan1': 3, 'HIS:plan': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'GLU:plan': 8, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 90 Time building chain proxies: 5.15, per 1000 atoms: 0.54 Number of scatterers: 9588 At special positions: 0 Unit cell: (119, 131, 91, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 42 16.00 O 1606 8.00 N 1572 7.00 C 6368 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.81 Conformation dependent library (CDL) restraints added in 1.6 seconds 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2340 Finding SS restraints... Secondary structure from input PDB file: 54 helices and 4 sheets defined 75.5% alpha, 4.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.99 Creating SS restraints... Processing helix chain 'A' and resid 4 through 31 Processing helix chain 'A' and resid 34 through 39 removed outlier: 3.605A pdb=" N TYR A 38 " --> pdb=" O ASN A 34 " (cutoff:3.500A) Processing helix chain 'A' and resid 71 through 74 Processing helix chain 'A' and resid 75 through 81 removed outlier: 3.755A pdb=" N LEU A 80 " --> pdb=" O MET A 76 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 118 removed outlier: 7.485A pdb=" N LEU A 93 " --> pdb=" O ASP A 89 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ASP A 94 " --> pdb=" O HIS A 90 " (cutoff:3.500A) removed outlier: 4.313A pdb=" N SER A 95 " --> pdb=" O ALA A 91 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL A 96 " --> pdb=" O GLY A 92 " (cutoff:3.500A) Proline residue: A 111 - end of helix Processing helix chain 'A' and resid 157 through 195 removed outlier: 3.793A pdb=" N ILE A 164 " --> pdb=" O TRP A 160 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET A 165 " --> pdb=" O ALA A 161 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 202 removed outlier: 3.743A pdb=" N PHE A 202 " --> pdb=" O ARG A 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 198 through 202' Processing helix chain 'A' and resid 216 through 229 Processing helix chain 'A' and resid 242 through 267 removed outlier: 3.660A pdb=" N TYR A 262 " --> pdb=" O TRP A 258 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR A 267 " --> pdb=" O GLN A 263 " (cutoff:3.500A) Processing helix chain 'A' and resid 292 through 314 Processing helix chain 'A' and resid 330 through 340 Processing helix chain 'A' and resid 361 through 365 Processing helix chain 'A' and resid 372 through 388 Processing helix chain 'A' and resid 390 through 402 removed outlier: 3.542A pdb=" N ILE A 394 " --> pdb=" O PHE A 390 " (cutoff:3.500A) Processing helix chain 'A' and resid 423 through 439 removed outlier: 3.953A pdb=" N GLY A 432 " --> pdb=" O GLY A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 441 through 453 Processing helix chain 'A' and resid 457 through 476 removed outlier: 3.625A pdb=" N VAL A 475 " --> pdb=" O ILE A 471 " (cutoff:3.500A) Processing helix chain 'A' and resid 478 through 491 removed outlier: 3.769A pdb=" N GLN A 490 " --> pdb=" O ALA A 486 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU A 491 " --> pdb=" O ALA A 487 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 524 removed outlier: 3.671A pdb=" N THR A 515 " --> pdb=" O PRO A 511 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE A 516 " --> pdb=" O MET A 512 " (cutoff:3.500A) Processing helix chain 'A' and resid 526 through 535 removed outlier: 4.012A pdb=" N LEU A 534 " --> pdb=" O ALA A 530 " (cutoff:3.500A) Processing helix chain 'A' and resid 535 through 548 Processing helix chain 'A' and resid 566 through 585 Proline residue: A 572 - end of helix Processing helix chain 'A' and resid 591 through 613 Processing helix chain 'A' and resid 624 through 648 removed outlier: 3.651A pdb=" N THR A 634 " --> pdb=" O GLY A 630 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY A 645 " --> pdb=" O LEU A 641 " (cutoff:3.500A) Processing helix chain 'A' and resid 654 through 682 removed outlier: 4.545A pdb=" N PHE A 658 " --> pdb=" O SER A 654 " (cutoff:3.500A) Proline residue: A 663 - end of helix Proline residue: A 679 - end of helix Processing helix chain 'A' and resid 685 through 700 Processing helix chain 'A' and resid 704 through 713 removed outlier: 4.386A pdb=" N TYR A 708 " --> pdb=" O ASN A 704 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N TYR A 713 " --> pdb=" O LEU A 709 " (cutoff:3.500A) Processing helix chain 'B' and resid 5 through 31 Processing helix chain 'B' and resid 34 through 39 removed outlier: 3.606A pdb=" N TYR B 38 " --> pdb=" O ASN B 34 " (cutoff:3.500A) Processing helix chain 'B' and resid 71 through 74 Processing helix chain 'B' and resid 75 through 81 removed outlier: 3.755A pdb=" N LEU B 80 " --> pdb=" O MET B 76 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 118 removed outlier: 7.485A pdb=" N LEU B 93 " --> pdb=" O ASP B 89 " (cutoff:3.500A) removed outlier: 9.706A pdb=" N ASP B 94 " --> pdb=" O HIS B 90 " (cutoff:3.500A) removed outlier: 4.312A pdb=" N SER B 95 " --> pdb=" O ALA B 91 " (cutoff:3.500A) removed outlier: 3.674A pdb=" N VAL B 96 " --> pdb=" O GLY B 92 " (cutoff:3.500A) Proline residue: B 111 - end of helix Processing helix chain 'B' and resid 157 through 195 removed outlier: 3.792A pdb=" N ILE B 164 " --> pdb=" O TRP B 160 " (cutoff:3.500A) removed outlier: 4.179A pdb=" N MET B 165 " --> pdb=" O ALA B 161 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 202 removed outlier: 3.744A pdb=" N PHE B 202 " --> pdb=" O ARG B 198 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 198 through 202' Processing helix chain 'B' and resid 216 through 229 Processing helix chain 'B' and resid 242 through 267 removed outlier: 3.659A pdb=" N TYR B 262 " --> pdb=" O TRP B 258 " (cutoff:3.500A) removed outlier: 4.340A pdb=" N THR B 267 " --> pdb=" O GLN B 263 " (cutoff:3.500A) Processing helix chain 'B' and resid 292 through 314 Processing helix chain 'B' and resid 330 through 340 Processing helix chain 'B' and resid 361 through 365 Processing helix chain 'B' and resid 372 through 388 Processing helix chain 'B' and resid 390 through 402 removed outlier: 3.542A pdb=" N ILE B 394 " --> pdb=" O PHE B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 423 through 439 removed outlier: 3.952A pdb=" N GLY B 432 " --> pdb=" O GLY B 428 " (cutoff:3.500A) Processing helix chain 'B' and resid 441 through 453 Processing helix chain 'B' and resid 457 through 476 removed outlier: 3.626A pdb=" N VAL B 475 " --> pdb=" O ILE B 471 " (cutoff:3.500A) Processing helix chain 'B' and resid 478 through 491 removed outlier: 3.768A pdb=" N GLN B 490 " --> pdb=" O ALA B 486 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N LEU B 491 " --> pdb=" O ALA B 487 " (cutoff:3.500A) Processing helix chain 'B' and resid 509 through 524 removed outlier: 3.672A pdb=" N THR B 515 " --> pdb=" O PRO B 511 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N PHE B 516 " --> pdb=" O MET B 512 " (cutoff:3.500A) Processing helix chain 'B' and resid 526 through 535 removed outlier: 4.012A pdb=" N LEU B 534 " --> pdb=" O ALA B 530 " (cutoff:3.500A) Processing helix chain 'B' and resid 535 through 548 Processing helix chain 'B' and resid 566 through 585 Proline residue: B 572 - end of helix Processing helix chain 'B' and resid 591 through 613 Processing helix chain 'B' and resid 624 through 648 removed outlier: 3.651A pdb=" N THR B 634 " --> pdb=" O GLY B 630 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N GLY B 645 " --> pdb=" O LEU B 641 " (cutoff:3.500A) Processing helix chain 'B' and resid 654 through 682 removed outlier: 4.546A pdb=" N PHE B 658 " --> pdb=" O SER B 654 " (cutoff:3.500A) Proline residue: B 663 - end of helix Proline residue: B 679 - end of helix Processing helix chain 'B' and resid 685 through 700 Processing helix chain 'B' and resid 704 through 713 removed outlier: 4.387A pdb=" N TYR B 708 " --> pdb=" O ASN B 704 " (cutoff:3.500A) removed outlier: 3.850A pdb=" N TYR B 713 " --> pdb=" O LEU B 709 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 233 through 235 removed outlier: 5.686A pdb=" N ALA A 323 " --> pdb=" O VAL A 239 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 233 through 235 Processing sheet with id=AA3, first strand: chain 'B' and resid 233 through 235 removed outlier: 5.686A pdb=" N ALA B 323 " --> pdb=" O VAL B 239 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 233 through 235 659 hydrogen bonds defined for protein. 1959 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: 3.24 Time building geometry restraints manager: 4.16 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2922 1.34 - 1.46: 2236 1.46 - 1.58: 4620 1.58 - 1.70: 0 1.70 - 1.81: 76 Bond restraints: 9854 Sorted by residual: bond pdb=" CB THR A 173 " pdb=" CG2 THR A 173 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 4.03e+00 bond pdb=" CB THR B 173 " pdb=" CG2 THR B 173 " ideal model delta sigma weight residual 1.521 1.455 0.066 3.30e-02 9.18e+02 3.99e+00 bond pdb=" CZ ARG B 29 " pdb=" NH2 ARG B 29 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.17e+00 bond pdb=" CZ ARG A 29 " pdb=" NH2 ARG A 29 " ideal model delta sigma weight residual 1.330 1.307 0.023 1.30e-02 5.92e+03 3.15e+00 bond pdb=" N ILE B 714 " pdb=" CA ILE B 714 " ideal model delta sigma weight residual 1.459 1.438 0.021 1.25e-02 6.40e+03 2.89e+00 ... (remaining 9849 not shown) Histogram of bond angle deviations from ideal: 98.30 - 105.45: 246 105.45 - 112.60: 5163 112.60 - 119.76: 3196 119.76 - 126.91: 4686 126.91 - 134.06: 147 Bond angle restraints: 13438 Sorted by residual: angle pdb=" N PRO B 275 " pdb=" CA PRO B 275 " pdb=" CB PRO B 275 " ideal model delta sigma weight residual 103.00 110.45 -7.45 1.10e+00 8.26e-01 4.59e+01 angle pdb=" N PRO A 275 " pdb=" CA PRO A 275 " pdb=" CB PRO A 275 " ideal model delta sigma weight residual 103.00 110.44 -7.44 1.10e+00 8.26e-01 4.58e+01 angle pdb=" C ASN B 612 " pdb=" N VAL B 613 " pdb=" CA VAL B 613 " ideal model delta sigma weight residual 123.16 117.82 5.34 1.06e+00 8.90e-01 2.54e+01 angle pdb=" C ASN A 612 " pdb=" N VAL A 613 " pdb=" CA VAL A 613 " ideal model delta sigma weight residual 123.16 117.85 5.31 1.06e+00 8.90e-01 2.51e+01 angle pdb=" N ILE B 714 " pdb=" CA ILE B 714 " pdb=" C ILE B 714 " ideal model delta sigma weight residual 109.34 101.30 8.04 2.08e+00 2.31e-01 1.49e+01 ... (remaining 13433 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.43: 5193 17.43 - 34.87: 407 34.87 - 52.30: 94 52.30 - 69.74: 28 69.74 - 87.17: 8 Dihedral angle restraints: 5730 sinusoidal: 2132 harmonic: 3598 Sorted by residual: dihedral pdb=" CA LEU A 703 " pdb=" C LEU A 703 " pdb=" N ASN A 704 " pdb=" CA ASN A 704 " ideal model delta harmonic sigma weight residual 180.00 156.95 23.05 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA LEU B 703 " pdb=" C LEU B 703 " pdb=" N ASN B 704 " pdb=" CA ASN B 704 " ideal model delta harmonic sigma weight residual 180.00 156.99 23.01 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA ASP B 316 " pdb=" C ASP B 316 " pdb=" N GLN B 317 " pdb=" CA GLN B 317 " ideal model delta harmonic sigma weight residual 180.00 -160.13 -19.87 0 5.00e+00 4.00e-02 1.58e+01 ... (remaining 5727 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.049: 1176 0.049 - 0.098: 318 0.098 - 0.147: 44 0.147 - 0.195: 4 0.195 - 0.244: 6 Chirality restraints: 1548 Sorted by residual: chirality pdb=" CA PRO B 275 " pdb=" N PRO B 275 " pdb=" C PRO B 275 " pdb=" CB PRO B 275 " both_signs ideal model delta sigma weight residual False 2.72 2.47 0.24 2.00e-01 2.50e+01 1.49e+00 chirality pdb=" CA PRO A 275 " pdb=" N PRO A 275 " pdb=" C PRO A 275 " pdb=" CB PRO A 275 " both_signs ideal model delta sigma weight residual False 2.72 2.48 0.24 2.00e-01 2.50e+01 1.46e+00 chirality pdb=" CA ILE B 714 " pdb=" N ILE B 714 " pdb=" C ILE B 714 " pdb=" CB ILE B 714 " both_signs ideal model delta sigma weight residual False 2.43 2.67 -0.23 2.00e-01 2.50e+01 1.37e+00 ... (remaining 1545 not shown) Planarity restraints: 1666 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C HIS A 715 " 0.050 5.00e-02 4.00e+02 7.56e-02 9.15e+00 pdb=" N PRO A 716 " -0.131 5.00e-02 4.00e+02 pdb=" CA PRO A 716 " 0.039 5.00e-02 4.00e+02 pdb=" CD PRO A 716 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C HIS B 715 " -0.050 5.00e-02 4.00e+02 7.56e-02 9.14e+00 pdb=" N PRO B 716 " 0.131 5.00e-02 4.00e+02 pdb=" CA PRO B 716 " -0.039 5.00e-02 4.00e+02 pdb=" CD PRO B 716 " -0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 181 " 0.007 2.00e-02 2.50e+03 1.44e-02 4.16e+00 pdb=" CG TYR B 181 " -0.005 2.00e-02 2.50e+03 pdb=" CD1 TYR B 181 " -0.011 2.00e-02 2.50e+03 pdb=" CD2 TYR B 181 " 0.015 2.00e-02 2.50e+03 pdb=" CE1 TYR B 181 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR B 181 " -0.028 2.00e-02 2.50e+03 pdb=" CZ TYR B 181 " 0.020 2.00e-02 2.50e+03 pdb=" OH TYR B 181 " 0.004 2.00e-02 2.50e+03 ... (remaining 1663 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 2523 2.79 - 3.32: 10181 3.32 - 3.84: 17986 3.84 - 4.37: 20781 4.37 - 4.90: 33304 Nonbonded interactions: 84775 Sorted by model distance: nonbonded pdb=" O ASN B 208 " pdb=" N TRP B 349 " model vdw 2.259 2.520 nonbonded pdb=" O ASN A 208 " pdb=" N TRP A 349 " model vdw 2.259 2.520 nonbonded pdb=" O ALA A 91 " pdb=" OG SER A 95 " model vdw 2.271 2.440 nonbonded pdb=" O ALA B 91 " pdb=" OG SER B 95 " model vdw 2.271 2.440 nonbonded pdb=" O ILE A 13 " pdb=" OG1 THR A 17 " model vdw 2.278 2.440 ... (remaining 84770 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' 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 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: 0.010 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.970 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.110 Check model and map are aligned: 0.140 Set scattering table: 0.090 Process input model: 28.940 Find NCS groups from input model: 0.660 Set up NCS constraints: 0.080 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:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.810 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7714 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 : 0.005 0.066 9854 Z= 0.298 Angle : 0.755 8.207 13438 Z= 0.414 Chirality : 0.045 0.244 1548 Planarity : 0.006 0.076 1666 Dihedral : 14.349 87.173 3390 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.50 % Allowed : 5.45 % Favored : 94.04 % Rotamer: Outliers : 4.55 % Allowed : 13.04 % Favored : 82.40 % 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 (0.21), residues: 1192 helix: -1.88 (0.15), residues: 832 sheet: -3.40 (0.87), residues: 24 loop : -3.03 (0.32), residues: 336 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP B 625 HIS 0.009 0.002 HIS B 608 PHE 0.017 0.002 PHE B 669 TYR 0.028 0.002 TYR B 181 ARG 0.004 0.001 ARG A 331 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 442 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 398 time to evaluate : 1.188 Fit side-chains revert: symmetry clash REVERT: A 17 THR cc_start: 0.9303 (m) cc_final: 0.8673 (t) REVERT: A 21 PHE cc_start: 0.8884 (m-10) cc_final: 0.8658 (m-80) REVERT: A 86 GLU cc_start: 0.8963 (OUTLIER) cc_final: 0.8432 (tp30) REVERT: A 89 ASP cc_start: 0.9066 (t70) cc_final: 0.8840 (t0) REVERT: A 94 ASP cc_start: 0.8651 (p0) cc_final: 0.8329 (p0) REVERT: A 102 TYR cc_start: 0.8961 (m-80) cc_final: 0.8743 (m-10) REVERT: A 115 LEU cc_start: 0.9365 (tt) cc_final: 0.9041 (tt) REVERT: A 190 GLN cc_start: 0.8650 (tt0) cc_final: 0.8141 (tm-30) REVERT: A 201 GLN cc_start: 0.8607 (mt0) cc_final: 0.8214 (mp10) REVERT: A 208 ASN cc_start: 0.8504 (m-40) cc_final: 0.8221 (m-40) REVERT: A 226 LEU cc_start: 0.9431 (mt) cc_final: 0.9091 (mt) REVERT: A 247 ASP cc_start: 0.8101 (t70) cc_final: 0.7779 (t0) REVERT: A 260 ASP cc_start: 0.8733 (m-30) cc_final: 0.8271 (t0) REVERT: A 361 TYR cc_start: 0.9014 (t80) cc_final: 0.8305 (t80) REVERT: A 363 PRO cc_start: 0.9530 (Cg_exo) cc_final: 0.9098 (Cg_endo) REVERT: A 364 ASN cc_start: 0.9112 (t0) cc_final: 0.8857 (t0) REVERT: A 376 ARG cc_start: 0.8461 (ttm110) cc_final: 0.8187 (mtm-85) REVERT: A 438 PHE cc_start: 0.8978 (m-10) cc_final: 0.8628 (m-10) REVERT: A 441 PHE cc_start: 0.8731 (m-80) cc_final: 0.8443 (m-80) REVERT: A 452 PHE cc_start: 0.9273 (t80) cc_final: 0.8725 (t80) REVERT: A 460 PHE cc_start: 0.8743 (t80) cc_final: 0.8531 (t80) REVERT: A 524 ASP cc_start: 0.9250 (t0) cc_final: 0.8998 (t70) REVERT: A 539 LEU cc_start: 0.9165 (tt) cc_final: 0.8962 (tp) REVERT: A 616 GLN cc_start: 0.8801 (mm110) cc_final: 0.8486 (mm110) REVERT: A 633 ILE cc_start: 0.9121 (OUTLIER) cc_final: 0.8840 (tp) REVERT: A 644 MET cc_start: 0.8496 (mtp) cc_final: 0.7983 (tmm) REVERT: A 688 GLU cc_start: 0.9270 (mm-30) cc_final: 0.9038 (mm-30) REVERT: B 86 GLU cc_start: 0.8912 (OUTLIER) cc_final: 0.8472 (tp30) REVERT: B 94 ASP cc_start: 0.8693 (p0) cc_final: 0.8375 (p0) REVERT: B 102 TYR cc_start: 0.9075 (m-80) cc_final: 0.8869 (m-10) REVERT: B 115 LEU cc_start: 0.9333 (tt) cc_final: 0.9013 (tt) REVERT: B 201 GLN cc_start: 0.8600 (mt0) cc_final: 0.8172 (mp10) REVERT: B 208 ASN cc_start: 0.8672 (m-40) cc_final: 0.8387 (m-40) REVERT: B 222 GLU cc_start: 0.8542 (tm-30) cc_final: 0.7946 (tm-30) REVERT: B 226 LEU cc_start: 0.9350 (mt) cc_final: 0.8933 (mt) REVERT: B 260 ASP cc_start: 0.8704 (m-30) cc_final: 0.8253 (t70) REVERT: B 361 TYR cc_start: 0.9009 (t80) cc_final: 0.8456 (t80) REVERT: B 364 ASN cc_start: 0.9156 (t0) cc_final: 0.8834 (t0) REVERT: B 376 ARG cc_start: 0.8341 (ttm110) cc_final: 0.8116 (mtm-85) REVERT: B 438 PHE cc_start: 0.9083 (m-10) cc_final: 0.8711 (m-10) REVERT: B 441 PHE cc_start: 0.8867 (m-80) cc_final: 0.8597 (m-80) REVERT: B 452 PHE cc_start: 0.9305 (t80) cc_final: 0.8729 (t80) REVERT: B 460 PHE cc_start: 0.8580 (t80) cc_final: 0.8366 (t80) REVERT: B 524 ASP cc_start: 0.9291 (t0) cc_final: 0.9015 (t70) REVERT: B 539 LEU cc_start: 0.9258 (tt) cc_final: 0.9030 (tp) REVERT: B 616 GLN cc_start: 0.8844 (mm110) cc_final: 0.8578 (mm110) REVERT: B 633 ILE cc_start: 0.9132 (OUTLIER) cc_final: 0.8827 (tp) REVERT: B 644 MET cc_start: 0.8440 (mtp) cc_final: 0.7855 (tmm) REVERT: B 688 GLU cc_start: 0.9262 (mm-30) cc_final: 0.8978 (mm-30) outliers start: 44 outliers final: 13 residues processed: 418 average time/residue: 0.2175 time to fit residues: 130.9665 Evaluate side-chains 305 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 288 time to evaluate : 1.415 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 86 GLU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 86 GLU Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 306 ILE Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 103 optimal weight: 0.9980 chunk 92 optimal weight: 0.8980 chunk 51 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 62 optimal weight: 0.6980 chunk 49 optimal weight: 0.6980 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 58 optimal weight: 1.9990 chunk 71 optimal weight: 6.9990 chunk 110 optimal weight: 0.8980 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 14 ASN ** A 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 14 ASN ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 342 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7683 moved from start: 0.2375 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.053 9854 Z= 0.248 Angle : 0.725 8.263 13438 Z= 0.363 Chirality : 0.043 0.163 1548 Planarity : 0.006 0.064 1666 Dihedral : 7.442 56.245 1342 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.29 % Favored : 94.71 % Rotamer: Outliers : 6.00 % Allowed : 20.39 % Favored : 73.60 % 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: -2.03 (0.23), residues: 1192 helix: -0.62 (0.17), residues: 842 sheet: -3.60 (0.91), residues: 24 loop : -2.86 (0.32), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP A 625 HIS 0.005 0.001 HIS B 294 PHE 0.040 0.002 PHE B 21 TYR 0.020 0.002 TYR B 181 ARG 0.005 0.001 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 401 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 343 time to evaluate : 1.079 Fit side-chains revert: symmetry clash REVERT: A 17 THR cc_start: 0.9373 (m) cc_final: 0.8760 (t) REVERT: A 30 LEU cc_start: 0.8980 (mt) cc_final: 0.8597 (pp) REVERT: A 72 PHE cc_start: 0.7142 (t80) cc_final: 0.6597 (t80) REVERT: A 76 MET cc_start: 0.7612 (ttt) cc_final: 0.7154 (tpp) REVERT: A 89 ASP cc_start: 0.9017 (t70) cc_final: 0.8748 (m-30) REVERT: A 115 LEU cc_start: 0.9372 (tt) cc_final: 0.9003 (tt) REVERT: A 176 MET cc_start: 0.8758 (tpp) cc_final: 0.8436 (tpp) REVERT: A 201 GLN cc_start: 0.8864 (mt0) cc_final: 0.8527 (mp10) REVERT: A 208 ASN cc_start: 0.8490 (m-40) cc_final: 0.8246 (m-40) REVERT: A 226 LEU cc_start: 0.9429 (mt) cc_final: 0.9078 (mt) REVERT: A 247 ASP cc_start: 0.8059 (t70) cc_final: 0.7737 (t0) REVERT: A 257 ASN cc_start: 0.9256 (p0) cc_final: 0.8929 (m-40) REVERT: A 260 ASP cc_start: 0.8686 (m-30) cc_final: 0.8363 (t70) REVERT: A 360 ILE cc_start: 0.9179 (pt) cc_final: 0.8964 (pt) REVERT: A 361 TYR cc_start: 0.8880 (t80) cc_final: 0.8163 (t80) REVERT: A 363 PRO cc_start: 0.9495 (Cg_exo) cc_final: 0.8930 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8946 (m-10) cc_final: 0.8646 (m-10) REVERT: A 441 PHE cc_start: 0.8352 (m-80) cc_final: 0.7967 (m-80) REVERT: A 460 PHE cc_start: 0.8691 (t80) cc_final: 0.8447 (t80) REVERT: A 465 SER cc_start: 0.9520 (t) cc_final: 0.9274 (m) REVERT: A 479 LEU cc_start: 0.8187 (OUTLIER) cc_final: 0.7842 (mp) REVERT: A 524 ASP cc_start: 0.9148 (t0) cc_final: 0.8887 (t70) REVERT: A 633 ILE cc_start: 0.9247 (OUTLIER) cc_final: 0.8896 (tp) REVERT: A 644 MET cc_start: 0.8075 (mtp) cc_final: 0.7396 (tmm) REVERT: A 688 GLU cc_start: 0.9211 (mm-30) cc_final: 0.8575 (mm-30) REVERT: B 30 LEU cc_start: 0.8980 (mt) cc_final: 0.8595 (pp) REVERT: B 31 GLN cc_start: 0.6665 (mm110) cc_final: 0.6439 (mm110) REVERT: B 72 PHE cc_start: 0.6999 (t80) cc_final: 0.6749 (t80) REVERT: B 102 TYR cc_start: 0.9011 (m-80) cc_final: 0.8731 (m-10) REVERT: B 115 LEU cc_start: 0.9366 (OUTLIER) cc_final: 0.8898 (tt) REVERT: B 176 MET cc_start: 0.8637 (tpp) cc_final: 0.8274 (tpp) REVERT: B 208 ASN cc_start: 0.8614 (m-40) cc_final: 0.8362 (m-40) REVERT: B 226 LEU cc_start: 0.9396 (mt) cc_final: 0.9080 (mt) REVERT: B 247 ASP cc_start: 0.7999 (t70) cc_final: 0.7709 (t0) REVERT: B 257 ASN cc_start: 0.8541 (m-40) cc_final: 0.8109 (p0) REVERT: B 260 ASP cc_start: 0.8676 (m-30) cc_final: 0.8286 (t70) REVERT: B 344 ARG cc_start: 0.9116 (OUTLIER) cc_final: 0.8424 (ttm110) REVERT: B 360 ILE cc_start: 0.9167 (pt) cc_final: 0.8949 (pt) REVERT: B 361 TYR cc_start: 0.8902 (t80) cc_final: 0.8358 (t80) REVERT: B 394 ILE cc_start: 0.9329 (OUTLIER) cc_final: 0.9127 (tp) REVERT: B 430 LEU cc_start: 0.7959 (tp) cc_final: 0.7717 (tt) REVERT: B 438 PHE cc_start: 0.9080 (m-10) cc_final: 0.8763 (m-10) REVERT: B 441 PHE cc_start: 0.8475 (m-80) cc_final: 0.8085 (m-80) REVERT: B 460 PHE cc_start: 0.8559 (t80) cc_final: 0.8331 (t80) REVERT: B 479 LEU cc_start: 0.8059 (OUTLIER) cc_final: 0.7598 (mp) REVERT: B 489 GLU cc_start: 0.8990 (mm-30) cc_final: 0.8689 (mm-30) REVERT: B 522 MET cc_start: 0.8766 (mmm) cc_final: 0.8052 (mmm) REVERT: B 565 ILE cc_start: 0.9199 (tp) cc_final: 0.8915 (tp) REVERT: B 616 GLN cc_start: 0.8824 (mm110) cc_final: 0.8591 (mm110) REVERT: B 633 ILE cc_start: 0.9228 (OUTLIER) cc_final: 0.8856 (tp) REVERT: B 644 MET cc_start: 0.8066 (mtp) cc_final: 0.7351 (tmm) outliers start: 58 outliers final: 28 residues processed: 379 average time/residue: 0.1838 time to fit residues: 100.1164 Evaluate side-chains 332 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 297 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 14 ASN Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 336 VAL Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 633 ILE Chi-restraints excluded: chain A residue 634 THR Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 14 ASN Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 336 VAL Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 633 ILE Chi-restraints excluded: chain B residue 634 THR Chi-restraints excluded: chain B residue 714 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 61 optimal weight: 10.0000 chunk 34 optimal weight: 0.5980 chunk 92 optimal weight: 0.9990 chunk 75 optimal weight: 0.0570 chunk 30 optimal weight: 0.6980 chunk 110 optimal weight: 0.9980 chunk 119 optimal weight: 0.9990 chunk 98 optimal weight: 3.9990 chunk 37 optimal weight: 0.7980 chunk 89 optimal weight: 0.9990 chunk 109 optimal weight: 0.4980 overall best weight: 0.5298 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN A 640 GLN ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 294 HIS ** B 339 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN ** B 640 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.3179 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 9854 Z= 0.220 Angle : 0.684 9.351 13438 Z= 0.345 Chirality : 0.042 0.165 1548 Planarity : 0.005 0.055 1666 Dihedral : 6.400 51.702 1334 Min Nonbonded Distance : 2.104 Molprobity Statistics. All-atom Clashscore : 20.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.87 % Favored : 94.13 % Rotamer: Outliers : 6.00 % Allowed : 22.57 % Favored : 71.43 % 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: -1.41 (0.24), residues: 1192 helix: -0.14 (0.17), residues: 846 sheet: -3.83 (0.88), residues: 24 loop : -2.69 (0.33), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP A 625 HIS 0.004 0.001 HIS B 294 PHE 0.013 0.002 PHE B 598 TYR 0.015 0.002 TYR A 102 ARG 0.005 0.001 ARG B 197 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 389 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 58 poor density : 331 time to evaluate : 1.190 Fit side-chains revert: symmetry clash REVERT: A 21 PHE cc_start: 0.8892 (m-80) cc_final: 0.8401 (m-80) REVERT: A 30 LEU cc_start: 0.8955 (mt) cc_final: 0.8606 (pp) REVERT: A 36 ARG cc_start: 0.8914 (mtp180) cc_final: 0.8405 (mmm160) REVERT: A 72 PHE cc_start: 0.7097 (t80) cc_final: 0.6872 (t80) REVERT: A 76 MET cc_start: 0.7485 (ttt) cc_final: 0.7188 (tpp) REVERT: A 86 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8630 (tp30) REVERT: A 89 ASP cc_start: 0.8968 (t70) cc_final: 0.8717 (m-30) REVERT: A 102 TYR cc_start: 0.8744 (m-10) cc_final: 0.8292 (m-10) REVERT: A 115 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.8935 (tt) REVERT: A 208 ASN cc_start: 0.8505 (t0) cc_final: 0.8268 (m-40) REVERT: A 226 LEU cc_start: 0.9402 (mt) cc_final: 0.9078 (mt) REVERT: A 247 ASP cc_start: 0.8047 (t70) cc_final: 0.7727 (t0) REVERT: A 260 ASP cc_start: 0.8700 (m-30) cc_final: 0.8499 (t70) REVERT: A 361 TYR cc_start: 0.8941 (t80) cc_final: 0.8249 (t80) REVERT: A 363 PRO cc_start: 0.9459 (Cg_exo) cc_final: 0.9034 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8976 (m-10) cc_final: 0.8634 (m-10) REVERT: A 441 PHE cc_start: 0.8204 (m-80) cc_final: 0.7765 (m-80) REVERT: A 452 PHE cc_start: 0.9145 (t80) cc_final: 0.8859 (t80) REVERT: A 460 PHE cc_start: 0.8617 (t80) cc_final: 0.8306 (t80) REVERT: A 465 SER cc_start: 0.9521 (t) cc_final: 0.9261 (m) REVERT: A 479 LEU cc_start: 0.8076 (OUTLIER) cc_final: 0.7661 (mp) REVERT: A 510 ILE cc_start: 0.7509 (OUTLIER) cc_final: 0.6998 (mt) REVERT: A 522 MET cc_start: 0.8880 (mmm) cc_final: 0.8155 (mmp) REVERT: A 524 ASP cc_start: 0.9146 (t0) cc_final: 0.8848 (t70) REVERT: A 526 TRP cc_start: 0.8653 (m-10) cc_final: 0.8290 (m-10) REVERT: A 686 LEU cc_start: 0.9575 (mt) cc_final: 0.9373 (mt) REVERT: A 688 GLU cc_start: 0.9035 (mm-30) cc_final: 0.8474 (mm-30) REVERT: B 21 PHE cc_start: 0.8789 (m-80) cc_final: 0.8331 (m-80) REVERT: B 30 LEU cc_start: 0.8894 (mt) cc_final: 0.8574 (pp) REVERT: B 82 MET cc_start: 0.8716 (tpt) cc_final: 0.8325 (ttt) REVERT: B 86 GLU cc_start: 0.9026 (mt-10) cc_final: 0.8678 (tp30) REVERT: B 94 ASP cc_start: 0.8612 (p0) cc_final: 0.8288 (p0) REVERT: B 107 LYS cc_start: 0.8441 (mttt) cc_final: 0.8234 (mtpt) REVERT: B 115 LEU cc_start: 0.9338 (tt) cc_final: 0.8974 (tt) REVERT: B 208 ASN cc_start: 0.8626 (t0) cc_final: 0.8382 (m-40) REVERT: B 226 LEU cc_start: 0.9376 (mt) cc_final: 0.9095 (mt) REVERT: B 247 ASP cc_start: 0.7674 (t70) cc_final: 0.7401 (t0) REVERT: B 344 ARG cc_start: 0.9131 (OUTLIER) cc_final: 0.8428 (ttm110) REVERT: B 361 TYR cc_start: 0.8969 (t80) cc_final: 0.8238 (t80) REVERT: B 363 PRO cc_start: 0.9478 (Cg_exo) cc_final: 0.8964 (Cg_endo) REVERT: B 394 ILE cc_start: 0.9300 (OUTLIER) cc_final: 0.9081 (tp) REVERT: B 430 LEU cc_start: 0.7788 (tp) cc_final: 0.7530 (tt) REVERT: B 438 PHE cc_start: 0.9107 (m-10) cc_final: 0.8785 (m-10) REVERT: B 441 PHE cc_start: 0.8287 (m-80) cc_final: 0.7859 (m-80) REVERT: B 447 MET cc_start: 0.9123 (tpt) cc_final: 0.8843 (tpp) REVERT: B 460 PHE cc_start: 0.8610 (t80) cc_final: 0.8278 (t80) REVERT: B 479 LEU cc_start: 0.8060 (OUTLIER) cc_final: 0.7630 (mp) REVERT: B 522 MET cc_start: 0.8865 (mmm) cc_final: 0.8223 (mmp) REVERT: B 524 ASP cc_start: 0.9245 (t0) cc_final: 0.8776 (t70) REVERT: B 526 TRP cc_start: 0.8704 (m-10) cc_final: 0.8434 (m-10) REVERT: B 534 LEU cc_start: 0.9406 (mm) cc_final: 0.9133 (mm) REVERT: B 575 GLN cc_start: 0.8956 (mm-40) cc_final: 0.8732 (mm110) REVERT: B 686 LEU cc_start: 0.9597 (mt) cc_final: 0.9347 (mt) REVERT: B 688 GLU cc_start: 0.9030 (mm-30) cc_final: 0.8787 (mm-30) outliers start: 58 outliers final: 28 residues processed: 362 average time/residue: 0.1832 time to fit residues: 98.5674 Evaluate side-chains 336 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 302 time to evaluate : 1.097 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 106 LEU Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 83 optimal weight: 10.0000 chunk 57 optimal weight: 0.6980 chunk 12 optimal weight: 0.5980 chunk 52 optimal weight: 0.6980 chunk 74 optimal weight: 0.8980 chunk 111 optimal weight: 3.9990 chunk 117 optimal weight: 0.6980 chunk 58 optimal weight: 0.9980 chunk 105 optimal weight: 0.9980 chunk 31 optimal weight: 0.9990 chunk 98 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 243 ASN ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 715 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 229 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7657 moved from start: 0.3621 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 9854 Z= 0.223 Angle : 0.681 10.097 13438 Z= 0.340 Chirality : 0.043 0.181 1548 Planarity : 0.005 0.054 1666 Dihedral : 6.073 57.738 1328 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 20.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.04 % Favored : 93.96 % Rotamer: Outliers : 5.07 % Allowed : 24.53 % Favored : 70.39 % 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: -1.08 (0.24), residues: 1192 helix: 0.12 (0.18), residues: 838 sheet: -3.94 (0.89), residues: 24 loop : -2.49 (0.34), residues: 330 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 625 HIS 0.003 0.001 HIS A 608 PHE 0.021 0.002 PHE A 396 TYR 0.013 0.001 TYR B 102 ARG 0.004 0.000 ARG B 683 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 368 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 319 time to evaluate : 1.033 Fit side-chains REVERT: A 14 ASN cc_start: 0.9331 (m-40) cc_final: 0.9022 (t0) REVERT: A 21 PHE cc_start: 0.8842 (m-80) cc_final: 0.8310 (m-80) REVERT: A 30 LEU cc_start: 0.8914 (mt) cc_final: 0.8592 (pp) REVERT: A 72 PHE cc_start: 0.7115 (t80) cc_final: 0.6890 (t80) REVERT: A 76 MET cc_start: 0.7468 (ttt) cc_final: 0.7131 (tpp) REVERT: A 102 TYR cc_start: 0.8762 (m-10) cc_final: 0.8362 (m-10) REVERT: A 115 LEU cc_start: 0.9336 (OUTLIER) cc_final: 0.8849 (tt) REVERT: A 172 TRP cc_start: 0.8241 (t-100) cc_final: 0.8017 (t-100) REVERT: A 176 MET cc_start: 0.8526 (tpp) cc_final: 0.8119 (tpp) REVERT: A 208 ASN cc_start: 0.8566 (t0) cc_final: 0.8324 (m-40) REVERT: A 226 LEU cc_start: 0.9367 (mt) cc_final: 0.9106 (mt) REVERT: A 247 ASP cc_start: 0.8093 (t70) cc_final: 0.7763 (t0) REVERT: A 361 TYR cc_start: 0.8913 (t80) cc_final: 0.8234 (t80) REVERT: A 363 PRO cc_start: 0.9427 (Cg_exo) cc_final: 0.8992 (Cg_endo) REVERT: A 438 PHE cc_start: 0.8997 (m-10) cc_final: 0.8647 (m-10) REVERT: A 441 PHE cc_start: 0.8209 (m-80) cc_final: 0.7776 (m-80) REVERT: A 452 PHE cc_start: 0.9136 (t80) cc_final: 0.8913 (t80) REVERT: A 460 PHE cc_start: 0.8595 (t80) cc_final: 0.8331 (t80) REVERT: A 465 SER cc_start: 0.9505 (t) cc_final: 0.9247 (m) REVERT: A 469 TYR cc_start: 0.8915 (t80) cc_final: 0.8644 (t80) REVERT: A 479 LEU cc_start: 0.8104 (OUTLIER) cc_final: 0.7735 (mp) REVERT: A 510 ILE cc_start: 0.7333 (OUTLIER) cc_final: 0.6862 (mt) REVERT: A 522 MET cc_start: 0.8813 (mmm) cc_final: 0.8077 (mmp) REVERT: A 524 ASP cc_start: 0.9145 (t0) cc_final: 0.8728 (t70) REVERT: A 526 TRP cc_start: 0.8593 (m-10) cc_final: 0.8183 (m-10) REVERT: A 560 MET cc_start: 0.5339 (tpp) cc_final: 0.4804 (ttm) REVERT: A 616 GLN cc_start: 0.8461 (mm110) cc_final: 0.8172 (mm110) REVERT: A 644 MET cc_start: 0.7682 (mmm) cc_final: 0.6338 (tmm) REVERT: A 688 GLU cc_start: 0.8924 (mm-30) cc_final: 0.8178 (mm-30) REVERT: B 14 ASN cc_start: 0.9258 (m-40) cc_final: 0.8951 (t0) REVERT: B 21 PHE cc_start: 0.8797 (m-80) cc_final: 0.8099 (m-80) REVERT: B 30 LEU cc_start: 0.8882 (mt) cc_final: 0.8576 (pp) REVERT: B 72 PHE cc_start: 0.6717 (t80) cc_final: 0.6446 (t80) REVERT: B 76 MET cc_start: 0.7415 (ttt) cc_final: 0.6918 (tpp) REVERT: B 82 MET cc_start: 0.8774 (tpt) cc_final: 0.8463 (ttt) REVERT: B 86 GLU cc_start: 0.9054 (mt-10) cc_final: 0.8652 (tp30) REVERT: B 89 ASP cc_start: 0.8902 (m-30) cc_final: 0.8694 (m-30) REVERT: B 102 TYR cc_start: 0.8735 (m-10) cc_final: 0.8167 (m-10) REVERT: B 115 LEU cc_start: 0.9327 (OUTLIER) cc_final: 0.8783 (tt) REVERT: B 208 ASN cc_start: 0.8563 (t0) cc_final: 0.8323 (m-40) REVERT: B 226 LEU cc_start: 0.9384 (mt) cc_final: 0.9097 (mt) REVERT: B 344 ARG cc_start: 0.9075 (OUTLIER) cc_final: 0.8290 (ttm110) REVERT: B 361 TYR cc_start: 0.8949 (t80) cc_final: 0.8275 (t80) REVERT: B 363 PRO cc_start: 0.9474 (Cg_exo) cc_final: 0.9043 (Cg_endo) REVERT: B 394 ILE cc_start: 0.9310 (OUTLIER) cc_final: 0.8991 (tp) REVERT: B 438 PHE cc_start: 0.9135 (m-10) cc_final: 0.8815 (m-10) REVERT: B 441 PHE cc_start: 0.8261 (m-80) cc_final: 0.7958 (m-80) REVERT: B 447 MET cc_start: 0.9107 (tpt) cc_final: 0.8808 (tpp) REVERT: B 460 PHE cc_start: 0.8584 (t80) cc_final: 0.8321 (t80) REVERT: B 479 LEU cc_start: 0.8032 (OUTLIER) cc_final: 0.7619 (mp) REVERT: B 522 MET cc_start: 0.8819 (mmm) cc_final: 0.7961 (mmp) REVERT: B 524 ASP cc_start: 0.9241 (t0) cc_final: 0.8965 (t70) REVERT: B 526 TRP cc_start: 0.8619 (m-10) cc_final: 0.8208 (m-10) REVERT: B 560 MET cc_start: 0.5316 (tpp) cc_final: 0.4761 (ttm) REVERT: B 644 MET cc_start: 0.7758 (mmm) cc_final: 0.6671 (tmm) REVERT: B 688 GLU cc_start: 0.8928 (mm-30) cc_final: 0.8563 (mm-30) outliers start: 49 outliers final: 31 residues processed: 343 average time/residue: 0.1645 time to fit residues: 83.8244 Evaluate side-chains 323 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 285 time to evaluate : 1.062 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 234 LEU Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 390 PHE Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 510 ILE Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 234 LEU Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 539 LEU Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 66 optimal weight: 5.9990 chunk 1 optimal weight: 1.9990 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 100 optimal weight: 0.8980 chunk 81 optimal weight: 6.9990 chunk 0 optimal weight: 9.9990 chunk 60 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 29 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 241 ASN ** A 616 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7652 moved from start: 0.3941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 9854 Z= 0.232 Angle : 0.688 10.406 13438 Z= 0.342 Chirality : 0.042 0.175 1548 Planarity : 0.005 0.051 1666 Dihedral : 5.816 43.263 1328 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 20.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.59 % Allowed : 27.12 % Favored : 67.29 % 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: -0.78 (0.24), residues: 1192 helix: 0.31 (0.18), residues: 842 sheet: -3.83 (0.90), residues: 24 loop : -2.32 (0.34), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP A 625 HIS 0.003 0.001 HIS A 608 PHE 0.016 0.001 PHE B 669 TYR 0.014 0.002 TYR B 102 ARG 0.003 0.000 ARG A 607 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 349 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 295 time to evaluate : 1.139 Fit side-chains revert: symmetry clash REVERT: A 14 ASN cc_start: 0.9297 (m-40) cc_final: 0.9011 (t0) REVERT: A 21 PHE cc_start: 0.8949 (m-80) cc_final: 0.8415 (m-80) REVERT: A 30 LEU cc_start: 0.8895 (mt) cc_final: 0.8602 (pp) REVERT: A 36 ARG cc_start: 0.8759 (mtp180) cc_final: 0.8397 (mtp180) REVERT: A 72 PHE cc_start: 0.7148 (t80) cc_final: 0.6910 (t80) REVERT: A 76 MET cc_start: 0.7355 (ttt) cc_final: 0.7071 (tpp) REVERT: A 102 TYR cc_start: 0.8788 (m-10) cc_final: 0.8430 (m-10) REVERT: A 115 LEU cc_start: 0.9264 (OUTLIER) cc_final: 0.8902 (tt) REVERT: A 172 TRP cc_start: 0.8192 (t-100) cc_final: 0.7951 (t-100) REVERT: A 176 MET cc_start: 0.8672 (tpp) cc_final: 0.8154 (tpp) REVERT: A 208 ASN cc_start: 0.8586 (t0) cc_final: 0.8331 (m-40) REVERT: A 226 LEU cc_start: 0.9360 (mt) cc_final: 0.9102 (mt) REVERT: A 247 ASP cc_start: 0.8101 (t70) cc_final: 0.7767 (t0) REVERT: A 361 TYR cc_start: 0.8847 (t80) cc_final: 0.8190 (t80) REVERT: A 363 PRO cc_start: 0.9428 (Cg_exo) cc_final: 0.8998 (Cg_endo) REVERT: A 379 MET cc_start: 0.8655 (mmm) cc_final: 0.8279 (mmm) REVERT: A 438 PHE cc_start: 0.8989 (m-10) cc_final: 0.8614 (m-10) REVERT: A 441 PHE cc_start: 0.8199 (m-80) cc_final: 0.7808 (m-80) REVERT: A 452 PHE cc_start: 0.9112 (t80) cc_final: 0.8370 (t80) REVERT: A 465 SER cc_start: 0.9514 (t) cc_final: 0.9237 (m) REVERT: A 469 TYR cc_start: 0.8942 (t80) cc_final: 0.8641 (t80) REVERT: A 479 LEU cc_start: 0.8150 (OUTLIER) cc_final: 0.7773 (mp) REVERT: A 522 MET cc_start: 0.8794 (mmm) cc_final: 0.8281 (mmp) REVERT: A 524 ASP cc_start: 0.9136 (t0) cc_final: 0.8658 (t70) REVERT: A 526 TRP cc_start: 0.8583 (m-10) cc_final: 0.8213 (m-10) REVERT: A 688 GLU cc_start: 0.8724 (mm-30) cc_final: 0.8083 (mm-30) REVERT: B 14 ASN cc_start: 0.9162 (m-40) cc_final: 0.8899 (t0) REVERT: B 21 PHE cc_start: 0.8796 (m-80) cc_final: 0.8029 (m-80) REVERT: B 30 LEU cc_start: 0.8856 (mt) cc_final: 0.8577 (pp) REVERT: B 72 PHE cc_start: 0.6789 (t80) cc_final: 0.6504 (t80) REVERT: B 76 MET cc_start: 0.7612 (ttt) cc_final: 0.7177 (tpp) REVERT: B 86 GLU cc_start: 0.9039 (mt-10) cc_final: 0.8789 (mt-10) REVERT: B 102 TYR cc_start: 0.8725 (m-10) cc_final: 0.8218 (m-10) REVERT: B 115 LEU cc_start: 0.9242 (OUTLIER) cc_final: 0.8901 (tt) REVERT: B 208 ASN cc_start: 0.8568 (t0) cc_final: 0.8340 (m-40) REVERT: B 226 LEU cc_start: 0.9385 (mt) cc_final: 0.9078 (mt) REVERT: B 344 ARG cc_start: 0.9058 (OUTLIER) cc_final: 0.8290 (ttm110) REVERT: B 361 TYR cc_start: 0.8941 (t80) cc_final: 0.8246 (t80) REVERT: B 363 PRO cc_start: 0.9468 (Cg_exo) cc_final: 0.9036 (Cg_endo) REVERT: B 394 ILE cc_start: 0.9110 (OUTLIER) cc_final: 0.8798 (tp) REVERT: B 438 PHE cc_start: 0.9160 (m-10) cc_final: 0.8787 (m-10) REVERT: B 441 PHE cc_start: 0.8254 (m-80) cc_final: 0.7962 (m-80) REVERT: B 447 MET cc_start: 0.9063 (tpt) cc_final: 0.8728 (tpp) REVERT: B 460 PHE cc_start: 0.8529 (t80) cc_final: 0.8254 (t80) REVERT: B 465 SER cc_start: 0.9550 (t) cc_final: 0.9244 (m) REVERT: B 479 LEU cc_start: 0.8084 (OUTLIER) cc_final: 0.7729 (mp) REVERT: B 510 ILE cc_start: 0.7475 (OUTLIER) cc_final: 0.7075 (mt) REVERT: B 522 MET cc_start: 0.8813 (mmm) cc_final: 0.7858 (mmp) REVERT: B 526 TRP cc_start: 0.8586 (m-10) cc_final: 0.8105 (m-10) REVERT: B 577 TYR cc_start: 0.7650 (m-80) cc_final: 0.7192 (m-80) REVERT: B 688 GLU cc_start: 0.8805 (mm-30) cc_final: 0.8555 (mm-30) outliers start: 54 outliers final: 35 residues processed: 323 average time/residue: 0.1604 time to fit residues: 78.4244 Evaluate side-chains 328 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 286 time to evaluate : 1.127 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 646 LEU Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 692 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 106 optimal weight: 0.0980 chunk 23 optimal weight: 1.9990 chunk 69 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 118 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 54 optimal weight: 5.9990 chunk 9 optimal weight: 4.9990 chunk 39 optimal weight: 0.9990 chunk 61 optimal weight: 10.0000 chunk 113 optimal weight: 0.7980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN B 609 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7643 moved from start: 0.4148 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 9854 Z= 0.231 Angle : 0.690 10.808 13438 Z= 0.339 Chirality : 0.042 0.191 1548 Planarity : 0.005 0.051 1666 Dihedral : 5.408 42.999 1322 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 20.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.62 % Favored : 94.38 % Rotamer: Outliers : 5.28 % Allowed : 27.23 % Favored : 67.49 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.65 (0.25), residues: 1192 helix: 0.41 (0.18), residues: 840 sheet: -3.71 (0.91), residues: 24 loop : -2.26 (0.34), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 625 HIS 0.003 0.001 HIS A 608 PHE 0.029 0.001 PHE A 396 TYR 0.014 0.001 TYR B 469 ARG 0.004 0.000 ARG A 468 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 365 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 51 poor density : 314 time to evaluate : 1.074 Fit side-chains REVERT: A 14 ASN cc_start: 0.9264 (m-40) cc_final: 0.8993 (t0) REVERT: A 30 LEU cc_start: 0.8890 (mt) cc_final: 0.8623 (pp) REVERT: A 36 ARG cc_start: 0.8899 (mtp180) cc_final: 0.8655 (mtp180) REVERT: A 72 PHE cc_start: 0.7144 (t80) cc_final: 0.6911 (t80) REVERT: A 76 MET cc_start: 0.7354 (ttt) cc_final: 0.7069 (tpp) REVERT: A 102 TYR cc_start: 0.8820 (m-10) cc_final: 0.8504 (m-10) REVERT: A 115 LEU cc_start: 0.9257 (OUTLIER) cc_final: 0.8903 (tt) REVERT: A 172 TRP cc_start: 0.8142 (t-100) cc_final: 0.7938 (t-100) REVERT: A 176 MET cc_start: 0.8753 (tpp) cc_final: 0.8243 (tpp) REVERT: A 208 ASN cc_start: 0.8603 (t0) cc_final: 0.8371 (m-40) REVERT: A 226 LEU cc_start: 0.9366 (mt) cc_final: 0.9117 (mt) REVERT: A 247 ASP cc_start: 0.8095 (t70) cc_final: 0.7767 (t0) REVERT: A 337 CYS cc_start: 0.9073 (t) cc_final: 0.8846 (t) REVERT: A 361 TYR cc_start: 0.8843 (t80) cc_final: 0.8167 (t80) REVERT: A 363 PRO cc_start: 0.9421 (Cg_exo) cc_final: 0.8952 (Cg_endo) REVERT: A 379 MET cc_start: 0.8558 (mmm) cc_final: 0.8356 (mmm) REVERT: A 441 PHE cc_start: 0.8158 (m-80) cc_final: 0.7785 (m-80) REVERT: A 452 PHE cc_start: 0.9088 (t80) cc_final: 0.8335 (t80) REVERT: A 465 SER cc_start: 0.9513 (t) cc_final: 0.9243 (m) REVERT: A 479 LEU cc_start: 0.8142 (OUTLIER) cc_final: 0.7776 (mp) REVERT: A 522 MET cc_start: 0.8760 (mmm) cc_final: 0.8245 (mmp) REVERT: A 524 ASP cc_start: 0.9122 (t0) cc_final: 0.8577 (t70) REVERT: A 526 TRP cc_start: 0.8525 (m-10) cc_final: 0.8135 (m-10) REVERT: A 584 TYR cc_start: 0.8845 (m-10) cc_final: 0.8408 (m-10) REVERT: A 644 MET cc_start: 0.7736 (mmm) cc_final: 0.6267 (tmm) REVERT: A 688 GLU cc_start: 0.8653 (mm-30) cc_final: 0.8081 (mm-30) REVERT: B 14 ASN cc_start: 0.9149 (m-40) cc_final: 0.8908 (t0) REVERT: B 21 PHE cc_start: 0.8785 (m-80) cc_final: 0.8041 (m-80) REVERT: B 30 LEU cc_start: 0.8841 (mt) cc_final: 0.8596 (pp) REVERT: B 42 TRP cc_start: 0.8245 (m100) cc_final: 0.7505 (m100) REVERT: B 72 PHE cc_start: 0.6770 (t80) cc_final: 0.6437 (t80) REVERT: B 76 MET cc_start: 0.7624 (ttt) cc_final: 0.7171 (tpp) REVERT: B 102 TYR cc_start: 0.8762 (m-10) cc_final: 0.8225 (m-10) REVERT: B 115 LEU cc_start: 0.9288 (OUTLIER) cc_final: 0.8856 (tt) REVERT: B 208 ASN cc_start: 0.8561 (t0) cc_final: 0.8335 (m-40) REVERT: B 226 LEU cc_start: 0.9390 (mt) cc_final: 0.9074 (mt) REVERT: B 344 ARG cc_start: 0.9040 (OUTLIER) cc_final: 0.8261 (ttm110) REVERT: B 361 TYR cc_start: 0.8884 (t80) cc_final: 0.8208 (t80) REVERT: B 363 PRO cc_start: 0.9469 (Cg_exo) cc_final: 0.9037 (Cg_endo) REVERT: B 394 ILE cc_start: 0.9067 (OUTLIER) cc_final: 0.8753 (tp) REVERT: B 441 PHE cc_start: 0.8254 (m-80) cc_final: 0.7953 (m-80) REVERT: B 447 MET cc_start: 0.9062 (tpt) cc_final: 0.8695 (tpp) REVERT: B 460 PHE cc_start: 0.8525 (t80) cc_final: 0.8233 (t80) REVERT: B 465 SER cc_start: 0.9537 (t) cc_final: 0.9252 (m) REVERT: B 479 LEU cc_start: 0.8097 (OUTLIER) cc_final: 0.7730 (mp) REVERT: B 510 ILE cc_start: 0.7436 (OUTLIER) cc_final: 0.7068 (mt) REVERT: B 522 MET cc_start: 0.8805 (mmm) cc_final: 0.7887 (mmp) REVERT: B 526 TRP cc_start: 0.8582 (m-10) cc_final: 0.8072 (m-10) REVERT: B 577 TYR cc_start: 0.7944 (m-80) cc_final: 0.7421 (m-80) REVERT: B 644 MET cc_start: 0.7944 (mmm) cc_final: 0.6550 (tmm) outliers start: 51 outliers final: 38 residues processed: 337 average time/residue: 0.1652 time to fit residues: 83.6772 Evaluate side-chains 327 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 282 time to evaluate : 1.115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 667 ILE Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 115 LEU Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 575 GLN Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 13 optimal weight: 2.9990 chunk 67 optimal weight: 0.9990 chunk 86 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 99 optimal weight: 0.8980 chunk 65 optimal weight: 8.9990 chunk 117 optimal weight: 0.9980 chunk 73 optimal weight: 0.7980 chunk 71 optimal weight: 0.0470 chunk 54 optimal weight: 0.0770 chunk 72 optimal weight: 0.7980 overall best weight: 0.5236 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 543 HIS B 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7619 moved from start: 0.4406 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9854 Z= 0.218 Angle : 0.705 11.063 13438 Z= 0.344 Chirality : 0.042 0.179 1548 Planarity : 0.005 0.047 1666 Dihedral : 5.374 43.129 1322 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 20.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.70 % Favored : 94.30 % Rotamer: Outliers : 5.59 % Allowed : 27.95 % Favored : 66.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.57 (0.25), residues: 1192 helix: 0.50 (0.18), residues: 840 sheet: -3.65 (0.91), residues: 24 loop : -2.36 (0.33), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP B 625 HIS 0.003 0.001 HIS A 608 PHE 0.025 0.001 PHE B 169 TYR 0.016 0.001 TYR B 181 ARG 0.004 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 352 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 54 poor density : 298 time to evaluate : 0.996 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8893 (mt) cc_final: 0.8649 (pp) REVERT: A 36 ARG cc_start: 0.8847 (mtp180) cc_final: 0.8601 (mtp180) REVERT: A 72 PHE cc_start: 0.7077 (t80) cc_final: 0.6864 (t80) REVERT: A 76 MET cc_start: 0.7369 (ttt) cc_final: 0.7081 (tpp) REVERT: A 102 TYR cc_start: 0.8752 (m-10) cc_final: 0.8426 (m-10) REVERT: A 115 LEU cc_start: 0.9272 (OUTLIER) cc_final: 0.8925 (tt) REVERT: A 176 MET cc_start: 0.8768 (tpp) cc_final: 0.8230 (tpp) REVERT: A 208 ASN cc_start: 0.8518 (t0) cc_final: 0.8309 (m-40) REVERT: A 226 LEU cc_start: 0.9380 (mt) cc_final: 0.9043 (mt) REVERT: A 247 ASP cc_start: 0.8072 (t70) cc_final: 0.7740 (t0) REVERT: A 337 CYS cc_start: 0.8992 (t) cc_final: 0.8663 (t) REVERT: A 361 TYR cc_start: 0.8808 (t80) cc_final: 0.8197 (t80) REVERT: A 363 PRO cc_start: 0.9417 (Cg_exo) cc_final: 0.8990 (Cg_endo) REVERT: A 441 PHE cc_start: 0.8041 (m-80) cc_final: 0.7685 (m-80) REVERT: A 452 PHE cc_start: 0.9033 (t80) cc_final: 0.8341 (t80) REVERT: A 465 SER cc_start: 0.9508 (t) cc_final: 0.9213 (m) REVERT: A 479 LEU cc_start: 0.8116 (OUTLIER) cc_final: 0.7748 (mp) REVERT: A 524 ASP cc_start: 0.9134 (t0) cc_final: 0.8817 (t70) REVERT: A 644 MET cc_start: 0.7741 (mmm) cc_final: 0.6258 (tmm) REVERT: B 21 PHE cc_start: 0.8756 (m-80) cc_final: 0.8001 (m-80) REVERT: B 30 LEU cc_start: 0.8850 (mt) cc_final: 0.8621 (pp) REVERT: B 31 GLN cc_start: 0.6162 (mm110) cc_final: 0.5935 (mm-40) REVERT: B 42 TRP cc_start: 0.8282 (m100) cc_final: 0.7571 (m100) REVERT: B 72 PHE cc_start: 0.6768 (t80) cc_final: 0.6463 (t80) REVERT: B 76 MET cc_start: 0.7563 (ttt) cc_final: 0.7160 (tpp) REVERT: B 102 TYR cc_start: 0.8638 (m-10) cc_final: 0.8146 (m-10) REVERT: B 176 MET cc_start: 0.8811 (tpp) cc_final: 0.8491 (tpp) REVERT: B 226 LEU cc_start: 0.9405 (mt) cc_final: 0.9089 (mt) REVERT: B 361 TYR cc_start: 0.8853 (t80) cc_final: 0.8202 (t80) REVERT: B 363 PRO cc_start: 0.9451 (Cg_exo) cc_final: 0.9047 (Cg_endo) REVERT: B 394 ILE cc_start: 0.9014 (OUTLIER) cc_final: 0.8713 (tp) REVERT: B 441 PHE cc_start: 0.8228 (m-80) cc_final: 0.7925 (m-80) REVERT: B 447 MET cc_start: 0.9059 (tpt) cc_final: 0.8693 (tpp) REVERT: B 465 SER cc_start: 0.9527 (t) cc_final: 0.9267 (m) REVERT: B 479 LEU cc_start: 0.8057 (OUTLIER) cc_final: 0.7690 (mp) REVERT: B 510 ILE cc_start: 0.7441 (OUTLIER) cc_final: 0.7122 (mt) REVERT: B 522 MET cc_start: 0.8754 (mmm) cc_final: 0.7843 (mmp) REVERT: B 526 TRP cc_start: 0.8538 (m-10) cc_final: 0.8015 (m-10) REVERT: B 577 TYR cc_start: 0.8034 (m-80) cc_final: 0.7410 (m-80) REVERT: B 584 TYR cc_start: 0.8788 (m-10) cc_final: 0.8529 (m-10) REVERT: B 644 MET cc_start: 0.7961 (mmm) cc_final: 0.6568 (tmm) outliers start: 54 outliers final: 41 residues processed: 323 average time/residue: 0.1651 time to fit residues: 79.9537 Evaluate side-chains 329 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 46 poor density : 283 time to evaluate : 1.126 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 194 SER Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 114 MET Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 390 PHE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 692 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 46 optimal weight: 0.7980 chunk 70 optimal weight: 5.9990 chunk 35 optimal weight: 2.9990 chunk 23 optimal weight: 6.9990 chunk 22 optimal weight: 1.9990 chunk 74 optimal weight: 0.5980 chunk 80 optimal weight: 0.9980 chunk 58 optimal weight: 5.9990 chunk 10 optimal weight: 0.0770 chunk 92 optimal weight: 0.8980 chunk 106 optimal weight: 0.0470 overall best weight: 0.4836 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 575 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7601 moved from start: 0.4645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 9854 Z= 0.216 Angle : 0.708 11.327 13438 Z= 0.343 Chirality : 0.042 0.166 1548 Planarity : 0.005 0.047 1666 Dihedral : 5.529 48.921 1322 Min Nonbonded Distance : 2.118 Molprobity Statistics. All-atom Clashscore : 20.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 5.07 % Allowed : 28.67 % Favored : 66.25 % 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: -0.50 (0.25), residues: 1192 helix: 0.57 (0.18), residues: 842 sheet: -3.50 (0.96), residues: 24 loop : -2.39 (0.33), residues: 326 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 625 HIS 0.004 0.001 HIS A 608 PHE 0.038 0.001 PHE A 396 TYR 0.017 0.002 TYR A 577 ARG 0.004 0.000 ARG A 683 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 342 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 49 poor density : 293 time to evaluate : 1.000 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8889 (mt) cc_final: 0.8621 (pp) REVERT: A 36 ARG cc_start: 0.8872 (mtp180) cc_final: 0.8626 (mtp180) REVERT: A 42 TRP cc_start: 0.8260 (m100) cc_final: 0.7577 (m100) REVERT: A 76 MET cc_start: 0.7373 (ttt) cc_final: 0.6997 (mmm) REVERT: A 102 TYR cc_start: 0.8733 (m-10) cc_final: 0.8413 (m-10) REVERT: A 115 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8922 (tt) REVERT: A 176 MET cc_start: 0.8662 (tpp) cc_final: 0.8388 (tpp) REVERT: A 226 LEU cc_start: 0.9390 (mt) cc_final: 0.9048 (mt) REVERT: A 247 ASP cc_start: 0.7994 (t70) cc_final: 0.7656 (t0) REVERT: A 337 CYS cc_start: 0.9012 (t) cc_final: 0.8657 (t) REVERT: A 361 TYR cc_start: 0.8827 (t80) cc_final: 0.8215 (t80) REVERT: A 363 PRO cc_start: 0.9411 (Cg_exo) cc_final: 0.8988 (Cg_endo) REVERT: A 441 PHE cc_start: 0.8035 (m-80) cc_final: 0.7668 (m-80) REVERT: A 452 PHE cc_start: 0.9006 (t80) cc_final: 0.8476 (t80) REVERT: A 479 LEU cc_start: 0.8112 (OUTLIER) cc_final: 0.7755 (mp) REVERT: A 522 MET cc_start: 0.8994 (mmp) cc_final: 0.8089 (mmp) REVERT: A 526 TRP cc_start: 0.8575 (m-10) cc_final: 0.7994 (m-10) REVERT: A 577 TYR cc_start: 0.7481 (m-80) cc_final: 0.7094 (m-80) REVERT: A 584 TYR cc_start: 0.8802 (m-10) cc_final: 0.8548 (m-10) REVERT: A 644 MET cc_start: 0.7756 (mmm) cc_final: 0.6278 (tmm) REVERT: B 30 LEU cc_start: 0.8841 (mt) cc_final: 0.8626 (pp) REVERT: B 31 GLN cc_start: 0.6167 (mm110) cc_final: 0.5952 (mm-40) REVERT: B 72 PHE cc_start: 0.6784 (t80) cc_final: 0.6462 (t80) REVERT: B 76 MET cc_start: 0.7553 (ttt) cc_final: 0.7159 (tpp) REVERT: B 102 TYR cc_start: 0.8573 (m-10) cc_final: 0.8149 (m-10) REVERT: B 176 MET cc_start: 0.8883 (tpp) cc_final: 0.8632 (tpp) REVERT: B 226 LEU cc_start: 0.9412 (mt) cc_final: 0.9096 (mt) REVERT: B 361 TYR cc_start: 0.8782 (t80) cc_final: 0.8078 (t80) REVERT: B 363 PRO cc_start: 0.9421 (Cg_exo) cc_final: 0.9028 (Cg_endo) REVERT: B 394 ILE cc_start: 0.8974 (OUTLIER) cc_final: 0.8670 (tp) REVERT: B 441 PHE cc_start: 0.8155 (m-80) cc_final: 0.7744 (m-80) REVERT: B 465 SER cc_start: 0.9518 (t) cc_final: 0.9234 (m) REVERT: B 479 LEU cc_start: 0.8046 (OUTLIER) cc_final: 0.7693 (mp) REVERT: B 522 MET cc_start: 0.8611 (mmm) cc_final: 0.8132 (mmp) REVERT: B 526 TRP cc_start: 0.8290 (m-10) cc_final: 0.8004 (m-10) REVERT: B 577 TYR cc_start: 0.7930 (m-80) cc_final: 0.7488 (m-80) REVERT: B 584 TYR cc_start: 0.8740 (m-10) cc_final: 0.8451 (m-10) REVERT: B 644 MET cc_start: 0.8060 (mmm) cc_final: 0.6617 (tmm) outliers start: 49 outliers final: 38 residues processed: 316 average time/residue: 0.1584 time to fit residues: 76.5646 Evaluate side-chains 325 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 283 time to evaluate : 0.980 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 112 optimal weight: 0.9980 chunk 102 optimal weight: 0.9980 chunk 109 optimal weight: 2.9990 chunk 65 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 86 optimal weight: 3.9990 chunk 33 optimal weight: 1.9990 chunk 99 optimal weight: 0.9990 chunk 103 optimal weight: 0.8980 chunk 71 optimal weight: 0.4980 chunk 115 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 575 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7625 moved from start: 0.4732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 9854 Z= 0.242 Angle : 0.712 11.135 13438 Z= 0.349 Chirality : 0.043 0.174 1548 Planarity : 0.005 0.046 1666 Dihedral : 5.544 51.483 1322 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.63 % Favored : 93.37 % Rotamer: Outliers : 4.97 % Allowed : 29.30 % Favored : 65.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.40 (0.25), residues: 1192 helix: 0.65 (0.18), residues: 842 sheet: -3.38 (0.82), residues: 34 loop : -2.32 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 625 HIS 0.003 0.001 HIS B 608 PHE 0.042 0.001 PHE A 396 TYR 0.018 0.002 TYR B 181 ARG 0.003 0.000 ARG B 631 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 333 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 48 poor density : 285 time to evaluate : 1.207 Fit side-chains REVERT: A 30 LEU cc_start: 0.8915 (mt) cc_final: 0.8624 (pp) REVERT: A 36 ARG cc_start: 0.8851 (mtp180) cc_final: 0.8643 (mtp180) REVERT: A 72 PHE cc_start: 0.7442 (t80) cc_final: 0.6955 (t80) REVERT: A 76 MET cc_start: 0.7262 (ttt) cc_final: 0.7014 (tpp) REVERT: A 102 TYR cc_start: 0.8845 (m-10) cc_final: 0.8508 (m-10) REVERT: A 115 LEU cc_start: 0.9275 (OUTLIER) cc_final: 0.9054 (tt) REVERT: A 176 MET cc_start: 0.8774 (tpp) cc_final: 0.8457 (tpp) REVERT: A 226 LEU cc_start: 0.9399 (mt) cc_final: 0.9049 (mt) REVERT: A 247 ASP cc_start: 0.8015 (t70) cc_final: 0.7681 (t0) REVERT: A 337 CYS cc_start: 0.9042 (t) cc_final: 0.8823 (t) REVERT: A 361 TYR cc_start: 0.8879 (t80) cc_final: 0.8269 (t80) REVERT: A 363 PRO cc_start: 0.9415 (Cg_exo) cc_final: 0.8934 (Cg_endo) REVERT: A 441 PHE cc_start: 0.8075 (m-80) cc_final: 0.7716 (m-80) REVERT: A 452 PHE cc_start: 0.8672 (t80) cc_final: 0.8343 (t80) REVERT: A 479 LEU cc_start: 0.8144 (OUTLIER) cc_final: 0.7785 (mp) REVERT: A 522 MET cc_start: 0.8795 (mmp) cc_final: 0.8381 (mmp) REVERT: A 526 TRP cc_start: 0.8448 (m-10) cc_final: 0.7956 (m-10) REVERT: A 577 TYR cc_start: 0.7440 (m-80) cc_final: 0.7060 (m-80) REVERT: A 584 TYR cc_start: 0.8823 (m-10) cc_final: 0.8520 (m-10) REVERT: A 644 MET cc_start: 0.7791 (mmm) cc_final: 0.6287 (tmm) REVERT: B 30 LEU cc_start: 0.8851 (mt) cc_final: 0.8635 (pp) REVERT: B 31 GLN cc_start: 0.6218 (mm110) cc_final: 0.5999 (mm-40) REVERT: B 72 PHE cc_start: 0.6691 (t80) cc_final: 0.6348 (t80) REVERT: B 76 MET cc_start: 0.7644 (ttt) cc_final: 0.7191 (tpp) REVERT: B 102 TYR cc_start: 0.8675 (m-10) cc_final: 0.8343 (m-10) REVERT: B 176 MET cc_start: 0.8945 (tpp) cc_final: 0.8463 (tpp) REVERT: B 226 LEU cc_start: 0.9419 (mt) cc_final: 0.9059 (mt) REVERT: B 344 ARG cc_start: 0.9134 (OUTLIER) cc_final: 0.8381 (ttm110) REVERT: B 361 TYR cc_start: 0.8827 (t80) cc_final: 0.8199 (t80) REVERT: B 363 PRO cc_start: 0.9435 (Cg_exo) cc_final: 0.8947 (Cg_endo) REVERT: B 394 ILE cc_start: 0.9006 (OUTLIER) cc_final: 0.8709 (tp) REVERT: B 441 PHE cc_start: 0.8191 (m-80) cc_final: 0.7797 (m-80) REVERT: B 452 PHE cc_start: 0.8959 (t80) cc_final: 0.8546 (t80) REVERT: B 460 PHE cc_start: 0.8522 (t80) cc_final: 0.8232 (t80) REVERT: B 465 SER cc_start: 0.9527 (t) cc_final: 0.9242 (m) REVERT: B 479 LEU cc_start: 0.8061 (OUTLIER) cc_final: 0.7710 (mp) REVERT: B 522 MET cc_start: 0.8651 (mmm) cc_final: 0.8157 (mmp) REVERT: B 526 TRP cc_start: 0.8261 (m-10) cc_final: 0.7990 (m-10) REVERT: B 577 TYR cc_start: 0.8118 (m-80) cc_final: 0.7753 (m-80) REVERT: B 582 LEU cc_start: 0.9109 (mt) cc_final: 0.8864 (mt) REVERT: B 584 TYR cc_start: 0.8817 (m-10) cc_final: 0.8328 (m-10) REVERT: B 611 ILE cc_start: 0.8787 (mm) cc_final: 0.8554 (mt) REVERT: B 644 MET cc_start: 0.7921 (mmm) cc_final: 0.6592 (tmm) outliers start: 48 outliers final: 39 residues processed: 307 average time/residue: 0.1833 time to fit residues: 85.9236 Evaluate side-chains 320 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 44 poor density : 276 time to evaluate : 1.018 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 9 VAL Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 240 CYS Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 9 VAL Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 240 CYS Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 377 LEU Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 70 optimal weight: 6.9990 chunk 54 optimal weight: 1.9990 chunk 80 optimal weight: 0.9990 chunk 121 optimal weight: 3.9990 chunk 111 optimal weight: 2.9990 chunk 96 optimal weight: 1.9990 chunk 10 optimal weight: 0.0980 chunk 74 optimal weight: 0.7980 chunk 59 optimal weight: 0.6980 chunk 76 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 overall best weight: 0.7182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 31 GLN ** B 14 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 575 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7608 moved from start: 0.4873 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 9854 Z= 0.231 Angle : 0.714 11.220 13438 Z= 0.348 Chirality : 0.042 0.167 1548 Planarity : 0.005 0.047 1666 Dihedral : 5.489 53.589 1322 Min Nonbonded Distance : 2.151 Molprobity Statistics. All-atom Clashscore : 21.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.46 % Favored : 93.54 % Rotamer: Outliers : 4.24 % Allowed : 30.02 % Favored : 65.73 % 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: -0.38 (0.25), residues: 1192 helix: 0.69 (0.18), residues: 846 sheet: -3.34 (0.84), residues: 34 loop : -2.44 (0.34), residues: 312 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 625 HIS 0.004 0.001 HIS B 608 PHE 0.016 0.001 PHE B 669 TYR 0.017 0.001 TYR B 520 ARG 0.003 0.000 ARG A 683 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2384 Ramachandran restraints generated. 1192 Oldfield, 0 Emsley, 1192 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 332 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 291 time to evaluate : 1.102 Fit side-chains revert: symmetry clash REVERT: A 30 LEU cc_start: 0.8937 (mt) cc_final: 0.8649 (pp) REVERT: A 42 TRP cc_start: 0.8258 (m100) cc_final: 0.7532 (m100) REVERT: A 176 MET cc_start: 0.8821 (tpp) cc_final: 0.8528 (tpp) REVERT: A 226 LEU cc_start: 0.9402 (mt) cc_final: 0.9037 (mt) REVERT: A 247 ASP cc_start: 0.8027 (t70) cc_final: 0.7687 (t0) REVERT: A 327 SER cc_start: 0.9303 (m) cc_final: 0.9028 (t) REVERT: A 361 TYR cc_start: 0.8854 (t80) cc_final: 0.8234 (t80) REVERT: A 363 PRO cc_start: 0.9410 (Cg_exo) cc_final: 0.8924 (Cg_endo) REVERT: A 441 PHE cc_start: 0.8034 (m-80) cc_final: 0.7684 (m-80) REVERT: A 452 PHE cc_start: 0.8476 (t80) cc_final: 0.8247 (t80) REVERT: A 478 PHE cc_start: 0.9095 (t80) cc_final: 0.8874 (t80) REVERT: A 479 LEU cc_start: 0.8117 (OUTLIER) cc_final: 0.7738 (mp) REVERT: A 522 MET cc_start: 0.8807 (mmp) cc_final: 0.8368 (mmp) REVERT: A 526 TRP cc_start: 0.8405 (m-10) cc_final: 0.7949 (m-10) REVERT: A 577 TYR cc_start: 0.7317 (m-80) cc_final: 0.7014 (m-80) REVERT: A 584 TYR cc_start: 0.8846 (m-10) cc_final: 0.8488 (m-10) REVERT: A 644 MET cc_start: 0.7819 (mmm) cc_final: 0.6296 (tmm) REVERT: B 30 LEU cc_start: 0.8850 (mt) cc_final: 0.8635 (pp) REVERT: B 72 PHE cc_start: 0.6748 (t80) cc_final: 0.6443 (t80) REVERT: B 76 MET cc_start: 0.7588 (ttt) cc_final: 0.7164 (tpp) REVERT: B 102 TYR cc_start: 0.8693 (m-10) cc_final: 0.8365 (m-10) REVERT: B 176 MET cc_start: 0.8921 (tpp) cc_final: 0.8436 (tpp) REVERT: B 201 GLN cc_start: 0.8692 (mt0) cc_final: 0.8416 (pm20) REVERT: B 226 LEU cc_start: 0.9414 (mt) cc_final: 0.9044 (mt) REVERT: B 344 ARG cc_start: 0.9130 (OUTLIER) cc_final: 0.8361 (ttm110) REVERT: B 361 TYR cc_start: 0.8798 (t80) cc_final: 0.8138 (t80) REVERT: B 363 PRO cc_start: 0.9427 (Cg_exo) cc_final: 0.8921 (Cg_endo) REVERT: B 394 ILE cc_start: 0.9002 (OUTLIER) cc_final: 0.8698 (tp) REVERT: B 441 PHE cc_start: 0.8141 (m-80) cc_final: 0.7765 (m-80) REVERT: B 452 PHE cc_start: 0.8823 (t80) cc_final: 0.8554 (t80) REVERT: B 460 PHE cc_start: 0.8512 (t80) cc_final: 0.8237 (t80) REVERT: B 465 SER cc_start: 0.9520 (t) cc_final: 0.9254 (m) REVERT: B 479 LEU cc_start: 0.8071 (OUTLIER) cc_final: 0.7722 (mp) REVERT: B 522 MET cc_start: 0.8670 (mmm) cc_final: 0.8167 (mmp) REVERT: B 526 TRP cc_start: 0.8242 (m-10) cc_final: 0.7985 (m-10) REVERT: B 577 TYR cc_start: 0.8121 (m-80) cc_final: 0.7802 (m-80) REVERT: B 582 LEU cc_start: 0.9091 (mt) cc_final: 0.8833 (mt) REVERT: B 584 TYR cc_start: 0.8714 (m-10) cc_final: 0.8417 (m-10) REVERT: B 644 MET cc_start: 0.7920 (mmm) cc_final: 0.6589 (tmm) REVERT: B 678 GLU cc_start: 0.8901 (mt-10) cc_final: 0.8599 (mt-10) outliers start: 41 outliers final: 34 residues processed: 310 average time/residue: 0.1630 time to fit residues: 77.0303 Evaluate side-chains 314 residues out of total 1052 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 38 poor density : 276 time to evaluate : 1.088 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ILE Chi-restraints excluded: chain A residue 162 HIS Chi-restraints excluded: chain A residue 170 THR Chi-restraints excluded: chain A residue 238 VAL Chi-restraints excluded: chain A residue 239 VAL Chi-restraints excluded: chain A residue 259 LEU Chi-restraints excluded: chain A residue 260 ASP Chi-restraints excluded: chain A residue 360 ILE Chi-restraints excluded: chain A residue 377 LEU Chi-restraints excluded: chain A residue 392 ILE Chi-restraints excluded: chain A residue 461 LEU Chi-restraints excluded: chain A residue 479 LEU Chi-restraints excluded: chain A residue 482 VAL Chi-restraints excluded: chain A residue 588 THR Chi-restraints excluded: chain A residue 591 LEU Chi-restraints excluded: chain A residue 613 VAL Chi-restraints excluded: chain A residue 614 TYR Chi-restraints excluded: chain A residue 673 CYS Chi-restraints excluded: chain A residue 691 MET Chi-restraints excluded: chain B residue 112 ILE Chi-restraints excluded: chain B residue 162 HIS Chi-restraints excluded: chain B residue 170 THR Chi-restraints excluded: chain B residue 194 SER Chi-restraints excluded: chain B residue 238 VAL Chi-restraints excluded: chain B residue 259 LEU Chi-restraints excluded: chain B residue 260 ASP Chi-restraints excluded: chain B residue 344 ARG Chi-restraints excluded: chain B residue 360 ILE Chi-restraints excluded: chain B residue 394 ILE Chi-restraints excluded: chain B residue 479 LEU Chi-restraints excluded: chain B residue 482 VAL Chi-restraints excluded: chain B residue 510 ILE Chi-restraints excluded: chain B residue 588 THR Chi-restraints excluded: chain B residue 591 LEU Chi-restraints excluded: chain B residue 613 VAL Chi-restraints excluded: chain B residue 667 ILE Chi-restraints excluded: chain B residue 673 CYS Chi-restraints excluded: chain B residue 691 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 122 random chunks: chunk 29 optimal weight: 0.3980 chunk 89 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 26 optimal weight: 0.9980 chunk 96 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 99 optimal weight: 0.9980 chunk 12 optimal weight: 0.8980 chunk 17 optimal weight: 0.9990 chunk 85 optimal weight: 8.9990 chunk 5 optimal weight: 1.9990 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 31 GLN B 14 ASN B 31 GLN B 575 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3733 r_free = 0.3733 target = 0.132309 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3500 r_free = 0.3500 target = 0.115525 restraints weight = 18174.056| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3546 r_free = 0.3546 target = 0.118824 restraints weight = 8254.451| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.120953 restraints weight = 4854.351| |-----------------------------------------------------------------------------| r_work (final): 0.3580 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.4904 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 9854 Z= 0.249 Angle : 0.725 11.058 13438 Z= 0.354 Chirality : 0.043 0.166 1548 Planarity : 0.005 0.046 1666 Dihedral : 5.616 58.415 1322 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 21.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.54 % Favored : 93.46 % Rotamer: Outliers : 4.35 % Allowed : 30.64 % Favored : 65.01 % 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: -0.38 (0.25), residues: 1192 helix: 0.66 (0.18), residues: 848 sheet: -3.28 (0.87), residues: 34 loop : -2.38 (0.35), residues: 310 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 625 HIS 0.004 0.001 HIS B 608 PHE 0.027 0.001 PHE A 72 TYR 0.042 0.002 TYR A 102 ARG 0.003 0.000 ARG A 683 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2377.70 seconds wall clock time: 44 minutes 26.58 seconds (2666.58 seconds total)