Starting phenix.real_space_refine on Tue May 13 21:36:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfs_38308/05_2025/8xfs_38308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfs_38308/05_2025/8xfs_38308.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.2 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8xfs_38308/05_2025/8xfs_38308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfs_38308/05_2025/8xfs_38308.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfs_38308/05_2025/8xfs_38308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfs_38308/05_2025/8xfs_38308.cif" } resolution = 3.2 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= -0.000 sd= 0.019 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 80 5.16 5 C 7036 2.51 5 N 1857 2.21 5 O 2010 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 3 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 10983 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5722 Number of conformers: 1 Conformer: "" Number of residues, atoms: 736, 5722 Classifications: {'peptide': 736} Incomplete info: {'truncation_to_alanine': 5} Link IDs: {'PTRANS': 37, 'TRANS': 698} Chain breaks: 3 Unresolved non-hydrogen bonds: 18 Unresolved non-hydrogen angles: 20 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLU:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 7 Chain: "C" Number of atoms: 1408 Number of conformers: 1 Conformer: "" Number of residues, atoms: 185, 1408 Classifications: {'peptide': 185} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 11, 'TRANS': 173} Unresolved non-hydrogen bonds: 34 Unresolved non-hydrogen angles: 44 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 1, 'PHE:plan': 1, 'GLU:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 29 Chain: "F" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 106, 817 Classifications: {'peptide': 106} Link IDs: {'PTRANS': 3, 'TRANS': 102} Chain: "B" Number of atoms: 786 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 786 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 21 Unresolved non-hydrogen dihedrals: 13 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Chain: "E" Number of atoms: 1466 Number of conformers: 1 Conformer: "" Number of residues, atoms: 190, 1466 Classifications: {'peptide': 190} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 11, 'TRANS': 178} Unresolved non-hydrogen bonds: 20 Unresolved non-hydrogen angles: 24 Unresolved non-hydrogen dihedrals: 16 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 2} Unresolved non-hydrogen planarities: 18 Chain: "D" Number of atoms: 784 Number of conformers: 1 Conformer: "" Number of residues, atoms: 101, 784 Classifications: {'peptide': 101} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 4, 'TRANS': 96} Unresolved non-hydrogen bonds: 19 Unresolved non-hydrogen angles: 23 Unresolved non-hydrogen dihedrals: 15 Planarities with less than four sites: {'GLN:plan1': 1, 'GLU:plan': 1, 'ARG:plan': 1, 'ASP:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 8.64, per 1000 atoms: 0.79 Number of scatterers: 10983 At special positions: 0 Unit cell: (88.893, 116.739, 167.076, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 80 16.00 O 2010 8.00 N 1857 7.00 C 7036 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 339 " - pdb=" SG CYS A 364 " distance=2.04 Simple disulfide: pdb=" SG CYS A 470 " - pdb=" SG CYS A 522 " distance=2.03 Simple disulfide: pdb=" SG CYS A 471 " - pdb=" SG CYS A 532 " distance=2.03 Simple disulfide: pdb=" SG CYS F 447 " - pdb=" SG CYS F 520 " distance=2.03 Simple disulfide: pdb=" SG CYS B 55 " - pdb=" SG CYS B 74 " distance=2.02 Simple disulfide: pdb=" SG CYS B 78 " - pdb=" SG CYS B 93 " distance=2.03 Simple disulfide: pdb=" SG CYS B 96 " - pdb=" SG CYS B 104 " distance=2.03 Simple disulfide: pdb=" SG CYS B 101 " - pdb=" SG CYS B 110 " distance=2.03 Simple disulfide: pdb=" SG CYS B 113 " - pdb=" SG CYS B 124 " distance=2.03 Simple disulfide: pdb=" SG CYS B 128 " - pdb=" SG CYS B 141 " distance=2.03 Simple disulfide: pdb=" SG CYS D 55 " - pdb=" SG CYS D 74 " distance=2.03 Simple disulfide: pdb=" SG CYS D 78 " - pdb=" SG CYS D 93 " distance=2.03 Simple disulfide: pdb=" SG CYS D 96 " - pdb=" SG CYS D 104 " distance=2.03 Simple disulfide: pdb=" SG CYS D 128 " - pdb=" SG CYS D 141 " distance=2.03 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=0, symmetry=0 Time building additional restraints: 2.58 Conformation dependent library (CDL) restraints added in 1.3 seconds 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2650 Finding SS restraints... Secondary structure from input PDB file: 29 helices and 15 sheets defined 29.5% alpha, 17.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.26 Creating SS restraints... Processing helix chain 'A' and resid 121 through 126 removed outlier: 3.506A pdb=" N ARG A 126 " --> pdb=" O SER A 122 " (cutoff:3.500A) Processing helix chain 'A' and resid 169 through 174 Processing helix chain 'A' and resid 242 through 247 Processing helix chain 'A' and resid 381 through 386 removed outlier: 4.302A pdb=" N PHE A 385 " --> pdb=" O GLU A 382 " (cutoff:3.500A) Processing helix chain 'A' and resid 466 through 472 removed outlier: 3.840A pdb=" N CYS A 470 " --> pdb=" O TYR A 466 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N ALA A 472 " --> pdb=" O TYR A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 538 through 565 removed outlier: 3.622A pdb=" N ALA A 565 " --> pdb=" O LEU A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 571 through 601 Processing helix chain 'A' and resid 604 through 613 removed outlier: 4.059A pdb=" N PHE A 608 " --> pdb=" O ARG A 604 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N TRP A 611 " --> pdb=" O GLU A 607 " (cutoff:3.500A) removed outlier: 3.707A pdb=" N GLU A 613 " --> pdb=" O GLY A 609 " (cutoff:3.500A) Processing helix chain 'A' and resid 615 through 649 removed outlier: 4.084A pdb=" N LYS A 619 " --> pdb=" O GLY A 615 " (cutoff:3.500A) removed outlier: 3.642A pdb=" N ASP A 649 " --> pdb=" O LEU A 645 " (cutoff:3.500A) Processing helix chain 'A' and resid 658 through 683 Proline residue: A 680 - end of helix Processing helix chain 'A' and resid 706 through 732 Processing helix chain 'A' and resid 742 through 768 Proline residue: A 762 - end of helix removed outlier: 3.795A pdb=" N PHE A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 778 through 790 Processing helix chain 'A' and resid 791 through 805 Proline residue: A 798 - end of helix removed outlier: 3.592A pdb=" N ASN A 805 " --> pdb=" O TYR A 801 " (cutoff:3.500A) Processing helix chain 'A' and resid 805 through 821 Processing helix chain 'C' and resid 128 through 132 Processing helix chain 'C' and resid 138 through 150 Processing helix chain 'C' and resid 161 through 171 removed outlier: 3.540A pdb=" N ILE C 165 " --> pdb=" O ASN C 161 " (cutoff:3.500A) Processing helix chain 'C' and resid 184 through 198 Processing helix chain 'C' and resid 217 through 240 Processing helix chain 'F' and resid 486 through 489 Processing helix chain 'F' and resid 511 through 515 Processing helix chain 'F' and resid 533 through 537 removed outlier: 3.781A pdb=" N ILE F 536 " --> pdb=" O ASN F 533 " (cutoff:3.500A) removed outlier: 3.676A pdb=" N PHE F 537 " --> pdb=" O TRP F 534 " (cutoff:3.500A) No H-bonds generated for 'chain 'F' and resid 533 through 537' Processing helix chain 'E' and resid 102 through 106 removed outlier: 3.826A pdb=" N LEU E 106 " --> pdb=" O PRO E 103 " (cutoff:3.500A) Processing helix chain 'E' and resid 128 through 132 Processing helix chain 'E' and resid 138 through 150 Processing helix chain 'E' and resid 161 through 171 removed outlier: 4.282A pdb=" N ILE E 165 " --> pdb=" O ASN E 161 " (cutoff:3.500A) removed outlier: 3.831A pdb=" N ASP E 166 " --> pdb=" O PRO E 162 " (cutoff:3.500A) Processing helix chain 'E' and resid 185 through 198 Processing helix chain 'E' and resid 217 through 245 Processing sheet with id=AA1, first strand: chain 'A' and resid 41 through 42 removed outlier: 7.100A pdb=" N LEU A 134 " --> pdb=" O TRP A 159 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N THR A 183 " --> pdb=" O LEU A 158 " (cutoff:3.500A) removed outlier: 7.115A pdb=" N LEU A 253 " --> pdb=" O HIS A 278 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'A' and resid 191 through 192 removed outlier: 3.632A pdb=" N ILE A 192 " --> pdb=" O SER A 215 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'A' and resid 300 through 303 removed outlier: 3.516A pdb=" N LYS A 440 " --> pdb=" O LEU A 418 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'C' and resid 74 through 82 removed outlier: 4.411A pdb=" N LYS C 125 " --> pdb=" O MET C 101 " (cutoff:3.500A) removed outlier: 6.355A pdb=" N TRP C 120 " --> pdb=" O ALA C 153 " (cutoff:3.500A) removed outlier: 7.772A pdb=" N ILE C 155 " --> pdb=" O TRP C 120 " (cutoff:3.500A) removed outlier: 6.360A pdb=" N GLY C 122 " --> pdb=" O ILE C 155 " (cutoff:3.500A) removed outlier: 7.275A pdb=" N ASP C 157 " --> pdb=" O GLY C 122 " (cutoff:3.500A) removed outlier: 7.188A pdb=" N VAL C 124 " --> pdb=" O ASP C 157 " (cutoff:3.500A) removed outlier: 8.676A pdb=" N VAL C 181 " --> pdb=" O THR C 152 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N VAL C 154 " --> pdb=" O VAL C 181 " (cutoff:3.500A) removed outlier: 7.661A pdb=" N VAL C 183 " --> pdb=" O VAL C 154 " (cutoff:3.500A) removed outlier: 6.522A pdb=" N PHE C 156 " --> pdb=" O VAL C 183 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'F' and resid 443 through 448 Processing sheet with id=AA7, first strand: chain 'F' and resid 483 through 484 removed outlier: 6.908A pdb=" N TRP F 461 " --> pdb=" O VAL F 473 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR F 475 " --> pdb=" O MET F 459 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET F 459 " --> pdb=" O THR F 475 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N CYS F 458 " --> pdb=" O ARG F 523 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG F 523 " --> pdb=" O CYS F 458 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'F' and resid 483 through 484 removed outlier: 6.908A pdb=" N TRP F 461 " --> pdb=" O VAL F 473 " (cutoff:3.500A) removed outlier: 4.827A pdb=" N THR F 475 " --> pdb=" O MET F 459 " (cutoff:3.500A) removed outlier: 6.937A pdb=" N MET F 459 " --> pdb=" O THR F 475 " (cutoff:3.500A) removed outlier: 4.868A pdb=" N CYS F 458 " --> pdb=" O ARG F 523 " (cutoff:3.500A) removed outlier: 3.991A pdb=" N ARG F 523 " --> pdb=" O CYS F 458 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 60 through 66 Processing sheet with id=AB1, first strand: chain 'B' and resid 82 through 85 Processing sheet with id=AB2, first strand: chain 'B' and resid 101 through 106 removed outlier: 4.811A pdb=" N ASP B 102 " --> pdb=" O CYS B 113 " (cutoff:3.500A) removed outlier: 7.558A pdb=" N CYS B 113 " --> pdb=" O ASP B 102 " (cutoff:3.500A) removed outlier: 7.487A pdb=" N CYS B 104 " --> pdb=" O THR B 111 " (cutoff:3.500A) removed outlier: 5.911A pdb=" N THR B 111 " --> pdb=" O CYS B 104 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N PHE B 109 " --> pdb=" O SER B 106 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'B' and resid 118 through 119 Processing sheet with id=AB4, first strand: chain 'E' and resid 58 through 69 removed outlier: 3.813A pdb=" N ASP E 73 " --> pdb=" O SER E 69 " (cutoff:3.500A) removed outlier: 8.563A pdb=" N VAL E 181 " --> pdb=" O THR E 152 " (cutoff:3.500A) removed outlier: 5.910A pdb=" N VAL E 154 " --> pdb=" O VAL E 181 " (cutoff:3.500A) removed outlier: 7.227A pdb=" N VAL E 183 " --> pdb=" O VAL E 154 " (cutoff:3.500A) removed outlier: 5.639A pdb=" N PHE E 156 " --> pdb=" O VAL E 183 " (cutoff:3.500A) removed outlier: 6.780A pdb=" N TRP E 120 " --> pdb=" O ALA E 153 " (cutoff:3.500A) removed outlier: 8.042A pdb=" N ILE E 155 " --> pdb=" O TRP E 120 " (cutoff:3.500A) removed outlier: 6.420A pdb=" N GLY E 122 " --> pdb=" O ILE E 155 " (cutoff:3.500A) removed outlier: 7.571A pdb=" N ASP E 157 " --> pdb=" O GLY E 122 " (cutoff:3.500A) removed outlier: 7.307A pdb=" N VAL E 124 " --> pdb=" O ASP E 157 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'D' and resid 60 through 66 Processing sheet with id=AB6, first strand: chain 'D' and resid 82 through 86 435 hydrogen bonds defined for protein. 1200 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: 3.76 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 3552 1.34 - 1.46: 2545 1.46 - 1.58: 5029 1.58 - 1.70: 0 1.70 - 1.82: 103 Bond restraints: 11229 Sorted by residual: bond pdb=" CA VAL C 158 " pdb=" CB VAL C 158 " ideal model delta sigma weight residual 1.540 1.524 0.016 1.36e-02 5.41e+03 1.45e+00 bond pdb=" C THR A 523 " pdb=" N PRO A 524 " ideal model delta sigma weight residual 1.334 1.361 -0.027 2.34e-02 1.83e+03 1.30e+00 bond pdb=" CB PRO C 210 " pdb=" CG PRO C 210 " ideal model delta sigma weight residual 1.492 1.534 -0.042 5.00e-02 4.00e+02 7.15e-01 bond pdb=" CA THR A 698 " pdb=" CB THR A 698 " ideal model delta sigma weight residual 1.530 1.543 -0.013 1.69e-02 3.50e+03 6.11e-01 bond pdb=" C ARG C 211 " pdb=" N GLN C 212 " ideal model delta sigma weight residual 1.331 1.347 -0.016 2.07e-02 2.33e+03 6.03e-01 ... (remaining 11224 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.97: 15056 1.97 - 3.95: 145 3.95 - 5.92: 21 5.92 - 7.90: 4 7.90 - 9.87: 1 Bond angle restraints: 15227 Sorted by residual: angle pdb=" C ARG C 211 " pdb=" N GLN C 212 " pdb=" CA GLN C 212 " ideal model delta sigma weight residual 121.80 131.67 -9.87 2.44e+00 1.68e-01 1.64e+01 angle pdb=" CA GLY E 96 " pdb=" C GLY E 96 " pdb=" N GLU E 97 " ideal model delta sigma weight residual 114.48 117.07 -2.59 1.19e+00 7.06e-01 4.75e+00 angle pdb=" N GLY E 96 " pdb=" CA GLY E 96 " pdb=" C GLY E 96 " ideal model delta sigma weight residual 110.63 113.72 -3.09 1.45e+00 4.76e-01 4.54e+00 angle pdb=" CA LEU A 279 " pdb=" CB LEU A 279 " pdb=" CG LEU A 279 " ideal model delta sigma weight residual 116.30 123.74 -7.44 3.50e+00 8.16e-02 4.51e+00 angle pdb=" CA LEU A 101 " pdb=" CB LEU A 101 " pdb=" CG LEU A 101 " ideal model delta sigma weight residual 116.30 123.70 -7.40 3.50e+00 8.16e-02 4.47e+00 ... (remaining 15222 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.18: 6390 17.18 - 34.35: 286 34.35 - 51.52: 63 51.52 - 68.70: 7 68.70 - 85.87: 2 Dihedral angle restraints: 6748 sinusoidal: 2649 harmonic: 4099 Sorted by residual: dihedral pdb=" CB CYS B 78 " pdb=" SG CYS B 78 " pdb=" SG CYS B 93 " pdb=" CB CYS B 93 " ideal model delta sinusoidal sigma weight residual 93.00 144.18 -51.18 1 1.00e+01 1.00e-02 3.58e+01 dihedral pdb=" CA ARG F 525 " pdb=" C ARG F 525 " pdb=" N ALA F 526 " pdb=" CA ALA F 526 " ideal model delta harmonic sigma weight residual 180.00 159.39 20.61 0 5.00e+00 4.00e-02 1.70e+01 dihedral pdb=" CA GLN C 212 " pdb=" C GLN C 212 " pdb=" N PRO C 213 " pdb=" CA PRO C 213 " ideal model delta harmonic sigma weight residual -180.00 -162.53 -17.47 0 5.00e+00 4.00e-02 1.22e+01 ... (remaining 6745 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.027: 1030 0.027 - 0.054: 417 0.054 - 0.081: 164 0.081 - 0.109: 93 0.109 - 0.136: 27 Chirality restraints: 1731 Sorted by residual: chirality pdb=" CA ILE A 334 " pdb=" N ILE A 334 " pdb=" C ILE A 334 " pdb=" CB ILE A 334 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.61e-01 chirality pdb=" CA THR A 698 " pdb=" N THR A 698 " pdb=" C THR A 698 " pdb=" CB THR A 698 " both_signs ideal model delta sigma weight residual False 2.53 2.39 0.13 2.00e-01 2.50e+01 4.38e-01 chirality pdb=" CA ILE A 277 " pdb=" N ILE A 277 " pdb=" C ILE A 277 " pdb=" CB ILE A 277 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.13 2.00e-01 2.50e+01 4.13e-01 ... (remaining 1728 not shown) Planarity restraints: 1954 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLN C 212 " 0.031 5.00e-02 4.00e+02 4.69e-02 3.52e+00 pdb=" N PRO C 213 " -0.081 5.00e-02 4.00e+02 pdb=" CA PRO C 213 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO C 213 " 0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ARG E 208 " -0.027 5.00e-02 4.00e+02 4.04e-02 2.61e+00 pdb=" N PRO E 209 " 0.070 5.00e-02 4.00e+02 pdb=" CA PRO E 209 " -0.021 5.00e-02 4.00e+02 pdb=" CD PRO E 209 " -0.022 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C THR A 523 " -0.020 5.00e-02 4.00e+02 2.94e-02 1.38e+00 pdb=" N PRO A 524 " 0.051 5.00e-02 4.00e+02 pdb=" CA PRO A 524 " -0.014 5.00e-02 4.00e+02 pdb=" CD PRO A 524 " -0.017 5.00e-02 4.00e+02 ... (remaining 1951 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 617 2.73 - 3.27: 11290 3.27 - 3.82: 17859 3.82 - 4.36: 20716 4.36 - 4.90: 36291 Nonbonded interactions: 86773 Sorted by model distance: nonbonded pdb=" OE1 GLN A 113 " pdb=" OG SER B 77 " model vdw 2.191 3.040 nonbonded pdb=" OG SER A 65 " pdb=" O ALA A 89 " model vdw 2.237 3.040 nonbonded pdb=" OD1 ASP A 161 " pdb=" OG1 THR A 183 " model vdw 2.246 3.040 nonbonded pdb=" N ASN A 91 " pdb=" OD1 ASN A 91 " model vdw 2.271 3.120 nonbonded pdb=" OG1 THR A 229 " pdb=" OD2 ASP B 108 " model vdw 2.308 3.040 ... (remaining 86768 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 'B' and (resid 41 through 42 or (resid 43 and (name N or name CA or name \ C or name O or name CB )) or resid 44 through 123 or (resid 124 and (name N or n \ ame CA or name C or name O or name CB )) or resid 125 through 141)) selection = chain 'D' } ncs_group { reference = (chain 'C' and (resid 56 through 207 or (resid 208 and (name N or name CA or nam \ e C or name O or name CB )) or resid 209 through 240)) selection = (chain 'E' and (resid 56 through 109 or (resid 110 and (name N or name CA or nam \ e C or name O or name CB )) or resid 111 through 213 or (resid 214 through 217 a \ nd (name N or name CA or name C or name O or name CB )) or resid 218 through 240 \ )) } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.010 Normalize map: mean=0, sd=1: 8.020 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: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.130 Process input model: 29.520 Find NCS groups from input model: 0.260 Set up NCS constraints: 0.060 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:2.900 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 41.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7758 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 : 0.002 0.042 11243 Z= 0.106 Angle : 0.516 9.869 15255 Z= 0.259 Chirality : 0.040 0.136 1731 Planarity : 0.003 0.047 1954 Dihedral : 10.305 85.875 4056 Min Nonbonded Distance : 2.191 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.07 % Allowed : 5.14 % Favored : 94.79 % Rotamer: Outliers : 2.74 % Allowed : 6.06 % Favored : 91.20 % 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 (0.23), residues: 1401 helix: 2.57 (0.27), residues: 359 sheet: -0.18 (0.32), residues: 276 loop : -0.93 (0.23), residues: 766 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 159 HIS 0.002 0.000 HIS A 209 PHE 0.013 0.001 PHE A 255 TYR 0.008 0.001 TYR C 182 ARG 0.001 0.000 ARG E 202 Details of bonding type rmsd hydrogen bonds : bond 0.06870 ( 424) hydrogen bonds : angle 4.12440 ( 1200) SS BOND : bond 0.00254 ( 14) SS BOND : angle 0.74315 ( 28) covalent geometry : bond 0.00228 (11229) covalent geometry : angle 0.51561 (15227) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 230 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 197 time to evaluate : 1.409 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ASP cc_start: 0.7264 (t70) cc_final: 0.6839 (t0) REVERT: A 529 PHE cc_start: 0.8585 (OUTLIER) cc_final: 0.7951 (t80) REVERT: C 132 ASP cc_start: 0.8194 (t0) cc_final: 0.7925 (t0) REVERT: C 219 MET cc_start: 0.5898 (ppp) cc_final: 0.5617 (ppp) REVERT: F 518 TYR cc_start: 0.7247 (m-80) cc_final: 0.6874 (m-80) REVERT: D 75 LEU cc_start: 0.7983 (OUTLIER) cc_final: 0.7571 (pt) outliers start: 33 outliers final: 15 residues processed: 225 average time/residue: 0.2434 time to fit residues: 76.7442 Evaluate side-chains 167 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 150 time to evaluate : 1.171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 67 ASN Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 183 THR Chi-restraints excluded: chain A residue 329 THR Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 236 LEU Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 135 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.9980 chunk 106 optimal weight: 2.9990 chunk 58 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 71 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 109 optimal weight: 3.9990 chunk 42 optimal weight: 2.9990 chunk 66 optimal weight: 0.8980 chunk 81 optimal weight: 0.1980 chunk 127 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN A 742 GLN C 108 ASN C 169 ASN C 206 GLN E 244 GLN D 56 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3828 r_free = 0.3828 target = 0.109831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077492 restraints weight = 24638.754| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.01 r_work: 0.3096 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 11243 Z= 0.140 Angle : 0.599 10.849 15255 Z= 0.294 Chirality : 0.042 0.261 1731 Planarity : 0.004 0.045 1954 Dihedral : 5.673 56.678 1540 Min Nonbonded Distance : 2.415 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.28 % Favored : 94.58 % Rotamer: Outliers : 2.82 % Allowed : 10.38 % Favored : 86.79 % 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: 0.20 (0.23), residues: 1401 helix: 2.42 (0.27), residues: 358 sheet: -0.02 (0.33), residues: 270 loop : -0.94 (0.23), residues: 773 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.004 0.001 HIS B 76 PHE 0.017 0.001 PHE A 718 TYR 0.037 0.001 TYR E 216 ARG 0.007 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03526 ( 424) hydrogen bonds : angle 4.17386 ( 1200) SS BOND : bond 0.00308 ( 14) SS BOND : angle 1.17525 ( 28) covalent geometry : bond 0.00325 (11229) covalent geometry : angle 0.59732 (15227) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 191 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 157 time to evaluate : 1.294 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8800 (OUTLIER) cc_final: 0.8543 (pp) REVERT: A 281 ASP cc_start: 0.9239 (t70) cc_final: 0.8549 (t0) REVERT: A 529 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8013 (t80) REVERT: A 812 TRP cc_start: 0.7288 (OUTLIER) cc_final: 0.6534 (t-100) REVERT: C 132 ASP cc_start: 0.8785 (t0) cc_final: 0.8352 (t0) REVERT: C 169 ASN cc_start: 0.9139 (m-40) cc_final: 0.8860 (m110) REVERT: C 208 ARG cc_start: 0.8109 (tmm-80) cc_final: 0.7662 (tpt170) REVERT: F 500 LYS cc_start: 0.7578 (pttm) cc_final: 0.7363 (pttm) REVERT: B 139 MET cc_start: 0.8569 (mmm) cc_final: 0.8198 (tpp) REVERT: E 192 MET cc_start: 0.8648 (mmm) cc_final: 0.8408 (mmm) REVERT: D 75 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7259 (pt) REVERT: D 90 MET cc_start: 0.8633 (ptp) cc_final: 0.8292 (pmm) REVERT: D 121 ARG cc_start: 0.8153 (ttp80) cc_final: 0.7888 (ttp80) REVERT: D 139 MET cc_start: 0.3533 (tpt) cc_final: 0.2978 (tpp) outliers start: 34 outliers final: 22 residues processed: 184 average time/residue: 0.2325 time to fit residues: 60.4924 Evaluate side-chains 175 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 149 time to evaluate : 1.177 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 101 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 135 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 32 optimal weight: 2.9990 chunk 138 optimal weight: 8.9990 chunk 1 optimal weight: 3.9990 chunk 66 optimal weight: 0.6980 chunk 129 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 18 optimal weight: 2.9990 chunk 97 optimal weight: 0.7980 chunk 92 optimal weight: 0.1980 chunk 99 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN A 584 ASN A 714 ASN A 797 ASN C 206 GLN E 169 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3798 r_free = 0.3798 target = 0.107815 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.075306 restraints weight = 25047.250| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 4.00 r_work: 0.3050 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3050 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1440 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 11243 Z= 0.213 Angle : 0.628 10.654 15255 Z= 0.313 Chirality : 0.044 0.157 1731 Planarity : 0.004 0.043 1954 Dihedral : 5.708 57.199 1532 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.14 % Favored : 93.72 % Rotamer: Outliers : 3.57 % Allowed : 10.96 % Favored : 85.47 % 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: 0.04 (0.23), residues: 1401 helix: 2.29 (0.27), residues: 354 sheet: -0.16 (0.33), residues: 272 loop : -1.02 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 159 HIS 0.004 0.001 HIS B 76 PHE 0.017 0.001 PHE A 255 TYR 0.033 0.001 TYR E 216 ARG 0.004 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03875 ( 424) hydrogen bonds : angle 4.31952 ( 1200) SS BOND : bond 0.00393 ( 14) SS BOND : angle 1.24811 ( 28) covalent geometry : bond 0.00499 (11229) covalent geometry : angle 0.62597 (15227) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 203 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 160 time to evaluate : 1.213 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 281 ASP cc_start: 0.9242 (t70) cc_final: 0.8551 (t0) REVERT: A 529 PHE cc_start: 0.8541 (OUTLIER) cc_final: 0.8044 (t80) REVERT: A 593 ILE cc_start: 0.7490 (OUTLIER) cc_final: 0.6922 (tp) REVERT: A 808 PHE cc_start: 0.7163 (m-80) cc_final: 0.6930 (m-80) REVERT: A 812 TRP cc_start: 0.7382 (OUTLIER) cc_final: 0.6631 (t-100) REVERT: C 117 GLU cc_start: 0.8364 (pm20) cc_final: 0.8133 (pm20) REVERT: C 132 ASP cc_start: 0.8820 (t0) cc_final: 0.8407 (t0) REVERT: C 169 ASN cc_start: 0.9229 (m-40) cc_final: 0.8948 (m110) REVERT: F 500 LYS cc_start: 0.7852 (pttm) cc_final: 0.7639 (pttm) REVERT: B 132 PHE cc_start: 0.8226 (m-80) cc_final: 0.7995 (m-80) REVERT: E 114 ASP cc_start: 0.7779 (m-30) cc_final: 0.6846 (t0) REVERT: E 192 MET cc_start: 0.8695 (mmm) cc_final: 0.8388 (mmm) REVERT: D 75 LEU cc_start: 0.7468 (OUTLIER) cc_final: 0.7217 (pt) REVERT: D 121 ARG cc_start: 0.8205 (ttp80) cc_final: 0.7925 (ttp80) REVERT: D 139 MET cc_start: 0.3724 (OUTLIER) cc_final: 0.3244 (tpp) outliers start: 43 outliers final: 29 residues processed: 192 average time/residue: 0.2478 time to fit residues: 68.9388 Evaluate side-chains 183 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 149 time to evaluate : 1.215 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 509 SER Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 134 optimal weight: 10.0000 chunk 118 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 3.9990 chunk 31 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 0.9980 chunk 56 optimal weight: 0.9990 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 108 ASN C 206 GLN E 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3809 r_free = 0.3809 target = 0.108582 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.076210 restraints weight = 24828.135| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.00 r_work: 0.3071 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7814 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11243 Z= 0.157 Angle : 0.613 11.676 15255 Z= 0.300 Chirality : 0.043 0.190 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.326 55.748 1528 Min Nonbonded Distance : 2.477 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.07 % Favored : 93.79 % Rotamer: Outliers : 3.24 % Allowed : 13.29 % Favored : 83.47 % 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: 0.05 (0.23), residues: 1401 helix: 2.28 (0.27), residues: 355 sheet: -0.13 (0.33), residues: 266 loop : -1.02 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS B 76 PHE 0.015 0.001 PHE A 255 TYR 0.027 0.001 TYR E 216 ARG 0.005 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03640 ( 424) hydrogen bonds : angle 4.29943 ( 1200) SS BOND : bond 0.00330 ( 14) SS BOND : angle 0.90840 ( 28) covalent geometry : bond 0.00368 (11229) covalent geometry : angle 0.61201 (15227) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 158 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 125 ILE cc_start: 0.9024 (OUTLIER) cc_final: 0.8766 (mp) REVERT: A 281 ASP cc_start: 0.9237 (t70) cc_final: 0.8526 (t0) REVERT: A 529 PHE cc_start: 0.8523 (OUTLIER) cc_final: 0.8009 (t80) REVERT: A 593 ILE cc_start: 0.7461 (OUTLIER) cc_final: 0.6892 (tp) REVERT: A 771 LEU cc_start: 0.8954 (tt) cc_final: 0.8427 (mp) REVERT: A 808 PHE cc_start: 0.7084 (m-80) cc_final: 0.6820 (m-80) REVERT: A 812 TRP cc_start: 0.7389 (OUTLIER) cc_final: 0.6647 (t-100) REVERT: C 117 GLU cc_start: 0.8346 (pm20) cc_final: 0.8086 (pm20) REVERT: C 132 ASP cc_start: 0.8814 (t0) cc_final: 0.8394 (t0) REVERT: C 169 ASN cc_start: 0.9292 (m-40) cc_final: 0.8975 (m110) REVERT: C 208 ARG cc_start: 0.8199 (tmm-80) cc_final: 0.7702 (tpt170) REVERT: F 468 LYS cc_start: 0.8562 (ptpp) cc_final: 0.8356 (ptpp) REVERT: F 500 LYS cc_start: 0.7837 (pttm) cc_final: 0.7593 (pttm) REVERT: B 132 PHE cc_start: 0.8175 (m-80) cc_final: 0.7903 (m-80) REVERT: B 139 MET cc_start: 0.8567 (mmm) cc_final: 0.8284 (tpp) REVERT: E 114 ASP cc_start: 0.7722 (m-30) cc_final: 0.6915 (t0) REVERT: E 192 MET cc_start: 0.8667 (mmm) cc_final: 0.8380 (mmm) REVERT: D 75 LEU cc_start: 0.7513 (OUTLIER) cc_final: 0.7249 (pt) REVERT: D 90 MET cc_start: 0.8657 (ptp) cc_final: 0.8399 (pmm) REVERT: D 99 GLU cc_start: 0.8663 (pm20) cc_final: 0.8269 (pm20) REVERT: D 139 MET cc_start: 0.3644 (OUTLIER) cc_final: 0.3221 (tpp) outliers start: 39 outliers final: 27 residues processed: 186 average time/residue: 0.2315 time to fit residues: 61.2609 Evaluate side-chains 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 33 poor density : 153 time to evaluate : 1.387 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 112 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 4.9990 chunk 127 optimal weight: 9.9990 chunk 89 optimal weight: 9.9990 chunk 99 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 116 optimal weight: 7.9990 chunk 67 optimal weight: 0.7980 chunk 109 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 108 ASN C 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.107999 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 72)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.075344 restraints weight = 24993.984| |-----------------------------------------------------------------------------| r_work (start): 0.3219 rms_B_bonded: 4.03 r_work: 0.3051 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3051 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7826 moved from start: 0.1718 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11243 Z= 0.184 Angle : 0.634 11.606 15255 Z= 0.311 Chirality : 0.044 0.405 1731 Planarity : 0.004 0.042 1954 Dihedral : 5.418 53.909 1528 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.42 % Favored : 93.43 % Rotamer: Outliers : 3.82 % Allowed : 13.29 % Favored : 82.89 % 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: -0.06 (0.23), residues: 1401 helix: 2.16 (0.28), residues: 355 sheet: -0.23 (0.33), residues: 268 loop : -1.05 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS B 76 PHE 0.016 0.001 PHE A 255 TYR 0.041 0.001 TYR E 216 ARG 0.005 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03829 ( 424) hydrogen bonds : angle 4.35186 ( 1200) SS BOND : bond 0.00408 ( 14) SS BOND : angle 1.55292 ( 28) covalent geometry : bond 0.00433 (11229) covalent geometry : angle 0.63113 (15227) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 46 poor density : 156 time to evaluate : 1.400 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ILE cc_start: 0.9005 (OUTLIER) cc_final: 0.8711 (mp) REVERT: A 281 ASP cc_start: 0.9239 (t70) cc_final: 0.8532 (t0) REVERT: A 529 PHE cc_start: 0.8540 (OUTLIER) cc_final: 0.8026 (t80) REVERT: A 593 ILE cc_start: 0.7488 (OUTLIER) cc_final: 0.6926 (tp) REVERT: A 771 LEU cc_start: 0.8980 (tt) cc_final: 0.8467 (mp) REVERT: A 812 TRP cc_start: 0.7349 (OUTLIER) cc_final: 0.6610 (t-100) REVERT: C 117 GLU cc_start: 0.8405 (pm20) cc_final: 0.8171 (pm20) REVERT: C 132 ASP cc_start: 0.8868 (t0) cc_final: 0.8470 (t0) REVERT: C 169 ASN cc_start: 0.9310 (m-40) cc_final: 0.8992 (m110) REVERT: C 208 ARG cc_start: 0.8196 (tmm-80) cc_final: 0.7671 (tpt170) REVERT: F 500 LYS cc_start: 0.7890 (pttm) cc_final: 0.7607 (pttm) REVERT: B 139 MET cc_start: 0.8640 (mmm) cc_final: 0.8350 (tpp) REVERT: E 114 ASP cc_start: 0.7807 (m-30) cc_final: 0.7025 (t0) REVERT: E 192 MET cc_start: 0.8684 (mmm) cc_final: 0.8394 (mmm) REVERT: D 75 LEU cc_start: 0.7493 (OUTLIER) cc_final: 0.7290 (pt) REVERT: D 90 MET cc_start: 0.8634 (ptp) cc_final: 0.8384 (pmm) REVERT: D 99 GLU cc_start: 0.8696 (pm20) cc_final: 0.8325 (pm20) REVERT: D 139 MET cc_start: 0.3636 (OUTLIER) cc_final: 0.3257 (tpp) outliers start: 46 outliers final: 35 residues processed: 188 average time/residue: 0.2308 time to fit residues: 62.0271 Evaluate side-chains 191 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 150 time to evaluate : 1.374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 509 SER Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 23 optimal weight: 2.9990 chunk 9 optimal weight: 0.8980 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 132 optimal weight: 3.9990 chunk 67 optimal weight: 1.9990 chunk 24 optimal weight: 0.4980 chunk 22 optimal weight: 1.9990 chunk 133 optimal weight: 3.9990 chunk 129 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 108 ASN C 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.108124 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075492 restraints weight = 25097.955| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 4.03 r_work: 0.3054 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3054 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7820 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 11243 Z= 0.175 Angle : 0.635 11.680 15255 Z= 0.310 Chirality : 0.044 0.338 1731 Planarity : 0.003 0.042 1954 Dihedral : 5.395 52.938 1528 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.14 % Favored : 93.72 % Rotamer: Outliers : 3.57 % Allowed : 14.62 % Favored : 81.81 % 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: -0.05 (0.23), residues: 1401 helix: 2.20 (0.28), residues: 355 sheet: -0.25 (0.33), residues: 268 loop : -1.04 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS B 76 PHE 0.021 0.001 PHE F 492 TYR 0.025 0.001 TYR E 216 ARG 0.006 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 424) hydrogen bonds : angle 4.36089 ( 1200) SS BOND : bond 0.00350 ( 14) SS BOND : angle 1.21695 ( 28) covalent geometry : bond 0.00410 (11229) covalent geometry : angle 0.63311 (15227) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 43 poor density : 154 time to evaluate : 1.182 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8914 (OUTLIER) cc_final: 0.8602 (m-40) REVERT: A 125 ILE cc_start: 0.9004 (OUTLIER) cc_final: 0.8722 (mp) REVERT: A 281 ASP cc_start: 0.9248 (t70) cc_final: 0.8544 (t0) REVERT: A 529 PHE cc_start: 0.8537 (OUTLIER) cc_final: 0.8035 (t80) REVERT: A 593 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.6910 (tp) REVERT: A 771 LEU cc_start: 0.8988 (tt) cc_final: 0.8451 (mp) REVERT: A 812 TRP cc_start: 0.7355 (OUTLIER) cc_final: 0.6647 (t-100) REVERT: C 117 GLU cc_start: 0.8496 (pm20) cc_final: 0.8223 (pm20) REVERT: C 132 ASP cc_start: 0.8861 (t0) cc_final: 0.8453 (t0) REVERT: C 169 ASN cc_start: 0.9304 (m-40) cc_final: 0.8976 (m110) REVERT: C 208 ARG cc_start: 0.8215 (tmm-80) cc_final: 0.7686 (tpt170) REVERT: F 500 LYS cc_start: 0.8008 (pttm) cc_final: 0.7788 (pttm) REVERT: B 139 MET cc_start: 0.8653 (mmm) cc_final: 0.8313 (tpp) REVERT: E 114 ASP cc_start: 0.7963 (m-30) cc_final: 0.7081 (t0) REVERT: E 192 MET cc_start: 0.8662 (mmm) cc_final: 0.8381 (mmm) REVERT: D 90 MET cc_start: 0.8605 (ptp) cc_final: 0.8387 (pmm) REVERT: D 99 GLU cc_start: 0.8688 (pm20) cc_final: 0.8352 (pm20) REVERT: D 123 ARG cc_start: 0.9047 (ttm110) cc_final: 0.8616 (mmp80) REVERT: D 139 MET cc_start: 0.3506 (OUTLIER) cc_final: 0.3122 (tpp) outliers start: 43 outliers final: 32 residues processed: 184 average time/residue: 0.2261 time to fit residues: 59.5905 Evaluate side-chains 189 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 151 time to evaluate : 1.357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 0.7980 chunk 41 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 113 optimal weight: 5.9990 chunk 25 optimal weight: 0.6980 chunk 121 optimal weight: 0.5980 chunk 24 optimal weight: 1.9990 chunk 52 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 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 714 ASN C 206 GLN F 506 GLN D 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3796 r_free = 0.3796 target = 0.107886 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075467 restraints weight = 25172.960| |-----------------------------------------------------------------------------| r_work (start): 0.3222 rms_B_bonded: 4.01 r_work: 0.3053 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3053 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7831 moved from start: 0.1838 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11243 Z= 0.174 Angle : 0.631 12.185 15255 Z= 0.310 Chirality : 0.043 0.279 1731 Planarity : 0.004 0.042 1954 Dihedral : 5.347 52.935 1524 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.35 % Favored : 93.50 % Rotamer: Outliers : 3.65 % Allowed : 14.70 % Favored : 81.64 % 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: -0.04 (0.23), residues: 1401 helix: 2.20 (0.28), residues: 355 sheet: -0.21 (0.33), residues: 266 loop : -1.05 (0.22), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS B 76 PHE 0.027 0.001 PHE F 492 TYR 0.042 0.001 TYR E 216 ARG 0.005 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03763 ( 424) hydrogen bonds : angle 4.34876 ( 1200) SS BOND : bond 0.00355 ( 14) SS BOND : angle 1.08191 ( 28) covalent geometry : bond 0.00409 (11229) covalent geometry : angle 0.63036 (15227) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 1.330 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8917 (OUTLIER) cc_final: 0.8604 (m-40) REVERT: A 92 ASP cc_start: 0.8615 (t70) cc_final: 0.8266 (t70) REVERT: A 125 ILE cc_start: 0.8995 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 281 ASP cc_start: 0.9242 (t70) cc_final: 0.8531 (t0) REVERT: A 529 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8052 (t80) REVERT: A 593 ILE cc_start: 0.7479 (OUTLIER) cc_final: 0.6916 (tp) REVERT: A 771 LEU cc_start: 0.8987 (tt) cc_final: 0.8446 (mp) REVERT: A 808 PHE cc_start: 0.7160 (m-10) cc_final: 0.6913 (m-80) REVERT: A 812 TRP cc_start: 0.7354 (OUTLIER) cc_final: 0.6643 (t-100) REVERT: C 87 ARG cc_start: 0.8673 (mtp-110) cc_final: 0.8131 (mtm110) REVERT: C 117 GLU cc_start: 0.8530 (pm20) cc_final: 0.8281 (pm20) REVERT: C 132 ASP cc_start: 0.8860 (t0) cc_final: 0.8448 (t0) REVERT: C 169 ASN cc_start: 0.9307 (m-40) cc_final: 0.8781 (m110) REVERT: C 208 ARG cc_start: 0.8211 (tmm-80) cc_final: 0.7692 (tpt170) REVERT: F 500 LYS cc_start: 0.8042 (pttm) cc_final: 0.7831 (pttm) REVERT: B 45 SER cc_start: 0.9127 (t) cc_final: 0.8820 (p) REVERT: E 114 ASP cc_start: 0.8063 (m-30) cc_final: 0.7172 (t0) REVERT: E 192 MET cc_start: 0.8677 (mmm) cc_final: 0.8397 (mmm) REVERT: D 90 MET cc_start: 0.8603 (ptp) cc_final: 0.8386 (pmm) REVERT: D 99 GLU cc_start: 0.8688 (pm20) cc_final: 0.8329 (pm20) REVERT: D 121 ARG cc_start: 0.8269 (ttp80) cc_final: 0.7980 (ttp80) REVERT: D 139 MET cc_start: 0.3282 (OUTLIER) cc_final: 0.2978 (tpp) outliers start: 44 outliers final: 33 residues processed: 184 average time/residue: 0.2573 time to fit residues: 68.5719 Evaluate side-chains 191 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 152 time to evaluate : 1.298 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 50 optimal weight: 0.9980 chunk 83 optimal weight: 2.9990 chunk 135 optimal weight: 9.9990 chunk 69 optimal weight: 0.8980 chunk 107 optimal weight: 0.5980 chunk 74 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 chunk 9 optimal weight: 0.8980 chunk 67 optimal weight: 0.2980 chunk 10 optimal weight: 0.8980 chunk 49 optimal weight: 0.6980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3886 r_free = 0.3886 target = 0.112364 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3408 r_free = 0.3408 target = 0.078509 restraints weight = 25999.473| |-----------------------------------------------------------------------------| r_work (start): 0.3341 rms_B_bonded: 3.78 r_work: 0.3224 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3224 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8028 moved from start: 0.1836 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 11243 Z= 0.131 Angle : 0.612 12.579 15255 Z= 0.299 Chirality : 0.042 0.265 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.167 52.630 1524 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 6.41 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 2.99 % Allowed : 15.03 % Favored : 81.98 % 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: 0.04 (0.23), residues: 1401 helix: 2.30 (0.28), residues: 355 sheet: -0.21 (0.33), residues: 268 loop : -1.00 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.002 0.000 HIS B 120 PHE 0.028 0.001 PHE F 492 TYR 0.034 0.001 TYR E 216 ARG 0.008 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03527 ( 424) hydrogen bonds : angle 4.31055 ( 1200) SS BOND : bond 0.00283 ( 14) SS BOND : angle 0.92280 ( 28) covalent geometry : bond 0.00306 (11229) covalent geometry : angle 0.61121 (15227) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 158 time to evaluate : 1.279 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8893 (OUTLIER) cc_final: 0.8643 (m-40) REVERT: A 92 ASP cc_start: 0.8516 (t70) cc_final: 0.8184 (t70) REVERT: A 125 ILE cc_start: 0.9061 (OUTLIER) cc_final: 0.8775 (mp) REVERT: A 281 ASP cc_start: 0.9145 (t70) cc_final: 0.8434 (t0) REVERT: A 529 PHE cc_start: 0.8724 (OUTLIER) cc_final: 0.8147 (t80) REVERT: A 593 ILE cc_start: 0.7625 (OUTLIER) cc_final: 0.7020 (tp) REVERT: A 771 LEU cc_start: 0.9012 (tt) cc_final: 0.8468 (mp) REVERT: A 808 PHE cc_start: 0.7048 (m-10) cc_final: 0.6819 (m-80) REVERT: A 812 TRP cc_start: 0.7498 (OUTLIER) cc_final: 0.6759 (t-100) REVERT: C 87 ARG cc_start: 0.8712 (mtp-110) cc_final: 0.8209 (mtm110) REVERT: C 132 ASP cc_start: 0.8889 (t0) cc_final: 0.8464 (t0) REVERT: C 169 ASN cc_start: 0.9280 (m-40) cc_final: 0.8800 (m110) REVERT: C 208 ARG cc_start: 0.8231 (tmm-80) cc_final: 0.7758 (tpt170) REVERT: F 500 LYS cc_start: 0.8129 (pttm) cc_final: 0.7918 (pttm) REVERT: B 45 SER cc_start: 0.9072 (t) cc_final: 0.8840 (p) REVERT: E 114 ASP cc_start: 0.8146 (m-30) cc_final: 0.7272 (t0) REVERT: E 192 MET cc_start: 0.8745 (mmm) cc_final: 0.8514 (mmm) REVERT: D 90 MET cc_start: 0.8625 (ptp) cc_final: 0.8414 (pmm) REVERT: D 99 GLU cc_start: 0.8735 (pm20) cc_final: 0.8398 (pm20) REVERT: D 121 ARG cc_start: 0.8263 (ttp80) cc_final: 0.7608 (ttp80) REVERT: D 123 ARG cc_start: 0.9011 (ttm110) cc_final: 0.8404 (ptt-90) REVERT: D 139 MET cc_start: 0.3566 (OUTLIER) cc_final: 0.3211 (tpp) outliers start: 36 outliers final: 28 residues processed: 185 average time/residue: 0.2425 time to fit residues: 64.0169 Evaluate side-chains 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 150 time to evaluate : 1.188 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 0.1980 chunk 108 optimal weight: 2.9990 chunk 115 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 10 optimal weight: 0.9990 chunk 136 optimal weight: 0.9990 chunk 35 optimal weight: 0.8980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 148 GLN C 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3814 r_free = 0.3814 target = 0.109096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3292 r_free = 0.3292 target = 0.076781 restraints weight = 25097.359| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.02 r_work: 0.3081 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3081 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 11243 Z= 0.138 Angle : 0.627 12.715 15255 Z= 0.305 Chirality : 0.042 0.235 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.148 52.719 1524 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 3.16 % Allowed : 15.20 % Favored : 81.64 % 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: 0.04 (0.23), residues: 1401 helix: 2.34 (0.28), residues: 354 sheet: -0.24 (0.33), residues: 270 loop : -1.00 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.003 0.000 HIS B 76 PHE 0.015 0.001 PHE A 255 TYR 0.033 0.001 TYR E 216 ARG 0.007 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03533 ( 424) hydrogen bonds : angle 4.29160 ( 1200) SS BOND : bond 0.00297 ( 14) SS BOND : angle 0.88706 ( 28) covalent geometry : bond 0.00324 (11229) covalent geometry : angle 0.62633 (15227) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 152 time to evaluate : 1.322 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8843 (mmm) cc_final: 0.8547 (mmm) REVERT: A 91 ASN cc_start: 0.8915 (OUTLIER) cc_final: 0.8630 (m-40) REVERT: A 92 ASP cc_start: 0.8611 (t70) cc_final: 0.8250 (t70) REVERT: A 125 ILE cc_start: 0.8992 (OUTLIER) cc_final: 0.8706 (mp) REVERT: A 281 ASP cc_start: 0.9252 (t70) cc_final: 0.8534 (t0) REVERT: A 529 PHE cc_start: 0.8527 (OUTLIER) cc_final: 0.8065 (t80) REVERT: A 593 ILE cc_start: 0.7340 (OUTLIER) cc_final: 0.6767 (tp) REVERT: A 771 LEU cc_start: 0.9008 (tt) cc_final: 0.8439 (mp) REVERT: A 808 PHE cc_start: 0.7058 (m-80) cc_final: 0.6807 (m-80) REVERT: A 812 TRP cc_start: 0.7354 (OUTLIER) cc_final: 0.6751 (t-100) REVERT: C 84 ARG cc_start: 0.7109 (mmm160) cc_final: 0.6639 (ttm-80) REVERT: C 87 ARG cc_start: 0.8677 (mtp-110) cc_final: 0.8148 (mtm110) REVERT: C 132 ASP cc_start: 0.8842 (t0) cc_final: 0.8412 (t0) REVERT: C 169 ASN cc_start: 0.9297 (m-40) cc_final: 0.8837 (m110) REVERT: C 208 ARG cc_start: 0.8199 (tmm-80) cc_final: 0.7700 (tpt170) REVERT: B 45 SER cc_start: 0.9199 (t) cc_final: 0.8891 (p) REVERT: E 114 ASP cc_start: 0.8050 (m-30) cc_final: 0.7150 (t0) REVERT: E 192 MET cc_start: 0.8644 (mmm) cc_final: 0.8365 (mmm) REVERT: D 90 MET cc_start: 0.8612 (ptp) cc_final: 0.8393 (pmm) REVERT: D 99 GLU cc_start: 0.8746 (pm20) cc_final: 0.8409 (pm20) REVERT: D 121 ARG cc_start: 0.8300 (ttp80) cc_final: 0.7631 (ttp80) REVERT: D 123 ARG cc_start: 0.9020 (ttm110) cc_final: 0.8395 (ptt-90) REVERT: D 139 MET cc_start: 0.3688 (OUTLIER) cc_final: 0.3287 (tpp) outliers start: 38 outliers final: 31 residues processed: 179 average time/residue: 0.2370 time to fit residues: 60.2497 Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 150 time to evaluate : 1.237 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 299 HIS Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.5980 chunk 123 optimal weight: 2.9990 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 0.7980 chunk 42 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.0970 chunk 110 optimal weight: 6.9990 chunk 135 optimal weight: 0.9990 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 2.9990 overall best weight: 0.6982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3815 r_free = 0.3815 target = 0.109134 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.076835 restraints weight = 24820.880| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 4.01 r_work: 0.3084 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3084 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.1929 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11243 Z= 0.139 Angle : 0.625 12.614 15255 Z= 0.305 Chirality : 0.042 0.224 1731 Planarity : 0.004 0.043 1954 Dihedral : 5.136 52.743 1524 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.09 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.07 % Favored : 93.79 % Rotamer: Outliers : 3.24 % Allowed : 15.20 % Favored : 81.56 % 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: 0.02 (0.23), residues: 1401 helix: 2.33 (0.28), residues: 354 sheet: -0.24 (0.33), residues: 270 loop : -1.02 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.003 0.001 HIS B 76 PHE 0.019 0.001 PHE C 225 TYR 0.044 0.001 TYR E 216 ARG 0.007 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03525 ( 424) hydrogen bonds : angle 4.28929 ( 1200) SS BOND : bond 0.00292 ( 14) SS BOND : angle 0.91737 ( 28) covalent geometry : bond 0.00327 (11229) covalent geometry : angle 0.62420 (15227) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 153 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 66 MET cc_start: 0.8885 (mmm) cc_final: 0.8609 (mmm) REVERT: A 91 ASN cc_start: 0.8902 (OUTLIER) cc_final: 0.8621 (m-40) REVERT: A 92 ASP cc_start: 0.8610 (t70) cc_final: 0.8250 (t70) REVERT: A 125 ILE cc_start: 0.8999 (OUTLIER) cc_final: 0.8713 (mp) REVERT: A 281 ASP cc_start: 0.9256 (t70) cc_final: 0.8538 (t0) REVERT: A 529 PHE cc_start: 0.8542 (OUTLIER) cc_final: 0.8064 (t80) REVERT: A 593 ILE cc_start: 0.7335 (OUTLIER) cc_final: 0.6763 (tp) REVERT: A 771 LEU cc_start: 0.8970 (tt) cc_final: 0.8415 (mp) REVERT: A 812 TRP cc_start: 0.7338 (OUTLIER) cc_final: 0.6729 (t-100) REVERT: C 84 ARG cc_start: 0.7122 (mmm160) cc_final: 0.6654 (ttm-80) REVERT: C 87 ARG cc_start: 0.8685 (mtp-110) cc_final: 0.8152 (mtm110) REVERT: C 132 ASP cc_start: 0.8842 (t0) cc_final: 0.8409 (t0) REVERT: C 169 ASN cc_start: 0.9318 (m-40) cc_final: 0.8876 (m110) REVERT: C 208 ARG cc_start: 0.8199 (tmm-80) cc_final: 0.7710 (tpt170) REVERT: B 45 SER cc_start: 0.9196 (t) cc_final: 0.8891 (p) REVERT: E 114 ASP cc_start: 0.8106 (m-30) cc_final: 0.7262 (t0) REVERT: E 192 MET cc_start: 0.8655 (mmm) cc_final: 0.8372 (mmm) REVERT: D 90 MET cc_start: 0.8600 (ptp) cc_final: 0.8381 (pmm) REVERT: D 99 GLU cc_start: 0.8766 (pm20) cc_final: 0.8423 (pm20) REVERT: D 121 ARG cc_start: 0.8319 (ttp80) cc_final: 0.7694 (ttp80) REVERT: D 123 ARG cc_start: 0.9023 (ttm110) cc_final: 0.8389 (ptt-90) REVERT: D 139 MET cc_start: 0.3718 (OUTLIER) cc_final: 0.3309 (tpp) outliers start: 39 outliers final: 30 residues processed: 182 average time/residue: 0.2330 time to fit residues: 60.4059 Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 151 time to evaluate : 1.201 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 540 MET Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 0.4980 chunk 34 optimal weight: 1.9990 chunk 86 optimal weight: 0.9980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 1.9990 chunk 135 optimal weight: 1.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.0060 chunk 118 optimal weight: 0.9990 chunk 19 optimal weight: 0.4980 chunk 107 optimal weight: 0.8980 overall best weight: 0.5596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 148 GLN C 206 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3824 r_free = 0.3824 target = 0.109727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077487 restraints weight = 24719.232| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 4.01 r_work: 0.3096 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3096 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7776 moved from start: 0.1956 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 11243 Z= 0.125 Angle : 0.614 12.581 15255 Z= 0.300 Chirality : 0.042 0.209 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.028 52.507 1524 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.64 % Favored : 94.22 % Rotamer: Outliers : 3.07 % Allowed : 15.53 % Favored : 81.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1401 helix: 2.38 (0.28), residues: 354 sheet: -0.27 (0.34), residues: 266 loop : -0.97 (0.23), residues: 781 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.003 0.000 HIS B 76 PHE 0.021 0.001 PHE A 765 TYR 0.044 0.001 TYR E 216 ARG 0.007 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03384 ( 424) hydrogen bonds : angle 4.25232 ( 1200) SS BOND : bond 0.00271 ( 14) SS BOND : angle 0.85317 ( 28) covalent geometry : bond 0.00291 (11229) covalent geometry : angle 0.61356 (15227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6684.80 seconds wall clock time: 116 minutes 24.10 seconds (6984.10 seconds total)