Starting phenix.real_space_refine on Sat Jul 20 17:25:22 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/07_2024/8xaj_38200.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/07_2024/8xaj_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/07_2024/8xaj_38200.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/07_2024/8xaj_38200.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/07_2024/8xaj_38200.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8xaj_38200/07_2024/8xaj_38200.cif" } resolution = 3.29 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.017 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 Residue "A ARG 29": "NH1" <-> "NH2" Residue "A PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 137": "NH1" <-> "NH2" Residue "A GLU 154": "OE1" <-> "OE2" Residue "A GLU 219": "OE1" <-> "OE2" Residue "A GLU 308": "OE1" <-> "OE2" Residue "A ARG 357": "NH1" <-> "NH2" Residue "A GLU 531": "OE1" <-> "OE2" Residue "A ARG 606": "NH1" <-> "NH2" Residue "A GLU 677": "OE1" <-> "OE2" Residue "B ARG 29": "NH1" <-> "NH2" Residue "B PHE 72": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 137": "NH1" <-> "NH2" Residue "B GLU 154": "OE1" <-> "OE2" Residue "B GLU 219": "OE1" <-> "OE2" Residue "B GLU 308": "OE1" <-> "OE2" Residue "B ARG 357": "NH1" <-> "NH2" Residue "B GLU 531": "OE1" <-> "OE2" Residue "B ARG 606": "NH1" <-> "NH2" Residue "B GLU 677": "OE1" <-> "OE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/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: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, '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: {'GLN:plan1': 2, 'PHE:plan': 1, 'ARG:plan': 2, 'ASN:plan1': 2, '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: 6.88, per 1000 atoms: 0.59 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=7, symmetry=0 Number of additional bonds: simple=7, symmetry=0 Coordination: Other bonds: Time building additional restraints: 4.93 Conformation dependent library (CDL) restraints added in 2.2 seconds 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: 1.24 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: 3.16 Time building geometry restraints manager: 5.34 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: 95.72 - 103.39: 161 103.39 - 111.05: 4450 111.05 - 118.72: 5033 118.72 - 126.38: 6367 126.38 - 134.04: 210 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 2.520 nonbonded pdb=" NH1 ARG B 188 " pdb=" O ALA B 620 " model vdw 1.550 2.520 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 2.520 ... (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 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: 0.680 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.120 Process input model: 33.500 Find NCS groups from input model: 0.510 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.630 Set ADP refinement strategy: 0.010 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 38.010 ------------------------------------------------------------------------------- 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 11977 Z= 0.572 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 : 16.03 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.52 (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 TRP 0.014 0.002 TRP B 624 HIS 0.004 0.001 HIS A 90 PHE 0.017 0.002 PHE B 598 TYR 0.030 0.002 TYR B 181 ARG 0.014 0.001 ARG B 630 *********************** 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 fitting. rotamer outliers: 0 poor density : 197 time to evaluate : 1.157 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: 0.2461 time to fit residues: 68.3779 Evaluate side-chains 155 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 155 time to evaluate : 1.246 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 1.9990 chunk 106 optimal weight: 0.7980 chunk 58 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 71 optimal weight: 0.8980 chunk 56 optimal weight: 0.8980 chunk 109 optimal weight: 0.0040 chunk 42 optimal weight: 0.7980 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 0.9990 chunk 127 optimal weight: 0.9980 overall best weight: 0.6592 ------------------------------------------------------------------------------- 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 701 ASN B 124 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 489 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.1329 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 11977 Z= 0.201 Angle : 0.698 7.847 16221 Z= 0.357 Chirality : 0.044 0.163 1793 Planarity : 0.006 0.069 2002 Dihedral : 14.551 150.362 1831 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 12.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.70 % Favored : 89.30 % Rotamer: Outliers : 1.51 % Allowed : 7.39 % Favored : 91.09 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.52 (0.24), residues: 1402 helix: 1.15 (0.19), residues: 826 sheet: -1.89 (1.05), residues: 24 loop : -2.75 (0.26), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.003 0.001 HIS B 232 PHE 0.032 0.002 PHE A 72 TYR 0.028 0.002 TYR B 181 ARG 0.016 0.001 ARG B 630 *********************** 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 202 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 184 time to evaluate : 1.264 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6554 (mmt) cc_final: 0.6342 (mmp) REVERT: A 263 GLN cc_start: 0.8681 (tm-30) cc_final: 0.8474 (pp30) REVERT: A 303 LYS cc_start: 0.9170 (tptm) cc_final: 0.8938 (tptp) REVERT: A 307 LYS cc_start: 0.8308 (tptp) cc_final: 0.7990 (tptp) REVERT: A 521 MET cc_start: 0.6785 (OUTLIER) cc_final: 0.6109 (mpp) REVERT: A 613 TYR cc_start: 0.6810 (m-80) cc_final: 0.6353 (m-80) REVERT: B 125 TRP cc_start: 0.7580 (t60) cc_final: 0.7278 (t-100) REVERT: B 165 MET cc_start: 0.8114 (mmp) cc_final: 0.7822 (mmt) REVERT: B 182 GLU cc_start: 0.7166 (tt0) cc_final: 0.6958 (tt0) REVERT: B 303 LYS cc_start: 0.9160 (tptm) cc_final: 0.8935 (tptp) REVERT: B 307 LYS cc_start: 0.8452 (tptp) cc_final: 0.8174 (tptp) REVERT: B 521 MET cc_start: 0.6834 (OUTLIER) cc_final: 0.6557 (mpp) REVERT: B 593 PHE cc_start: 0.6766 (m-10) cc_final: 0.6543 (m-80) REVERT: B 613 TYR cc_start: 0.6859 (m-80) cc_final: 0.6440 (m-80) outliers start: 18 outliers final: 6 residues processed: 189 average time/residue: 0.2153 time to fit residues: 59.6473 Evaluate side-chains 171 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 163 time to evaluate : 1.233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN 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 A residue 521 MET Chi-restraints excluded: chain B residue 94 ASP 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 70 optimal weight: 10.0000 chunk 39 optimal weight: 0.0070 chunk 105 optimal weight: 0.7980 chunk 86 optimal weight: 3.9990 chunk 35 optimal weight: 5.9990 chunk 127 optimal weight: 0.0870 chunk 137 optimal weight: 0.3980 chunk 113 optimal weight: 3.9990 chunk 126 optimal weight: 0.0980 chunk 43 optimal weight: 0.0270 chunk 102 optimal weight: 0.9980 overall best weight: 0.1234 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 574 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7359 moved from start: 0.1866 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 11977 Z= 0.165 Angle : 0.636 8.206 16221 Z= 0.324 Chirality : 0.042 0.162 1793 Planarity : 0.006 0.061 2002 Dihedral : 14.043 153.989 1831 Min Nonbonded Distance : 2.143 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.13 % Favored : 89.87 % Rotamer: Outliers : 2.02 % Allowed : 10.92 % Favored : 87.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.18 (0.24), residues: 1402 helix: 1.43 (0.19), residues: 844 sheet: -1.28 (1.11), residues: 22 loop : -2.77 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 624 HIS 0.002 0.000 HIS A 650 PHE 0.035 0.001 PHE B 72 TYR 0.020 0.001 TYR B 181 ARG 0.012 0.000 ARG A 630 *********************** 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 209 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 185 time to evaluate : 1.167 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6613 (mmt) cc_final: 0.6379 (mmp) REVERT: A 297 GLU cc_start: 0.6618 (OUTLIER) cc_final: 0.6183 (mp0) REVERT: A 303 LYS cc_start: 0.9155 (tptm) cc_final: 0.8918 (tptp) REVERT: A 307 LYS cc_start: 0.8373 (tptp) cc_final: 0.8054 (tptp) REVERT: A 589 MET cc_start: 0.7864 (mmm) cc_final: 0.7461 (mmm) REVERT: A 613 TYR cc_start: 0.6832 (m-80) cc_final: 0.6376 (m-80) REVERT: B 125 TRP cc_start: 0.7718 (t60) cc_final: 0.7227 (t-100) REVERT: B 165 MET cc_start: 0.8051 (mmp) cc_final: 0.7789 (mmp) REVERT: B 297 GLU cc_start: 0.7061 (OUTLIER) cc_final: 0.5568 (mp0) REVERT: B 300 LYS cc_start: 0.8857 (mtmm) cc_final: 0.8374 (mtmt) REVERT: B 303 LYS cc_start: 0.9167 (tptm) cc_final: 0.8942 (tptp) REVERT: B 307 LYS cc_start: 0.8453 (tptp) cc_final: 0.8192 (tptp) outliers start: 24 outliers final: 12 residues processed: 200 average time/residue: 0.2088 time to fit residues: 61.3591 Evaluate side-chains 182 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 168 time to evaluate : 1.153 ------------------------------------------------------------------------------- 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 297 GLU 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 A residue 549 VAL Chi-restraints excluded: chain B residue 94 ASP 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 517 ILE Chi-restraints excluded: chain B residue 549 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 125 optimal weight: 3.9990 chunk 95 optimal weight: 9.9990 chunk 66 optimal weight: 0.7980 chunk 14 optimal weight: 4.9990 chunk 60 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 127 optimal weight: 0.7980 chunk 135 optimal weight: 3.9990 chunk 121 optimal weight: 0.9980 chunk 36 optimal weight: 0.7980 chunk 112 optimal weight: 2.9990 overall best weight: 1.2782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7439 moved from start: 0.1865 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 11977 Z= 0.237 Angle : 0.658 7.889 16221 Z= 0.339 Chirality : 0.043 0.165 1793 Planarity : 0.006 0.057 2002 Dihedral : 13.667 165.096 1831 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 11.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.06 % Favored : 89.94 % Rotamer: Outliers : 2.61 % Allowed : 13.61 % Favored : 83.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.00 (0.24), residues: 1402 helix: 1.60 (0.19), residues: 828 sheet: -1.38 (1.12), residues: 24 loop : -2.61 (0.26), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 624 HIS 0.003 0.001 HIS B 628 PHE 0.030 0.001 PHE A 72 TYR 0.027 0.002 TYR B 181 ARG 0.012 0.000 ARG B 630 *********************** 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 208 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 31 poor density : 177 time to evaluate : 1.181 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6516 (mmt) cc_final: 0.6291 (mmp) REVERT: A 297 GLU cc_start: 0.6753 (OUTLIER) cc_final: 0.6243 (mp0) REVERT: A 303 LYS cc_start: 0.9144 (tptm) cc_final: 0.8897 (tptp) REVERT: A 307 LYS cc_start: 0.8386 (tptp) cc_final: 0.7947 (tptp) REVERT: A 521 MET cc_start: 0.6440 (OUTLIER) cc_final: 0.5618 (mpp) REVERT: A 589 MET cc_start: 0.8011 (mmm) cc_final: 0.7689 (mmm) REVERT: A 613 TYR cc_start: 0.7053 (m-80) cc_final: 0.6502 (m-80) REVERT: B 125 TRP cc_start: 0.7745 (t60) cc_final: 0.7271 (t-100) REVERT: B 297 GLU cc_start: 0.7046 (OUTLIER) cc_final: 0.6469 (mp0) REVERT: B 303 LYS cc_start: 0.9165 (tptm) cc_final: 0.8900 (tptp) REVERT: B 307 LYS cc_start: 0.8478 (tptp) cc_final: 0.8155 (tptp) outliers start: 31 outliers final: 19 residues processed: 191 average time/residue: 0.2067 time to fit residues: 58.3610 Evaluate side-chains 187 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 165 time to evaluate : 1.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 94 ASP 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 428 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 653 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 148 SER 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 521 MET Chi-restraints excluded: chain B residue 549 VAL Chi-restraints excluded: chain B residue 653 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 76 optimal weight: 4.9990 chunk 1 optimal weight: 0.9990 chunk 100 optimal weight: 1.9990 chunk 55 optimal weight: 0.4980 chunk 115 optimal weight: 1.9990 chunk 93 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 4.9990 chunk 121 optimal weight: 7.9990 chunk 34 optimal weight: 2.9990 chunk 45 optimal weight: 0.7980 overall best weight: 1.2586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 124 ASN ** A 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 615 GLN A 709 GLN ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 162 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.1979 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 11977 Z= 0.233 Angle : 0.656 8.067 16221 Z= 0.338 Chirality : 0.043 0.188 1793 Planarity : 0.005 0.056 2002 Dihedral : 13.405 174.174 1831 Min Nonbonded Distance : 2.222 Molprobity Statistics. All-atom Clashscore : 11.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 3.45 % Allowed : 14.71 % Favored : 81.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.24), residues: 1402 helix: 1.73 (0.19), residues: 818 sheet: -0.88 (1.17), residues: 22 loop : -2.53 (0.26), residues: 562 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 624 HIS 0.004 0.001 HIS B 628 PHE 0.031 0.001 PHE B 72 TYR 0.029 0.002 TYR B 181 ARG 0.012 0.000 ARG A 630 *********************** 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 211 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 170 time to evaluate : 1.245 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 70 MET cc_start: 0.6510 (mmt) cc_final: 0.6291 (mmp) REVERT: A 256 GLN cc_start: 0.9065 (mm-40) cc_final: 0.8737 (mm-40) REVERT: A 297 GLU cc_start: 0.6583 (OUTLIER) cc_final: 0.6113 (mp0) REVERT: A 303 LYS cc_start: 0.9147 (tptm) cc_final: 0.8903 (tptp) REVERT: A 307 LYS cc_start: 0.8412 (tptp) cc_final: 0.7982 (tptp) REVERT: A 521 MET cc_start: 0.6295 (OUTLIER) cc_final: 0.5457 (mpp) REVERT: A 613 TYR cc_start: 0.7066 (m-80) cc_final: 0.6516 (m-80) REVERT: B 125 TRP cc_start: 0.7648 (t60) cc_final: 0.7214 (t-100) REVERT: B 297 GLU cc_start: 0.7030 (OUTLIER) cc_final: 0.6485 (mp0) REVERT: B 307 LYS cc_start: 0.8517 (tptp) cc_final: 0.8185 (tptp) outliers start: 41 outliers final: 22 residues processed: 196 average time/residue: 0.2099 time to fit residues: 60.5645 Evaluate side-chains 189 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 164 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 94 ASP 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 A residue 653 LEU Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 482 ILE 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 121 optimal weight: 5.9990 chunk 26 optimal weight: 40.0000 chunk 79 optimal weight: 0.8980 chunk 33 optimal weight: 3.9990 chunk 135 optimal weight: 2.9990 chunk 112 optimal weight: 0.9980 chunk 62 optimal weight: 0.7980 chunk 11 optimal weight: 8.9990 chunk 44 optimal weight: 0.0970 chunk 71 optimal weight: 0.9980 chunk 130 optimal weight: 0.3980 overall best weight: 0.6378 ------------------------------------------------------------------------------- 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 709 GLN B 124 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11977 Z= 0.185 Angle : 0.652 9.437 16221 Z= 0.332 Chirality : 0.042 0.162 1793 Planarity : 0.005 0.056 2002 Dihedral : 13.156 178.824 1831 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 12.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.42 % Favored : 90.58 % Rotamer: Outliers : 2.52 % Allowed : 16.13 % Favored : 81.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.24), residues: 1402 helix: 1.74 (0.19), residues: 830 sheet: -0.85 (1.18), residues: 22 loop : -2.48 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 624 HIS 0.002 0.001 HIS B 628 PHE 0.030 0.001 PHE B 72 TYR 0.027 0.001 TYR A 181 ARG 0.012 0.000 ARG A 630 *********************** 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 203 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 173 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 GLU cc_start: 0.6594 (OUTLIER) cc_final: 0.6089 (mp0) REVERT: A 303 LYS cc_start: 0.9144 (tptm) cc_final: 0.8898 (tptp) REVERT: A 307 LYS cc_start: 0.8416 (tptp) cc_final: 0.8000 (tptp) REVERT: A 521 MET cc_start: 0.6291 (OUTLIER) cc_final: 0.5463 (mpp) REVERT: A 589 MET cc_start: 0.7988 (mmm) cc_final: 0.7704 (mmm) REVERT: A 613 TYR cc_start: 0.7027 (m-80) cc_final: 0.6477 (m-80) REVERT: B 124 ASN cc_start: 0.7977 (OUTLIER) cc_final: 0.7759 (t0) REVERT: B 125 TRP cc_start: 0.7635 (t60) cc_final: 0.7346 (t-100) REVERT: B 297 GLU cc_start: 0.6943 (OUTLIER) cc_final: 0.6224 (mp0) REVERT: B 303 LYS cc_start: 0.9030 (tptp) cc_final: 0.8759 (tptp) REVERT: B 307 LYS cc_start: 0.8521 (tptp) cc_final: 0.8236 (tptp) outliers start: 30 outliers final: 23 residues processed: 190 average time/residue: 0.2192 time to fit residues: 61.3043 Evaluate side-chains 194 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 167 time to evaluate : 1.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 88 ILE 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 231 ASP 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 A residue 709 GLN Chi-restraints excluded: chain B residue 94 ASP Chi-restraints excluded: chain B residue 124 ASN Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 482 ILE 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 15 optimal weight: 0.9990 chunk 77 optimal weight: 0.6980 chunk 98 optimal weight: 9.9990 chunk 76 optimal weight: 0.6980 chunk 114 optimal weight: 2.9990 chunk 75 optimal weight: 0.8980 chunk 134 optimal weight: 1.9990 chunk 84 optimal weight: 4.9990 chunk 82 optimal weight: 3.9990 chunk 62 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 162 HIS ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 11977 Z= 0.194 Angle : 0.657 9.428 16221 Z= 0.335 Chirality : 0.042 0.160 1793 Planarity : 0.005 0.056 2002 Dihedral : 12.986 175.156 1831 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 12.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.84 % Favored : 90.16 % Rotamer: Outliers : 2.94 % Allowed : 15.80 % Favored : 81.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1402 helix: 1.73 (0.19), residues: 830 sheet: -0.88 (1.16), residues: 22 loop : -2.45 (0.27), residues: 550 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 624 HIS 0.003 0.001 HIS B 628 PHE 0.031 0.001 PHE B 72 TYR 0.027 0.001 TYR A 181 ARG 0.012 0.000 ARG A 630 *********************** 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 206 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 171 time to evaluate : 1.299 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 GLU cc_start: 0.6576 (OUTLIER) cc_final: 0.6063 (mp0) REVERT: A 303 LYS cc_start: 0.9146 (tptm) cc_final: 0.8900 (tptp) REVERT: A 307 LYS cc_start: 0.8412 (tptp) cc_final: 0.7991 (tptp) REVERT: A 521 MET cc_start: 0.6375 (OUTLIER) cc_final: 0.5544 (mpp) REVERT: A 559 MET cc_start: 0.2711 (ptt) cc_final: 0.2203 (mpp) REVERT: A 613 TYR cc_start: 0.7106 (m-80) cc_final: 0.6540 (m-80) REVERT: B 125 TRP cc_start: 0.7798 (t60) cc_final: 0.7461 (t-100) REVERT: B 165 MET cc_start: 0.7884 (mmp) cc_final: 0.7550 (mmt) REVERT: B 297 GLU cc_start: 0.7090 (OUTLIER) cc_final: 0.6538 (mp0) REVERT: B 303 LYS cc_start: 0.9027 (tptp) cc_final: 0.8737 (mmmm) REVERT: B 307 LYS cc_start: 0.8526 (tptp) cc_final: 0.8274 (tptp) REVERT: B 603 ILE cc_start: 0.6669 (mm) cc_final: 0.6399 (mt) REVERT: B 613 TYR cc_start: 0.5529 (m-80) cc_final: 0.5230 (m-80) outliers start: 35 outliers final: 26 residues processed: 190 average time/residue: 0.2157 time to fit residues: 60.9615 Evaluate side-chains 197 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 168 time to evaluate : 1.294 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 43 TYR 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 231 ASP 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 612 VAL Chi-restraints excluded: chain B residue 44 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 482 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 53 optimal weight: 0.2980 chunk 80 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 26 optimal weight: 50.0000 chunk 85 optimal weight: 0.9980 chunk 91 optimal weight: 0.0170 chunk 66 optimal weight: 2.9990 chunk 12 optimal weight: 5.9990 chunk 106 optimal weight: 0.7980 chunk 122 optimal weight: 4.9990 chunk 129 optimal weight: 3.9990 overall best weight: 1.0220 ------------------------------------------------------------------------------- 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7416 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11977 Z= 0.213 Angle : 0.664 10.091 16221 Z= 0.338 Chirality : 0.043 0.166 1793 Planarity : 0.005 0.055 2002 Dihedral : 12.689 170.407 1831 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.70 % Favored : 90.30 % Rotamer: Outliers : 2.52 % Allowed : 16.81 % Favored : 80.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.07 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1402 helix: 1.62 (0.19), residues: 842 sheet: -0.90 (1.15), residues: 22 loop : -2.47 (0.27), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 624 HIS 0.003 0.001 HIS B 628 PHE 0.029 0.001 PHE B 72 TYR 0.029 0.001 TYR A 181 ARG 0.012 0.000 ARG A 630 *********************** 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 206 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 30 poor density : 176 time to evaluate : 1.212 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 297 GLU cc_start: 0.6561 (OUTLIER) cc_final: 0.6036 (mp0) REVERT: A 303 LYS cc_start: 0.9149 (tptm) cc_final: 0.8902 (tptp) REVERT: A 307 LYS cc_start: 0.8432 (tptp) cc_final: 0.8027 (tptp) REVERT: A 521 MET cc_start: 0.6356 (OUTLIER) cc_final: 0.5523 (mpp) REVERT: A 613 TYR cc_start: 0.7152 (m-80) cc_final: 0.6590 (m-80) REVERT: B 125 TRP cc_start: 0.7830 (t60) cc_final: 0.7488 (t-100) REVERT: B 297 GLU cc_start: 0.7118 (OUTLIER) cc_final: 0.6563 (mp0) REVERT: B 303 LYS cc_start: 0.9049 (tptp) cc_final: 0.8763 (mmmm) REVERT: B 307 LYS cc_start: 0.8554 (tptp) cc_final: 0.8311 (tptp) REVERT: B 603 ILE cc_start: 0.6669 (mm) cc_final: 0.6378 (mt) outliers start: 30 outliers final: 26 residues processed: 193 average time/residue: 0.2080 time to fit residues: 59.4137 Evaluate side-chains 199 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.203 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 88 ILE 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 231 ASP 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 B residue 44 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 482 ILE 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 117 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 129 optimal weight: 2.9990 chunk 75 optimal weight: 0.4980 chunk 54 optimal weight: 10.0000 chunk 98 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 113 optimal weight: 2.9990 chunk 118 optimal weight: 0.2980 chunk 82 optimal weight: 3.9990 chunk 132 optimal weight: 0.6980 overall best weight: 1.0582 ------------------------------------------------------------------------------- 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 124 ASN ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7419 moved from start: 0.2353 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11977 Z= 0.220 Angle : 0.680 9.998 16221 Z= 0.344 Chirality : 0.043 0.167 1793 Planarity : 0.005 0.055 2002 Dihedral : 12.445 166.882 1831 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.77 % Favored : 90.23 % Rotamer: Outliers : 2.77 % Allowed : 16.81 % Favored : 80.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.22 (0.24), residues: 1402 helix: 1.71 (0.19), residues: 830 sheet: -1.38 (1.22), residues: 20 loop : -2.40 (0.27), residues: 552 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 624 HIS 0.005 0.001 HIS A 650 PHE 0.028 0.001 PHE A 389 TYR 0.030 0.001 TYR A 181 ARG 0.012 0.000 ARG A 630 *********************** 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 206 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 173 time to evaluate : 1.323 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7350 (p0) cc_final: 0.6505 (m-40) REVERT: A 297 GLU cc_start: 0.6554 (OUTLIER) cc_final: 0.6039 (mp0) REVERT: A 303 LYS cc_start: 0.9146 (tptm) cc_final: 0.8897 (tptp) REVERT: A 307 LYS cc_start: 0.8455 (tptp) cc_final: 0.8039 (tptp) REVERT: A 521 MET cc_start: 0.6359 (OUTLIER) cc_final: 0.5532 (mpp) REVERT: A 559 MET cc_start: 0.2711 (ptt) cc_final: 0.2222 (mpp) REVERT: A 613 TYR cc_start: 0.7137 (m-80) cc_final: 0.6582 (m-80) REVERT: B 125 TRP cc_start: 0.7800 (t60) cc_final: 0.7489 (t-100) REVERT: B 297 GLU cc_start: 0.7097 (OUTLIER) cc_final: 0.6578 (mp0) REVERT: B 307 LYS cc_start: 0.8567 (tptp) cc_final: 0.8304 (tptp) REVERT: B 559 MET cc_start: 0.2636 (ptt) cc_final: 0.2326 (mpp) REVERT: B 613 TYR cc_start: 0.6374 (m-80) cc_final: 0.6084 (m-80) outliers start: 33 outliers final: 26 residues processed: 193 average time/residue: 0.2117 time to fit residues: 60.5005 Evaluate side-chains 199 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 170 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 231 ASP 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 44 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 482 ILE 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 81 optimal weight: 8.9990 chunk 63 optimal weight: 0.8980 chunk 92 optimal weight: 4.9990 chunk 139 optimal weight: 1.9990 chunk 128 optimal weight: 0.7980 chunk 111 optimal weight: 0.4980 chunk 11 optimal weight: 10.0000 chunk 85 optimal weight: 0.9980 chunk 68 optimal weight: 1.9990 chunk 88 optimal weight: 0.9980 chunk 118 optimal weight: 3.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7402 moved from start: 0.2451 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11977 Z= 0.204 Angle : 0.678 10.832 16221 Z= 0.344 Chirality : 0.043 0.178 1793 Planarity : 0.005 0.055 2002 Dihedral : 12.202 163.737 1831 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 13.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.34 % Favored : 90.66 % Rotamer: Outliers : 2.44 % Allowed : 17.56 % Favored : 80.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.24), residues: 1402 helix: 1.64 (0.19), residues: 842 sheet: -1.38 (1.22), residues: 20 loop : -2.42 (0.27), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 624 HIS 0.007 0.001 HIS A 650 PHE 0.030 0.001 PHE B 72 TYR 0.029 0.001 TYR A 181 ARG 0.012 0.000 ARG B 630 ********************** 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 202 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 173 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 127 ASN cc_start: 0.7368 (p0) cc_final: 0.6543 (m-40) REVERT: A 297 GLU cc_start: 0.6528 (OUTLIER) cc_final: 0.6029 (mp0) REVERT: A 303 LYS cc_start: 0.9147 (tptm) cc_final: 0.8898 (tptp) REVERT: A 307 LYS cc_start: 0.8468 (tptp) cc_final: 0.8044 (tptp) REVERT: A 521 MET cc_start: 0.6288 (OUTLIER) cc_final: 0.5475 (mpp) REVERT: A 613 TYR cc_start: 0.7148 (m-80) cc_final: 0.6578 (m-80) REVERT: B 125 TRP cc_start: 0.7814 (t60) cc_final: 0.7502 (t-100) REVERT: B 297 GLU cc_start: 0.7005 (OUTLIER) cc_final: 0.6507 (mp0) REVERT: B 303 LYS cc_start: 0.9004 (tptp) cc_final: 0.8792 (tptp) REVERT: B 307 LYS cc_start: 0.8586 (tptp) cc_final: 0.8301 (tptp) REVERT: B 559 MET cc_start: 0.2792 (ptt) cc_final: 0.2466 (mpp) outliers start: 29 outliers final: 26 residues processed: 189 average time/residue: 0.2254 time to fit residues: 63.1907 Evaluate side-chains 196 residues out of total 1224 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 29 poor density : 167 time to evaluate : 1.250 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 34 ASN Chi-restraints excluded: chain A residue 43 TYR Chi-restraints excluded: chain A residue 44 LEU Chi-restraints excluded: chain A residue 88 ILE Chi-restraints excluded: chain A residue 96 VAL Chi-restraints excluded: chain A residue 181 TYR Chi-restraints excluded: chain A residue 231 ASP 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 44 LEU Chi-restraints excluded: chain B residue 147 LEU Chi-restraints excluded: chain B residue 181 TYR Chi-restraints excluded: chain B residue 239 VAL Chi-restraints excluded: chain B residue 297 GLU Chi-restraints excluded: chain B residue 304 GLU Chi-restraints excluded: chain B residue 317 LYS Chi-restraints excluded: chain B residue 482 ILE 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 34 optimal weight: 0.7980 chunk 102 optimal weight: 2.9990 chunk 16 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 111 optimal weight: 1.9990 chunk 46 optimal weight: 3.9990 chunk 114 optimal weight: 2.9990 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 97 optimal weight: 20.0000 chunk 6 optimal weight: 5.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 574 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 124 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 257 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4164 r_free = 0.4164 target = 0.180228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.140198 restraints weight = 17963.802| |-----------------------------------------------------------------------------| r_work (start): 0.3682 rms_B_bonded: 2.49 r_work: 0.3577 rms_B_bonded: 3.14 restraints_weight: 0.5000 r_work (final): 0.3577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.2474 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 11977 Z= 0.216 Angle : 0.679 11.112 16221 Z= 0.345 Chirality : 0.043 0.188 1793 Planarity : 0.005 0.054 2002 Dihedral : 12.051 161.632 1831 Min Nonbonded Distance : 2.206 Molprobity Statistics. All-atom Clashscore : 13.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.49 % Favored : 90.51 % Rotamer: Outliers : 2.52 % Allowed : 17.82 % Favored : 79.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.24), residues: 1402 helix: 1.60 (0.19), residues: 844 sheet: -1.38 (1.22), residues: 20 loop : -2.40 (0.28), residues: 538 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 624 HIS 0.007 0.001 HIS A 650 PHE 0.029 0.001 PHE A 72 TYR 0.030 0.001 TYR A 181 ARG 0.011 0.000 ARG B 630 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2388.68 seconds wall clock time: 43 minutes 30.57 seconds (2610.57 seconds total)