Starting phenix.real_space_refine on Sat Aug 23 10:43:19 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xaj_38200/08_2025/8xaj_38200.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xaj_38200/08_2025/8xaj_38200.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.29 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xaj_38200/08_2025/8xaj_38200.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xaj_38200/08_2025/8xaj_38200.map" model { file = "/net/cci-nas-00/data/ceres_data/8xaj_38200/08_2025/8xaj_38200.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xaj_38200/08_2025/8xaj_38200.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } 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= 0.017 sd= 0.074 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 7 5.49 5 S 52 5.16 5 C 7776 2.51 5 N 1847 2.21 5 O 1986 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 20 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 11668 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 5645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5645 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "B" Number of atoms: 5645 Number of conformers: 1 Conformer: "" Number of residues, atoms: 705, 5645 Classifications: {'peptide': 705} Incomplete info: {'truncation_to_alanine': 17} Link IDs: {'PTRANS': 36, 'TRANS': 668} Chain breaks: 1 Unresolved non-hydrogen bonds: 70 Unresolved non-hydrogen angles: 88 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 5 Planarities with less than four sites: {'ARG:plan': 2, 'ASN:plan1': 2, 'GLN:plan1': 2, 'PHE:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 39 Chain: "A" Number of atoms: 378 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 378 Unusual residues: {'PCW': 7} Classifications: {'undetermined': 7} Link IDs: {None: 6} Residues with excluded nonbonded symmetry interactions: 7 residue: pdb=" N PCW A 801 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 801 " occ=0.00 residue: pdb=" N PCW A 802 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 802 " occ=0.00 residue: pdb=" N PCW A 803 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 803 " occ=0.00 residue: pdb=" N PCW A 804 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 804 " occ=0.00 residue: pdb=" N PCW A 805 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 805 " occ=0.00 residue: pdb=" N PCW A 806 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 806 " occ=0.00 residue: pdb=" N PCW A 807 " occ=0.00 ... (52 atoms not shown) pdb=" P PCW A 807 " occ=0.00 Time building chain proxies: 2.25, per 1000 atoms: 0.19 Number of scatterers: 11668 At special positions: 0 Unit cell: (98.115, 148.755, 99.17, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 52 16.00 P 7 15.00 O 1986 8.00 N 1847 7.00 C 7776 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 - 3.00 Amino acid : True - 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=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 1.02 Conformation dependent library (CDL) restraints added in 542.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2712 Finding SS restraints... Secondary structure from input PDB file: 56 helices and 2 sheets defined 67.4% alpha, 2.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing helix chain 'A' and resid 3 through 25 Processing helix chain 'A' and resid 26 through 28 No H-bonds generated for 'chain 'A' and resid 26 through 28' Processing helix chain 'A' and resid 39 through 43 removed outlier: 4.155A pdb=" N TRP A 42 " --> pdb=" O PHE A 39 " (cutoff:3.500A) Processing helix chain 'A' and resid 83 through 92 Processing helix chain 'A' and resid 92 through 125 removed outlier: 4.592A pdb=" N TYR A 102 " --> pdb=" O TYR A 98 " (cutoff:3.500A) Proline residue: A 111 - end of helix Proline residue: A 122 - end of helix Processing helix chain 'A' and resid 133 through 141 removed outlier: 3.795A pdb=" N LEU A 136 " --> pdb=" O ALA A 133 " (cutoff:3.500A) removed outlier: 5.785A pdb=" N ASN A 138 " --> pdb=" O GLN A 135 " (cutoff:3.500A) removed outlier: 6.412A pdb=" N VAL A 139 " --> pdb=" O LEU A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 148 through 152 Processing helix chain 'A' and resid 158 through 194 removed outlier: 3.874A pdb=" N HIS A 162 " --> pdb=" O ARG A 158 " (cutoff:3.500A) Processing helix chain 'A' and resid 198 through 201 Processing helix chain 'A' and resid 216 through 228 Processing helix chain 'A' and resid 243 through 269 Processing helix chain 'A' and resid 291 through 313 removed outlier: 3.937A pdb=" N GLU A 310 " --> pdb=" O SER A 306 " (cutoff:3.500A) removed outlier: 3.974A pdb=" N GLU A 311 " --> pdb=" O LYS A 307 " (cutoff:3.500A) removed outlier: 4.080A pdb=" N VAL A 313 " --> pdb=" O ARG A 309 " (cutoff:3.500A) Processing helix chain 'A' and resid 329 through 339 Processing helix chain 'A' and resid 367 through 388 Processing helix chain 'A' and resid 390 through 400 Processing helix chain 'A' and resid 408 through 412 removed outlier: 3.732A pdb=" N LEU A 412 " --> pdb=" O ALA A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 422 through 452 Proline residue: A 430 - end of helix removed outlier: 3.664A pdb=" N LEU A 434 " --> pdb=" O PRO A 430 " (cutoff:3.500A) Proline residue: A 442 - end of helix removed outlier: 3.760A pdb=" N GLU A 452 " --> pdb=" O MET A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 456 through 482 Processing helix chain 'A' and resid 485 through 495 Processing helix chain 'A' and resid 500 through 532 Proline residue: A 510 - end of helix removed outlier: 4.593A pdb=" N THR A 514 " --> pdb=" O PRO A 510 " (cutoff:3.500A) removed outlier: 4.595A pdb=" N PHE A 515 " --> pdb=" O MET A 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE A 532 " --> pdb=" O VAL A 528 " (cutoff:3.500A) Processing helix chain 'A' and resid 534 through 548 removed outlier: 4.025A pdb=" N LEU A 538 " --> pdb=" O MET A 534 " (cutoff:3.500A) removed outlier: 3.685A pdb=" N LEU A 543 " --> pdb=" O ILE A 539 " (cutoff:3.500A) removed outlier: 4.161A pdb=" N ALA A 546 " --> pdb=" O HIS A 542 " (cutoff:3.500A) Processing helix chain 'A' and resid 569 through 583 Processing helix chain 'A' and resid 589 through 612 removed outlier: 4.241A pdb=" N PHE A 593 " --> pdb=" O MET A 589 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N LEU A 595 " --> pdb=" O LEU A 591 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG A 606 " --> pdb=" O TYR A 602 " (cutoff:3.500A) Processing helix chain 'A' and resid 623 through 649 Processing helix chain 'A' and resid 654 through 676 Proline residue: A 662 - end of helix Processing helix chain 'A' and resid 677 through 681 Processing helix chain 'A' and resid 684 through 699 Processing helix chain 'A' and resid 703 through 709 removed outlier: 3.747A pdb=" N TYR A 707 " --> pdb=" O ASN A 703 " (cutoff:3.500A) Processing helix chain 'B' and resid 4 through 25 Processing helix chain 'B' and resid 26 through 28 No H-bonds generated for 'chain 'B' and resid 26 through 28' Processing helix chain 'B' and resid 39 through 43 removed outlier: 4.154A pdb=" N TRP B 42 " --> pdb=" O PHE B 39 " (cutoff:3.500A) Processing helix chain 'B' and resid 83 through 92 Processing helix chain 'B' and resid 92 through 125 removed outlier: 4.592A pdb=" N TYR B 102 " --> pdb=" O TYR B 98 " (cutoff:3.500A) Proline residue: B 111 - end of helix Proline residue: B 122 - end of helix Processing helix chain 'B' and resid 133 through 141 removed outlier: 3.794A pdb=" N LEU B 136 " --> pdb=" O ALA B 133 " (cutoff:3.500A) removed outlier: 5.786A pdb=" N ASN B 138 " --> pdb=" O GLN B 135 " (cutoff:3.500A) removed outlier: 6.413A pdb=" N VAL B 139 " --> pdb=" O LEU B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 148 through 152 Processing helix chain 'B' and resid 158 through 194 removed outlier: 3.875A pdb=" N HIS B 162 " --> pdb=" O ARG B 158 " (cutoff:3.500A) Processing helix chain 'B' and resid 198 through 201 Processing helix chain 'B' and resid 216 through 228 Processing helix chain 'B' and resid 243 through 269 Processing helix chain 'B' and resid 291 through 313 removed outlier: 3.936A pdb=" N GLU B 310 " --> pdb=" O SER B 306 " (cutoff:3.500A) removed outlier: 3.975A pdb=" N GLU B 311 " --> pdb=" O LYS B 307 " (cutoff:3.500A) removed outlier: 4.079A pdb=" N VAL B 313 " --> pdb=" O ARG B 309 " (cutoff:3.500A) Processing helix chain 'B' and resid 329 through 339 Processing helix chain 'B' and resid 367 through 388 Processing helix chain 'B' and resid 390 through 400 Processing helix chain 'B' and resid 408 through 412 removed outlier: 3.732A pdb=" N LEU B 412 " --> pdb=" O ALA B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 422 through 452 Proline residue: B 430 - end of helix removed outlier: 3.664A pdb=" N LEU B 434 " --> pdb=" O PRO B 430 " (cutoff:3.500A) Proline residue: B 442 - end of helix removed outlier: 3.761A pdb=" N GLU B 452 " --> pdb=" O MET B 448 " (cutoff:3.500A) Processing helix chain 'B' and resid 456 through 482 Processing helix chain 'B' and resid 485 through 495 Processing helix chain 'B' and resid 500 through 532 Proline residue: B 510 - end of helix removed outlier: 4.593A pdb=" N THR B 514 " --> pdb=" O PRO B 510 " (cutoff:3.500A) removed outlier: 4.596A pdb=" N PHE B 515 " --> pdb=" O MET B 511 " (cutoff:3.500A) removed outlier: 3.654A pdb=" N ILE B 532 " --> pdb=" O VAL B 528 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 548 removed outlier: 4.024A pdb=" N LEU B 538 " --> pdb=" O MET B 534 " (cutoff:3.500A) removed outlier: 3.686A pdb=" N LEU B 543 " --> pdb=" O ILE B 539 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N ALA B 546 " --> pdb=" O HIS B 542 " (cutoff:3.500A) Processing helix chain 'B' and resid 569 through 583 Processing helix chain 'B' and resid 589 through 612 removed outlier: 4.241A pdb=" N PHE B 593 " --> pdb=" O MET B 589 " (cutoff:3.500A) removed outlier: 3.571A pdb=" N LEU B 595 " --> pdb=" O LEU B 591 " (cutoff:3.500A) removed outlier: 4.008A pdb=" N ARG B 606 " --> pdb=" O TYR B 602 " (cutoff:3.500A) Processing helix chain 'B' and resid 623 through 649 Processing helix chain 'B' and resid 654 through 676 Proline residue: B 662 - end of helix Processing helix chain 'B' and resid 677 through 681 Processing helix chain 'B' and resid 684 through 699 Processing helix chain 'B' and resid 703 through 709 removed outlier: 3.746A pdb=" N TYR B 707 " --> pdb=" O ASN B 703 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 235 through 238 Processing sheet with id=AA2, first strand: chain 'B' and resid 235 through 238 685 hydrogen bonds defined for protein. 1983 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: 1.60 Time building geometry restraints manager: 1.33 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1762 1.31 - 1.44: 3314 1.44 - 1.56: 6753 1.56 - 1.69: 52 1.69 - 1.81: 96 Bond restraints: 11977 Sorted by residual: bond pdb=" C14 PCW A 804 " pdb=" C15 PCW A 804 " ideal model delta sigma weight residual 1.523 1.630 -0.107 2.00e-02 2.50e+03 2.87e+01 bond pdb=" C11 PCW A 807 " pdb=" O3 PCW A 807 " ideal model delta sigma weight residual 1.326 1.429 -0.103 2.00e-02 2.50e+03 2.64e+01 bond pdb=" C11 PCW A 804 " pdb=" O3 PCW A 804 " ideal model delta sigma weight residual 1.326 1.428 -0.102 2.00e-02 2.50e+03 2.60e+01 bond pdb=" C11 PCW A 806 " pdb=" O3 PCW A 806 " ideal model delta sigma weight residual 1.326 1.428 -0.102 2.00e-02 2.50e+03 2.58e+01 bond pdb=" C11 PCW A 801 " pdb=" O3 PCW A 801 " ideal model delta sigma weight residual 1.326 1.427 -0.101 2.00e-02 2.50e+03 2.55e+01 ... (remaining 11972 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.88: 15796 2.88 - 5.76: 330 5.76 - 8.64: 58 8.64 - 11.52: 23 11.52 - 14.40: 14 Bond angle restraints: 16221 Sorted by residual: angle pdb=" O3P PCW A 802 " pdb=" P PCW A 802 " pdb=" O4P PCW A 802 " ideal model delta sigma weight residual 96.85 111.25 -14.40 3.00e+00 1.11e-01 2.30e+01 angle pdb=" C5 PCW A 803 " pdb=" N PCW A 803 " pdb=" C7 PCW A 803 " ideal model delta sigma weight residual 107.31 120.91 -13.60 3.00e+00 1.11e-01 2.05e+01 angle pdb=" C5 PCW A 802 " pdb=" N PCW A 802 " pdb=" C7 PCW A 802 " ideal model delta sigma weight residual 107.31 120.83 -13.52 3.00e+00 1.11e-01 2.03e+01 angle pdb=" C ARG B 675 " pdb=" CA ARG B 675 " pdb=" CB ARG B 675 " ideal model delta sigma weight residual 111.03 102.78 8.25 1.87e+00 2.86e-01 1.95e+01 angle pdb=" O3P PCW A 801 " pdb=" P PCW A 801 " pdb=" O4P PCW A 801 " ideal model delta sigma weight residual 96.85 109.97 -13.12 3.00e+00 1.11e-01 1.91e+01 ... (remaining 16216 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.56: 6939 34.56 - 69.12: 196 69.12 - 103.68: 18 103.68 - 138.24: 4 138.24 - 172.80: 2 Dihedral angle restraints: 7159 sinusoidal: 2985 harmonic: 4174 Sorted by residual: dihedral pdb=" CA ARG B 682 " pdb=" C ARG B 682 " pdb=" N TYR B 683 " pdb=" CA TYR B 683 " ideal model delta harmonic sigma weight residual -180.00 -152.82 -27.18 0 5.00e+00 4.00e-02 2.96e+01 dihedral pdb=" CA ARG A 682 " pdb=" C ARG A 682 " pdb=" N TYR A 683 " pdb=" CA TYR A 683 " ideal model delta harmonic sigma weight residual 180.00 -152.83 -27.17 0 5.00e+00 4.00e-02 2.95e+01 dihedral pdb=" CA VAL B 612 " pdb=" C VAL B 612 " pdb=" N TYR B 613 " pdb=" CA TYR B 613 " ideal model delta harmonic sigma weight residual 180.00 154.17 25.83 0 5.00e+00 4.00e-02 2.67e+01 ... (remaining 7156 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.058: 1449 0.058 - 0.116: 290 0.116 - 0.174: 40 0.174 - 0.232: 10 0.232 - 0.290: 4 Chirality restraints: 1793 Sorted by residual: chirality pdb=" C2 PCW A 807 " pdb=" C1 PCW A 807 " pdb=" C3 PCW A 807 " pdb=" O2 PCW A 807 " both_signs ideal model delta sigma weight residual False -2.32 -2.61 0.29 2.00e-01 2.50e+01 2.10e+00 chirality pdb=" C2 PCW A 805 " pdb=" C1 PCW A 805 " pdb=" C3 PCW A 805 " pdb=" O2 PCW A 805 " both_signs ideal model delta sigma weight residual False -2.32 -2.58 0.25 2.00e-01 2.50e+01 1.59e+00 chirality pdb=" C2 PCW A 804 " pdb=" C1 PCW A 804 " pdb=" C3 PCW A 804 " pdb=" O2 PCW A 804 " both_signs ideal model delta sigma weight residual False -2.32 -2.56 0.24 2.00e-01 2.50e+01 1.43e+00 ... (remaining 1790 not shown) Planarity restraints: 2002 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C38 PCW A 804 " 0.022 2.00e-02 2.50e+03 3.97e-02 1.58e+01 pdb=" C39 PCW A 804 " -0.050 2.00e-02 2.50e+03 pdb=" C40 PCW A 804 " 0.052 2.00e-02 2.50e+03 pdb=" C41 PCW A 804 " -0.024 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLU A 84 " 0.059 5.00e-02 4.00e+02 8.93e-02 1.28e+01 pdb=" N PRO A 85 " -0.154 5.00e-02 4.00e+02 pdb=" CA PRO A 85 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO A 85 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLU B 84 " -0.059 5.00e-02 4.00e+02 8.93e-02 1.27e+01 pdb=" N PRO B 85 " 0.154 5.00e-02 4.00e+02 pdb=" CA PRO B 85 " -0.046 5.00e-02 4.00e+02 pdb=" CD PRO B 85 " -0.050 5.00e-02 4.00e+02 ... (remaining 1999 not shown) Histogram of nonbonded interaction distances: 1.55 - 2.22: 8 2.22 - 2.89: 4656 2.89 - 3.56: 17669 3.56 - 4.23: 25752 4.23 - 4.90: 44600 Nonbonded interactions: 92685 Sorted by model distance: nonbonded pdb=" NH1 ARG A 188 " pdb=" O ALA A 620 " model vdw 1.547 3.120 nonbonded pdb=" NH1 ARG B 188 " pdb=" O ALA B 620 " model vdw 1.550 3.120 nonbonded pdb=" NH1 ARG A 188 " pdb=" C ALA A 620 " model vdw 2.088 3.350 nonbonded pdb=" NH1 ARG B 188 " pdb=" C ALA B 620 " model vdw 2.092 3.350 nonbonded pdb=" ND2 ASN A 257 " pdb=" OD2 ASP A 554 " model vdw 2.194 3.120 ... (remaining 92680 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = (chain 'A' and resid 3 through 718) 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=0.00 max=1.00 mean=0.97 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.980 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: 0.170 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 10.080 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 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:1.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 12.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7482 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 : 0.009 0.107 11984 Z= 0.426 Angle : 1.091 14.398 16221 Z= 0.519 Chirality : 0.050 0.290 1793 Planarity : 0.007 0.089 2002 Dihedral : 16.782 172.801 4447 Min Nonbonded Distance : 1.547 Molprobity Statistics. All-atom Clashscore : 15.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.27 % Favored : 88.73 % Rotamer: Outliers : 0.00 % Allowed : 0.50 % Favored : 99.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.52 (0.22), residues: 1402 helix: 0.13 (0.18), residues: 832 sheet: None (None), residues: 0 loop : -2.81 (0.24), residues: 570 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.014 0.001 ARG B 630 TYR 0.030 0.002 TYR B 181 PHE 0.017 0.002 PHE B 598 TRP 0.014 0.002 TRP B 624 HIS 0.004 0.001 HIS A 90 Details of bonding type rmsd covalent geometry : bond 0.00860 (11977) covalent geometry : angle 1.09119 (16221) hydrogen bonds : bond 0.13776 ( 685) hydrogen bonds : angle 6.87951 ( 1983) Misc. bond : bond 0.04136 ( 7) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 197 time to evaluate : 0.412 Fit side-chains revert: symmetry clash REVERT: A 303 LYS cc_start: 0.9221 (tptm) cc_final: 0.8987 (tptp) REVERT: A 307 LYS cc_start: 0.8231 (tptp) cc_final: 0.7897 (tptp) REVERT: A 650 HIS cc_start: 0.7976 (m170) cc_final: 0.7753 (m170) REVERT: B 165 MET cc_start: 0.8072 (mmp) cc_final: 0.7587 (mmp) REVERT: B 167 TYR cc_start: 0.8730 (m-80) cc_final: 0.8447 (m-80) REVERT: B 300 LYS cc_start: 0.8883 (mtmm) cc_final: 0.8374 (mtmt) REVERT: B 303 LYS cc_start: 0.9190 (tptm) cc_final: 0.8952 (mmmm) REVERT: B 307 LYS cc_start: 0.8374 (tptp) cc_final: 0.8018 (tptp) outliers start: 0 outliers final: 0 residues processed: 197 average time/residue: 0.0996 time to fit residues: 28.0409 Evaluate side-chains 155 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 155 time to evaluate : 0.318 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 98 optimal weight: 7.9990 chunk 107 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 66 optimal weight: 0.6980 chunk 130 optimal weight: 0.8980 chunk 124 optimal weight: 1.9990 chunk 103 optimal weight: 0.9990 chunk 77 optimal weight: 0.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 0.6980 chunk 55 optimal weight: 1.9990 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 124 ASN A 257 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 257 ASN B 574 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.177700 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3666 r_free = 0.3666 target = 0.137367 restraints weight = 17906.163| |-----------------------------------------------------------------------------| r_work (start): 0.3648 rms_B_bonded: 2.43 r_work: 0.3544 rms_B_bonded: 3.06 restraints_weight: 0.5000 r_work: 0.3426 rms_B_bonded: 5.00 restraints_weight: 0.2500 r_work (final): 0.3426 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7476 moved from start: 0.1363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11984 Z= 0.153 Angle : 0.717 7.984 16221 Z= 0.368 Chirality : 0.044 0.158 1793 Planarity : 0.006 0.069 2002 Dihedral : 14.578 151.101 1831 Min Nonbonded Distance : 2.446 Molprobity Statistics. All-atom Clashscore : 10.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 1.43 % Allowed : 7.98 % Favored : 90.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.68 (0.23), residues: 1402 helix: 1.13 (0.19), residues: 812 sheet: -2.09 (0.86), residues: 34 loop : -2.90 (0.25), residues: 556 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 630 TYR 0.027 0.002 TYR B 181 PHE 0.031 0.002 PHE A 72 TRP 0.017 0.001 TRP A 624 HIS 0.002 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00336 (11977) covalent geometry : angle 0.71671 (16221) hydrogen bonds : bond 0.04446 ( 685) hydrogen bonds : angle 4.94532 ( 1983) Misc. bond : bond 0.00137 ( 7) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 184 time to evaluate : 0.320 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 303 LYS cc_start: 0.9282 (tptm) cc_final: 0.8956 (tptp) REVERT: A 307 LYS cc_start: 0.8621 (tptp) cc_final: 0.8172 (tptp) REVERT: A 451 PHE cc_start: 0.8504 (t80) cc_final: 0.8170 (t80) REVERT: A 613 TYR cc_start: 0.7038 (m-80) cc_final: 0.6374 (m-80) REVERT: A 650 HIS cc_start: 0.8220 (m170) cc_final: 0.7987 (m170) REVERT: B 124 ASN cc_start: 0.8037 (OUTLIER) cc_final: 0.7730 (t0) REVERT: B 125 TRP cc_start: 0.7880 (t60) cc_final: 0.7482 (t-100) REVERT: B 165 MET cc_start: 0.8122 (mmp) cc_final: 0.7855 (mmt) REVERT: B 182 GLU cc_start: 0.7988 (tt0) cc_final: 0.7734 (tt0) REVERT: B 303 LYS cc_start: 0.9292 (tptm) cc_final: 0.8968 (tptp) REVERT: B 307 LYS cc_start: 0.8680 (tptp) cc_final: 0.8280 (tptp) REVERT: B 521 MET cc_start: 0.6631 (OUTLIER) cc_final: 0.6297 (mpp) REVERT: B 613 TYR cc_start: 0.7075 (m-80) cc_final: 0.6504 (m-80) outliers start: 17 outliers final: 6 residues processed: 190 average time/residue: 0.0874 time to fit residues: 24.7901 Evaluate side-chains 170 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 162 time to evaluate : 0.253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 121 VAL Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 34 optimal weight: 4.9990 chunk 70 optimal weight: 10.0000 chunk 71 optimal weight: 1.9990 chunk 68 optimal weight: 3.9990 chunk 104 optimal weight: 4.9990 chunk 50 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 76 optimal weight: 0.9990 chunk 55 optimal weight: 4.9990 overall best weight: 1.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN B 489 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4114 r_free = 0.4114 target = 0.175333 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.134329 restraints weight = 18037.608| |-----------------------------------------------------------------------------| r_work (start): 0.3608 rms_B_bonded: 2.50 r_work: 0.3503 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7424 moved from start: 0.1568 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 11984 Z= 0.197 Angle : 0.712 8.469 16221 Z= 0.367 Chirality : 0.045 0.169 1793 Planarity : 0.006 0.064 2002 Dihedral : 14.222 151.846 1831 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.63 % Favored : 89.37 % Rotamer: Outliers : 2.10 % Allowed : 11.18 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.38 (0.24), residues: 1402 helix: 1.31 (0.19), residues: 814 sheet: -1.12 (1.13), residues: 22 loop : -2.72 (0.26), residues: 566 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 630 TYR 0.030 0.002 TYR B 181 PHE 0.031 0.002 PHE A 389 TRP 0.015 0.001 TRP A 624 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00464 (11977) covalent geometry : angle 0.71210 (16221) hydrogen bonds : bond 0.04392 ( 685) hydrogen bonds : angle 4.87677 ( 1983) Misc. bond : bond 0.00126 ( 7) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 166 time to evaluate : 0.474 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 86 GLU cc_start: 0.7919 (tp30) cc_final: 0.7622 (tp30) REVERT: A 181 TYR cc_start: 0.8318 (OUTLIER) cc_final: 0.7969 (t80) REVERT: A 297 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5916 (mp0) REVERT: A 303 LYS cc_start: 0.9275 (tptm) cc_final: 0.8954 (tptp) REVERT: A 304 GLU cc_start: 0.7372 (OUTLIER) cc_final: 0.7135 (pm20) REVERT: A 307 LYS cc_start: 0.8646 (tptp) cc_final: 0.8093 (tptp) REVERT: A 521 MET cc_start: 0.6427 (OUTLIER) cc_final: 0.5667 (mpp) REVERT: A 613 TYR cc_start: 0.7227 (m-80) cc_final: 0.6448 (m-80) REVERT: B 70 MET cc_start: 0.7197 (mmt) cc_final: 0.6994 (mmp) REVERT: B 125 TRP cc_start: 0.8298 (t60) cc_final: 0.7839 (t-100) REVERT: B 182 GLU cc_start: 0.7663 (tt0) cc_final: 0.7425 (tt0) REVERT: B 297 GLU cc_start: 0.6884 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: B 303 LYS cc_start: 0.9274 (tptm) cc_final: 0.8973 (tptp) REVERT: B 304 GLU cc_start: 0.7719 (mp0) cc_final: 0.7478 (mp0) REVERT: B 307 LYS cc_start: 0.8669 (tptp) cc_final: 0.8290 (tptp) REVERT: B 521 MET cc_start: 0.6668 (OUTLIER) cc_final: 0.6444 (mpp) REVERT: B 613 TYR cc_start: 0.7243 (m-80) cc_final: 0.6595 (m-80) outliers start: 25 outliers final: 11 residues processed: 182 average time/residue: 0.0852 time to fit residues: 23.3100 Evaluate side-chains 176 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 159 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 71 optimal weight: 0.9990 chunk 75 optimal weight: 10.0000 chunk 120 optimal weight: 1.9990 chunk 84 optimal weight: 0.9980 chunk 126 optimal weight: 0.7980 chunk 130 optimal weight: 4.9990 chunk 88 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 chunk 110 optimal weight: 7.9990 chunk 90 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 489 GLN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4139 r_free = 0.4139 target = 0.177927 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3667 r_free = 0.3667 target = 0.137538 restraints weight = 17965.161| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 2.49 r_work: 0.3541 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7349 moved from start: 0.1810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.055 11984 Z= 0.145 Angle : 0.661 7.875 16221 Z= 0.342 Chirality : 0.043 0.166 1793 Planarity : 0.006 0.059 2002 Dihedral : 13.794 162.625 1831 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 10.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.41 % Favored : 89.59 % Rotamer: Outliers : 2.35 % Allowed : 13.61 % Favored : 84.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.17 (0.24), residues: 1402 helix: 1.52 (0.19), residues: 812 sheet: -1.08 (1.11), residues: 22 loop : -2.67 (0.26), residues: 568 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 630 TYR 0.028 0.002 TYR A 181 PHE 0.031 0.001 PHE A 72 TRP 0.018 0.001 TRP A 624 HIS 0.003 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00326 (11977) covalent geometry : angle 0.66055 (16221) hydrogen bonds : bond 0.03984 ( 685) hydrogen bonds : angle 4.70119 ( 1983) Misc. bond : bond 0.00114 ( 7) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 174 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7337 (mmt) cc_final: 0.7060 (mmp) REVERT: A 297 GLU cc_start: 0.6450 (OUTLIER) cc_final: 0.6034 (mp0) REVERT: A 303 LYS cc_start: 0.9274 (tptm) cc_final: 0.8956 (tptp) REVERT: A 307 LYS cc_start: 0.8672 (tptp) cc_final: 0.8136 (tptp) REVERT: A 451 PHE cc_start: 0.8417 (t80) cc_final: 0.8201 (t80) REVERT: A 521 MET cc_start: 0.6237 (OUTLIER) cc_final: 0.5519 (mpp) REVERT: A 613 TYR cc_start: 0.7326 (m-80) cc_final: 0.6509 (m-80) REVERT: B 125 TRP cc_start: 0.8185 (t60) cc_final: 0.7831 (t-100) REVERT: B 182 GLU cc_start: 0.7653 (tt0) cc_final: 0.7439 (tt0) REVERT: B 297 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6446 (mp0) REVERT: B 303 LYS cc_start: 0.9276 (tptm) cc_final: 0.8967 (tptp) REVERT: B 307 LYS cc_start: 0.8721 (tptp) cc_final: 0.8303 (tptp) REVERT: B 613 TYR cc_start: 0.7208 (m-80) cc_final: 0.6582 (m-80) outliers start: 28 outliers final: 13 residues processed: 191 average time/residue: 0.0957 time to fit residues: 27.3999 Evaluate side-chains 179 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 163 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 128 optimal weight: 3.9990 chunk 14 optimal weight: 5.9990 chunk 22 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 1 optimal weight: 0.9980 chunk 126 optimal weight: 0.5980 chunk 82 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 48 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 122 optimal weight: 6.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 489 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4131 r_free = 0.4131 target = 0.177184 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3655 r_free = 0.3655 target = 0.136684 restraints weight = 17857.093| |-----------------------------------------------------------------------------| r_work (start): 0.3635 rms_B_bonded: 2.48 r_work: 0.3530 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3530 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7392 moved from start: 0.1941 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11984 Z= 0.160 Angle : 0.671 7.910 16221 Z= 0.345 Chirality : 0.044 0.167 1793 Planarity : 0.006 0.056 2002 Dihedral : 13.511 171.577 1831 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 10.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.86 % Allowed : 15.63 % Favored : 81.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.24), residues: 1402 helix: 1.58 (0.19), residues: 804 sheet: -0.89 (1.14), residues: 22 loop : -2.65 (0.26), residues: 576 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 630 TYR 0.028 0.002 TYR A 181 PHE 0.032 0.002 PHE B 72 TRP 0.015 0.001 TRP A 624 HIS 0.003 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00369 (11977) covalent geometry : angle 0.67095 (16221) hydrogen bonds : bond 0.03968 ( 685) hydrogen bonds : angle 4.68598 ( 1983) Misc. bond : bond 0.00101 ( 7) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 173 time to evaluate : 0.423 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7265 (mmt) cc_final: 0.6995 (mmp) REVERT: A 86 GLU cc_start: 0.8036 (tp30) cc_final: 0.7718 (tp30) REVERT: A 124 ASN cc_start: 0.8139 (OUTLIER) cc_final: 0.7792 (t0) REVERT: A 127 ASN cc_start: 0.7675 (p0) cc_final: 0.7046 (m-40) REVERT: A 263 GLN cc_start: 0.8789 (tm-30) cc_final: 0.8460 (pp30) REVERT: A 297 GLU cc_start: 0.6606 (OUTLIER) cc_final: 0.6055 (mp0) REVERT: A 303 LYS cc_start: 0.9246 (tptm) cc_final: 0.8925 (tptp) REVERT: A 307 LYS cc_start: 0.8671 (tptp) cc_final: 0.8154 (tptp) REVERT: A 437 PHE cc_start: 0.7786 (t80) cc_final: 0.7576 (t80) REVERT: A 579 LEU cc_start: 0.8535 (OUTLIER) cc_final: 0.8285 (mt) REVERT: A 589 MET cc_start: 0.8205 (mmm) cc_final: 0.7936 (mmm) REVERT: A 613 TYR cc_start: 0.7375 (m-80) cc_final: 0.6526 (m-80) REVERT: A 709 GLN cc_start: 0.8023 (OUTLIER) cc_final: 0.7710 (pp30) REVERT: B 125 TRP cc_start: 0.8128 (t60) cc_final: 0.7788 (t-100) REVERT: B 182 GLU cc_start: 0.7713 (tt0) cc_final: 0.7471 (tt0) REVERT: B 200 ASP cc_start: 0.8881 (p0) cc_final: 0.8622 (p0) REVERT: B 297 GLU cc_start: 0.6908 (OUTLIER) cc_final: 0.6570 (mp0) REVERT: B 303 LYS cc_start: 0.9248 (tptm) cc_final: 0.8945 (tptp) REVERT: B 307 LYS cc_start: 0.8741 (tptp) cc_final: 0.8322 (tptp) REVERT: B 573 ILE cc_start: 0.7530 (pt) cc_final: 0.7300 (tp) REVERT: B 613 TYR cc_start: 0.7270 (m-80) cc_final: 0.6586 (m-80) outliers start: 34 outliers final: 19 residues processed: 194 average time/residue: 0.0957 time to fit residues: 27.8096 Evaluate side-chains 190 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 166 time to evaluate : 0.417 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 124 ASN Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 26 optimal weight: 50.0000 chunk 87 optimal weight: 2.9990 chunk 122 optimal weight: 4.9990 chunk 28 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 93 optimal weight: 6.9990 chunk 61 optimal weight: 0.8980 chunk 84 optimal weight: 6.9990 chunk 1 optimal weight: 0.9990 chunk 117 optimal weight: 1.9990 chunk 11 optimal weight: 0.0980 overall best weight: 1.3986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4125 r_free = 0.4125 target = 0.176788 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3650 r_free = 0.3650 target = 0.136337 restraints weight = 17947.402| |-----------------------------------------------------------------------------| r_work (start): 0.3630 rms_B_bonded: 2.49 r_work: 0.3523 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.3523 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7364 moved from start: 0.2027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 11984 Z= 0.167 Angle : 0.680 9.106 16221 Z= 0.349 Chirality : 0.044 0.170 1793 Planarity : 0.005 0.055 2002 Dihedral : 13.355 177.006 1831 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.34 % Favored : 89.66 % Rotamer: Outliers : 2.94 % Allowed : 16.72 % Favored : 80.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.24), residues: 1402 helix: 1.58 (0.19), residues: 806 sheet: -0.82 (1.13), residues: 22 loop : -2.61 (0.26), residues: 574 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 630 TYR 0.029 0.002 TYR A 181 PHE 0.031 0.002 PHE A 389 TRP 0.016 0.001 TRP A 624 HIS 0.004 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00390 (11977) covalent geometry : angle 0.67986 (16221) hydrogen bonds : bond 0.03982 ( 685) hydrogen bonds : angle 4.69459 ( 1983) Misc. bond : bond 0.00094 ( 7) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 204 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 169 time to evaluate : 0.371 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.2937 (OUTLIER) cc_final: 0.2447 (tp) REVERT: A 70 MET cc_start: 0.7332 (mmt) cc_final: 0.7063 (mmp) REVERT: A 86 GLU cc_start: 0.7988 (tp30) cc_final: 0.7651 (tp30) REVERT: A 127 ASN cc_start: 0.7717 (p0) cc_final: 0.7022 (m-40) REVERT: A 263 GLN cc_start: 0.8790 (tm-30) cc_final: 0.8460 (pp30) REVERT: A 297 GLU cc_start: 0.6532 (OUTLIER) cc_final: 0.6016 (mp0) REVERT: A 303 LYS cc_start: 0.9266 (tptm) cc_final: 0.8942 (tptp) REVERT: A 307 LYS cc_start: 0.8700 (tptp) cc_final: 0.8186 (tptp) REVERT: A 437 PHE cc_start: 0.7738 (t80) cc_final: 0.7534 (t80) REVERT: A 573 ILE cc_start: 0.7586 (OUTLIER) cc_final: 0.7360 (pt) REVERT: A 579 LEU cc_start: 0.8505 (OUTLIER) cc_final: 0.8258 (mt) REVERT: A 589 MET cc_start: 0.8229 (mmm) cc_final: 0.7930 (mmm) REVERT: A 613 TYR cc_start: 0.7391 (m-80) cc_final: 0.6538 (m-80) REVERT: A 709 GLN cc_start: 0.7983 (OUTLIER) cc_final: 0.7718 (pp30) REVERT: B 125 TRP cc_start: 0.8125 (t60) cc_final: 0.7750 (t-100) REVERT: B 182 GLU cc_start: 0.7723 (tt0) cc_final: 0.7480 (tt0) REVERT: B 200 ASP cc_start: 0.8854 (p0) cc_final: 0.8627 (p0) REVERT: B 297 GLU cc_start: 0.6957 (OUTLIER) cc_final: 0.6398 (mp0) REVERT: B 303 LYS cc_start: 0.9275 (tptm) cc_final: 0.8961 (tptp) REVERT: B 307 LYS cc_start: 0.8749 (tptp) cc_final: 0.8367 (tptp) REVERT: B 573 ILE cc_start: 0.7531 (pt) cc_final: 0.7274 (tp) REVERT: B 598 PHE cc_start: 0.7173 (OUTLIER) cc_final: 0.6920 (m-10) REVERT: B 613 TYR cc_start: 0.7214 (m-80) cc_final: 0.6579 (m-80) outliers start: 35 outliers final: 24 residues processed: 190 average time/residue: 0.0906 time to fit residues: 25.7443 Evaluate side-chains 198 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 573 ILE Chi-restraints excluded: chain A residue 579 LEU Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 612 VAL Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 27 optimal weight: 9.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 102 optimal weight: 0.5980 chunk 82 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 93 optimal weight: 6.9990 chunk 132 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 31 optimal weight: 0.6980 chunk 91 optimal weight: 0.9990 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4140 r_free = 0.4140 target = 0.178160 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3665 r_free = 0.3665 target = 0.137638 restraints weight = 17963.530| |-----------------------------------------------------------------------------| r_work (start): 0.3646 rms_B_bonded: 2.51 r_work: 0.3541 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3541 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7370 moved from start: 0.2137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 11984 Z= 0.145 Angle : 0.666 8.493 16221 Z= 0.341 Chirality : 0.043 0.215 1793 Planarity : 0.005 0.055 2002 Dihedral : 13.145 177.777 1831 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.99 % Favored : 90.01 % Rotamer: Outliers : 2.86 % Allowed : 17.14 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.05 (0.24), residues: 1402 helix: 1.55 (0.19), residues: 818 sheet: -0.85 (1.12), residues: 22 loop : -2.56 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 630 TYR 0.028 0.001 TYR A 181 PHE 0.032 0.002 PHE A 169 TRP 0.017 0.001 TRP A 624 HIS 0.003 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00330 (11977) covalent geometry : angle 0.66617 (16221) hydrogen bonds : bond 0.03826 ( 685) hydrogen bonds : angle 4.65018 ( 1983) Misc. bond : bond 0.00088 ( 7) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 208 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 174 time to evaluate : 0.449 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.3179 (OUTLIER) cc_final: 0.2651 (tp) REVERT: A 70 MET cc_start: 0.7298 (mmt) cc_final: 0.7034 (mmp) REVERT: A 86 GLU cc_start: 0.8015 (tp30) cc_final: 0.7691 (tp30) REVERT: A 127 ASN cc_start: 0.7725 (p0) cc_final: 0.7219 (m-40) REVERT: A 297 GLU cc_start: 0.6475 (OUTLIER) cc_final: 0.5994 (mp0) REVERT: A 303 LYS cc_start: 0.9252 (tptm) cc_final: 0.8932 (tptp) REVERT: A 307 LYS cc_start: 0.8697 (tptp) cc_final: 0.8271 (tptp) REVERT: A 320 MET cc_start: 0.8390 (ptp) cc_final: 0.8044 (pmm) REVERT: A 389 PHE cc_start: 0.6695 (OUTLIER) cc_final: 0.5502 (t80) REVERT: A 521 MET cc_start: 0.6202 (OUTLIER) cc_final: 0.5385 (mpp) REVERT: A 589 MET cc_start: 0.8240 (mmm) cc_final: 0.7948 (mmm) REVERT: A 613 TYR cc_start: 0.7386 (m-80) cc_final: 0.6539 (m-80) REVERT: B 125 TRP cc_start: 0.8143 (t60) cc_final: 0.7699 (t-100) REVERT: B 182 GLU cc_start: 0.7728 (tt0) cc_final: 0.7501 (tt0) REVERT: B 200 ASP cc_start: 0.8799 (p0) cc_final: 0.8597 (p0) REVERT: B 297 GLU cc_start: 0.6964 (OUTLIER) cc_final: 0.6404 (mp0) REVERT: B 303 LYS cc_start: 0.9273 (tptm) cc_final: 0.8998 (tptp) REVERT: B 307 LYS cc_start: 0.8747 (tptp) cc_final: 0.8374 (tptp) REVERT: B 598 PHE cc_start: 0.7190 (OUTLIER) cc_final: 0.6957 (m-10) REVERT: B 613 TYR cc_start: 0.7197 (m-80) cc_final: 0.6497 (m-80) outliers start: 34 outliers final: 21 residues processed: 194 average time/residue: 0.0920 time to fit residues: 26.6908 Evaluate side-chains 192 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 165 time to evaluate : 0.390 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 598 PHE Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 44 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 124 optimal weight: 0.2980 chunk 135 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 15 optimal weight: 0.7980 chunk 117 optimal weight: 5.9990 chunk 83 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4154 r_free = 0.4154 target = 0.179664 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 66)----------------| | r_work = 0.3681 r_free = 0.3681 target = 0.139051 restraints weight = 18037.530| |-----------------------------------------------------------------------------| r_work (start): 0.3663 rms_B_bonded: 2.54 r_work: 0.3563 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.2288 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11984 Z= 0.141 Angle : 0.683 10.214 16221 Z= 0.352 Chirality : 0.043 0.185 1793 Planarity : 0.005 0.056 2002 Dihedral : 12.867 173.062 1831 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 10.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.69 % Allowed : 17.48 % Favored : 79.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.02 (0.24), residues: 1402 helix: 1.57 (0.19), residues: 818 sheet: -0.87 (1.13), residues: 22 loop : -2.55 (0.27), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 630 TYR 0.027 0.001 TYR A 181 PHE 0.031 0.001 PHE B 72 TRP 0.016 0.001 TRP B 624 HIS 0.003 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00315 (11977) covalent geometry : angle 0.68324 (16221) hydrogen bonds : bond 0.03710 ( 685) hydrogen bonds : angle 4.61263 ( 1983) Misc. bond : bond 0.00082 ( 7) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 207 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 0.403 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.7235 (mmt) cc_final: 0.6969 (mmp) REVERT: A 127 ASN cc_start: 0.7690 (p0) cc_final: 0.7026 (m-40) REVERT: A 180 GLU cc_start: 0.7791 (tp30) cc_final: 0.7587 (tp30) REVERT: A 297 GLU cc_start: 0.6540 (OUTLIER) cc_final: 0.6050 (mp0) REVERT: A 303 LYS cc_start: 0.9227 (tptm) cc_final: 0.8916 (tptp) REVERT: A 307 LYS cc_start: 0.8690 (tptp) cc_final: 0.8279 (tptp) REVERT: A 320 MET cc_start: 0.8389 (ptp) cc_final: 0.8076 (pmm) REVERT: A 389 PHE cc_start: 0.6758 (OUTLIER) cc_final: 0.5596 (t80) REVERT: A 521 MET cc_start: 0.6182 (OUTLIER) cc_final: 0.5340 (mpp) REVERT: A 589 MET cc_start: 0.8229 (mmm) cc_final: 0.7965 (mmm) REVERT: A 613 TYR cc_start: 0.7372 (m-80) cc_final: 0.6558 (m-80) REVERT: B 44 LEU cc_start: 0.3690 (OUTLIER) cc_final: 0.3375 (mp) REVERT: B 125 TRP cc_start: 0.8146 (t60) cc_final: 0.7823 (t-100) REVERT: B 182 GLU cc_start: 0.7776 (tt0) cc_final: 0.7551 (tt0) REVERT: B 297 GLU cc_start: 0.6888 (OUTLIER) cc_final: 0.6348 (mp0) REVERT: B 303 LYS cc_start: 0.9237 (tptm) cc_final: 0.8943 (tptp) REVERT: B 307 LYS cc_start: 0.8701 (tptp) cc_final: 0.8339 (tptp) REVERT: B 613 TYR cc_start: 0.7148 (m-80) cc_final: 0.6427 (m-80) outliers start: 32 outliers final: 22 residues processed: 193 average time/residue: 0.0926 time to fit residues: 26.9370 Evaluate side-chains 191 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 164 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 43 TYR Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 51 optimal weight: 5.9990 chunk 114 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 1 optimal weight: 0.9990 chunk 61 optimal weight: 0.5980 chunk 104 optimal weight: 0.5980 chunk 10 optimal weight: 4.9990 chunk 116 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 94 optimal weight: 6.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4148 r_free = 0.4148 target = 0.179020 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.138424 restraints weight = 18033.431| |-----------------------------------------------------------------------------| r_work (start): 0.3656 rms_B_bonded: 2.53 r_work: 0.3553 rms_B_bonded: 3.15 restraints_weight: 0.5000 r_work (final): 0.3553 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7404 moved from start: 0.2320 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.056 11984 Z= 0.151 Angle : 0.682 10.231 16221 Z= 0.352 Chirality : 0.044 0.211 1793 Planarity : 0.005 0.055 2002 Dihedral : 12.633 169.686 1831 Min Nonbonded Distance : 2.345 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.69 % Allowed : 17.56 % Favored : 79.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.11 (0.24), residues: 1402 helix: 1.45 (0.19), residues: 830 sheet: -1.37 (1.19), residues: 20 loop : -2.56 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 630 TYR 0.027 0.001 TYR A 181 PHE 0.042 0.002 PHE A 169 TRP 0.015 0.001 TRP B 624 HIS 0.003 0.001 HIS B 628 Details of bonding type rmsd covalent geometry : bond 0.00346 (11977) covalent geometry : angle 0.68167 (16221) hydrogen bonds : bond 0.03777 ( 685) hydrogen bonds : angle 4.62132 ( 1983) Misc. bond : bond 0.00077 ( 7) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 167 time to evaluate : 0.479 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.3253 (OUTLIER) cc_final: 0.2731 (tp) REVERT: A 127 ASN cc_start: 0.7717 (p0) cc_final: 0.7002 (m-40) REVERT: A 297 GLU cc_start: 0.6507 (OUTLIER) cc_final: 0.6026 (mp0) REVERT: A 303 LYS cc_start: 0.9235 (tptm) cc_final: 0.8922 (tptp) REVERT: A 307 LYS cc_start: 0.8713 (tptp) cc_final: 0.8286 (tptp) REVERT: A 320 MET cc_start: 0.8388 (ptp) cc_final: 0.8068 (pmm) REVERT: A 521 MET cc_start: 0.6149 (OUTLIER) cc_final: 0.5310 (mpp) REVERT: A 589 MET cc_start: 0.8251 (mmm) cc_final: 0.7979 (mmm) REVERT: A 613 TYR cc_start: 0.7389 (m-80) cc_final: 0.6601 (m-80) REVERT: B 44 LEU cc_start: 0.3696 (OUTLIER) cc_final: 0.3376 (mp) REVERT: B 125 TRP cc_start: 0.8124 (t60) cc_final: 0.7787 (t-100) REVERT: B 182 GLU cc_start: 0.7791 (tt0) cc_final: 0.7570 (tt0) REVERT: B 297 GLU cc_start: 0.6842 (OUTLIER) cc_final: 0.6314 (mp0) REVERT: B 303 LYS cc_start: 0.9264 (tptm) cc_final: 0.8974 (tptp) REVERT: B 307 LYS cc_start: 0.8732 (tptp) cc_final: 0.8370 (tptp) REVERT: B 613 TYR cc_start: 0.7156 (m-80) cc_final: 0.6474 (m-80) outliers start: 32 outliers final: 24 residues processed: 185 average time/residue: 0.0964 time to fit residues: 26.9919 Evaluate side-chains 195 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 166 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 147 LEU Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain A residue 709 GLN Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 72 optimal weight: 3.9990 chunk 121 optimal weight: 2.9990 chunk 27 optimal weight: 20.0000 chunk 62 optimal weight: 0.9990 chunk 84 optimal weight: 1.9990 chunk 98 optimal weight: 8.9990 chunk 54 optimal weight: 3.9990 chunk 8 optimal weight: 2.9990 chunk 59 optimal weight: 4.9990 chunk 31 optimal weight: 0.7980 chunk 95 optimal weight: 4.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 162 HIS ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 709 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 397 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175194 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.135026 restraints weight = 18070.738| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 2.48 r_work: 0.3503 rms_B_bonded: 3.13 restraints_weight: 0.5000 r_work (final): 0.3503 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7433 moved from start: 0.2262 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.073 11984 Z= 0.209 Angle : 0.738 10.579 16221 Z= 0.383 Chirality : 0.046 0.262 1793 Planarity : 0.006 0.054 2002 Dihedral : 12.453 166.255 1831 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.20 % Favored : 89.80 % Rotamer: Outliers : 2.52 % Allowed : 17.98 % Favored : 79.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.25 (0.24), residues: 1402 helix: 1.30 (0.19), residues: 830 sheet: -1.35 (1.20), residues: 20 loop : -2.56 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 630 TYR 0.033 0.002 TYR A 181 PHE 0.056 0.002 PHE A 169 TRP 0.011 0.001 TRP A 117 HIS 0.004 0.001 HIS A 628 Details of bonding type rmsd covalent geometry : bond 0.00498 (11977) covalent geometry : angle 0.73803 (16221) hydrogen bonds : bond 0.04219 ( 685) hydrogen bonds : angle 4.80306 ( 1983) Misc. bond : bond 0.00071 ( 7) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2804 Ramachandran restraints generated. 1402 Oldfield, 0 Emsley, 1402 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 170 time to evaluate : 0.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 44 LEU cc_start: 0.3062 (OUTLIER) cc_final: 0.2574 (tp) REVERT: A 70 MET cc_start: 0.7391 (mmt) cc_final: 0.7146 (mmp) REVERT: A 98 TYR cc_start: 0.7852 (t80) cc_final: 0.7469 (t80) REVERT: A 122 PRO cc_start: 0.9055 (Cg_exo) cc_final: 0.8710 (Cg_endo) REVERT: A 127 ASN cc_start: 0.7791 (p0) cc_final: 0.7217 (m-40) REVERT: A 180 GLU cc_start: 0.7914 (tp30) cc_final: 0.7686 (tp30) REVERT: A 297 GLU cc_start: 0.6502 (OUTLIER) cc_final: 0.6033 (mp0) REVERT: A 303 LYS cc_start: 0.9279 (tptm) cc_final: 0.8965 (tptp) REVERT: A 307 LYS cc_start: 0.8737 (tptp) cc_final: 0.8297 (tptp) REVERT: A 320 MET cc_start: 0.8427 (ptp) cc_final: 0.8064 (pmm) REVERT: A 521 MET cc_start: 0.6111 (OUTLIER) cc_final: 0.5324 (mpp) REVERT: A 613 TYR cc_start: 0.7343 (m-80) cc_final: 0.6573 (m-80) REVERT: B 44 LEU cc_start: 0.3686 (OUTLIER) cc_final: 0.3467 (mp) REVERT: B 125 TRP cc_start: 0.8230 (t60) cc_final: 0.7877 (t-100) REVERT: B 182 GLU cc_start: 0.7711 (tt0) cc_final: 0.7502 (tt0) REVERT: B 297 GLU cc_start: 0.6750 (OUTLIER) cc_final: 0.6240 (mp0) REVERT: B 303 LYS cc_start: 0.9292 (tptm) cc_final: 0.8989 (tptp) REVERT: B 307 LYS cc_start: 0.8770 (tptp) cc_final: 0.8389 (tptp) REVERT: B 613 TYR cc_start: 0.7177 (m-80) cc_final: 0.6522 (m-80) outliers start: 30 outliers final: 23 residues processed: 186 average time/residue: 0.0955 time to fit residues: 26.4140 Evaluate side-chains 197 residues out of total 1224 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 169 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 297 GLU Chi-restraints excluded: chain A residue 304 GLU Chi-restraints excluded: chain A residue 305 ILE Chi-restraints excluded: chain A residue 317 LYS Chi-restraints excluded: chain A residue 376 LEU Chi-restraints excluded: chain A residue 389 PHE Chi-restraints excluded: chain A residue 517 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain A residue 549 VAL Chi-restraints excluded: chain A residue 612 VAL Chi-restraints excluded: chain A residue 653 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 123 VAL Chi-restraints excluded: chain B residue 146 LYS Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 376 LEU Chi-restraints excluded: chain B residue 389 PHE Chi-restraints excluded: chain B residue 489 GLN Chi-restraints excluded: chain B residue 517 ILE Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 63 optimal weight: 1.9990 chunk 132 optimal weight: 0.7980 chunk 35 optimal weight: 1.9990 chunk 6 optimal weight: 0.0070 chunk 14 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 13 optimal weight: 0.6980 chunk 49 optimal weight: 1.9990 chunk 134 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 chunk 45 optimal weight: 0.9990 overall best weight: 0.7002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4155 r_free = 0.4155 target = 0.179640 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3691 r_free = 0.3691 target = 0.139620 restraints weight = 17971.550| |-----------------------------------------------------------------------------| r_work (start): 0.3675 rms_B_bonded: 2.50 r_work: 0.3570 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7385 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.072 11984 Z= 0.144 Angle : 0.699 11.045 16221 Z= 0.361 Chirality : 0.043 0.245 1793 Planarity : 0.005 0.055 2002 Dihedral : 12.213 163.524 1831 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 2.44 % Allowed : 18.15 % Favored : 79.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.12 (0.24), residues: 1402 helix: 1.45 (0.19), residues: 830 sheet: -1.44 (1.18), residues: 20 loop : -2.57 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 630 TYR 0.028 0.001 TYR A 181 PHE 0.032 0.001 PHE A 72 TRP 0.019 0.001 TRP A 624 HIS 0.006 0.001 HIS A 650 Details of bonding type rmsd covalent geometry : bond 0.00328 (11977) covalent geometry : angle 0.69915 (16221) hydrogen bonds : bond 0.03723 ( 685) hydrogen bonds : angle 4.64698 ( 1983) Misc. bond : bond 0.00071 ( 7) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2482.74 seconds wall clock time: 43 minutes 20.89 seconds (2600.89 seconds total)