Starting phenix.real_space_refine on Tue Jul 29 04:49:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfs_38308/07_2025/8xfs_38308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfs_38308/07_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_38308/07_2025/8xfs_38308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfs_38308/07_2025/8xfs_38308.map" model { file = "/net/cci-nas-00/data/ceres_data/8xfs_38308/07_2025/8xfs_38308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfs_38308/07_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.79, per 1000 atoms: 0.80 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: 2.67 Conformation dependent library (CDL) restraints added in 1.6 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: 1.17 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: 3.66 Time building geometry restraints manager: 3.20 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: 0.000 Normalize map: mean=0, sd=1: 8.700 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: 0.090 Set scattering table: 0.120 Process input model: 30.060 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.020 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 42.740 ------------------------------------------------------------------------------- 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 : 1.453 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: 0.2863 time to fit residues: 91.5994 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 : 1.981 ------------------------------------------------------------------------------- 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 = 63)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077484 restraints weight = 24638.745| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.01 r_work: 0.3096 rms_B_bonded: 4.37 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 1.17527 ( 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 : 1.175 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8798 (OUTLIER) cc_final: 0.8542 (pp) REVERT: A 281 ASP cc_start: 0.9241 (t70) cc_final: 0.8551 (t0) REVERT: A 529 PHE cc_start: 0.8478 (OUTLIER) cc_final: 0.8012 (t80) REVERT: A 812 TRP cc_start: 0.7292 (OUTLIER) cc_final: 0.6534 (t-100) REVERT: C 132 ASP cc_start: 0.8787 (t0) cc_final: 0.8352 (t0) REVERT: C 169 ASN cc_start: 0.9139 (m-40) cc_final: 0.8861 (m110) REVERT: C 208 ARG cc_start: 0.8108 (tmm-80) cc_final: 0.7662 (tpt170) REVERT: F 500 LYS cc_start: 0.7576 (pttm) cc_final: 0.7362 (pttm) REVERT: B 139 MET cc_start: 0.8569 (mmm) cc_final: 0.8199 (tpp) REVERT: E 192 MET cc_start: 0.8648 (mmm) cc_final: 0.8407 (mmm) REVERT: D 75 LEU cc_start: 0.7498 (OUTLIER) cc_final: 0.7263 (pt) REVERT: D 90 MET cc_start: 0.8637 (ptp) cc_final: 0.8295 (pmm) REVERT: D 121 ARG cc_start: 0.8154 (ttp80) cc_final: 0.7888 (ttp80) REVERT: D 139 MET cc_start: 0.3531 (tpt) cc_final: 0.2977 (tpp) outliers start: 34 outliers final: 22 residues processed: 184 average time/residue: 0.2345 time to fit residues: 61.4034 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 : 1.324 ------------------------------------------------------------------------------- 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: 0.7980 chunk 129 optimal weight: 10.0000 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 97 optimal weight: 0.3980 chunk 92 optimal weight: 0.2980 chunk 99 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 584 ASN A 714 ASN A 797 ASN C 206 GLN E 169 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3829 r_free = 0.3829 target = 0.109844 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.077462 restraints weight = 24933.547| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 4.03 r_work: 0.3094 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3094 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1264 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11243 Z= 0.133 Angle : 0.579 11.160 15255 Z= 0.286 Chirality : 0.042 0.157 1731 Planarity : 0.003 0.044 1954 Dihedral : 5.406 56.886 1532 Min Nonbonded Distance : 2.488 Molprobity Statistics. All-atom Clashscore : 6.18 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.64 % Favored : 94.22 % Rotamer: Outliers : 2.99 % Allowed : 11.38 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1401 helix: 2.42 (0.27), residues: 355 sheet: 0.01 (0.33), residues: 268 loop : -0.96 (0.23), residues: 778 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 0.014 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 0.03412 ( 424) hydrogen bonds : angle 4.17387 ( 1200) SS BOND : bond 0.00310 ( 14) SS BOND : angle 1.08784 ( 28) covalent geometry : bond 0.00307 (11229) covalent geometry : angle 0.57811 (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 195 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 159 time to evaluate : 2.094 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8785 (OUTLIER) cc_final: 0.8475 (pp) REVERT: A 281 ASP cc_start: 0.9245 (t70) cc_final: 0.8531 (t0) REVERT: A 529 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8016 (t80) REVERT: A 593 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6726 (tp) REVERT: A 812 TRP cc_start: 0.7267 (OUTLIER) cc_final: 0.6534 (t-100) REVERT: C 97 GLU cc_start: 0.8546 (pt0) cc_final: 0.8309 (pt0) REVERT: C 117 GLU cc_start: 0.8209 (pm20) cc_final: 0.7999 (pt0) REVERT: C 132 ASP cc_start: 0.8803 (t0) cc_final: 0.8385 (t0) REVERT: C 169 ASN cc_start: 0.9232 (m-40) cc_final: 0.8992 (m110) REVERT: F 500 LYS cc_start: 0.7812 (pttm) cc_final: 0.7540 (pttm) REVERT: F 504 TYR cc_start: 0.8335 (m-80) cc_final: 0.8133 (m-80) REVERT: B 132 PHE cc_start: 0.8203 (m-80) cc_final: 0.7944 (m-80) REVERT: E 114 ASP cc_start: 0.7654 (m-30) cc_final: 0.6741 (t0) REVERT: E 157 ASP cc_start: 0.8308 (m-30) cc_final: 0.8094 (m-30) REVERT: D 75 LEU cc_start: 0.7464 (OUTLIER) cc_final: 0.7221 (pt) REVERT: D 90 MET cc_start: 0.8626 (ptp) cc_final: 0.8285 (pmm) REVERT: D 139 MET cc_start: 0.3782 (OUTLIER) cc_final: 0.3237 (tpp) outliers start: 36 outliers final: 23 residues processed: 185 average time/residue: 0.2967 time to fit residues: 80.5665 Evaluate side-chains 179 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 150 time to evaluate : 1.371 ------------------------------------------------------------------------------- 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 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 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 C residue 144 LYS 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 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 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: 0.0000 chunk 118 optimal weight: 0.3980 chunk 14 optimal weight: 1.9990 chunk 70 optimal weight: 0.6980 chunk 39 optimal weight: 2.9990 chunk 93 optimal weight: 0.9980 chunk 101 optimal weight: 4.9990 chunk 31 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 50 optimal weight: 0.7980 chunk 56 optimal weight: 0.9990 overall best weight: 0.5784 ------------------------------------------------------------------------------- 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 = 0.3833 r_free = 0.3833 target = 0.110162 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3313 r_free = 0.3313 target = 0.077864 restraints weight = 24770.136| |-----------------------------------------------------------------------------| r_work (start): 0.3270 rms_B_bonded: 4.01 r_work: 0.3103 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7782 moved from start: 0.1418 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11243 Z= 0.122 Angle : 0.584 11.342 15255 Z= 0.286 Chirality : 0.042 0.200 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.241 56.304 1530 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 2.91 % Allowed : 12.96 % Favored : 84.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.23), residues: 1401 helix: 2.41 (0.28), residues: 355 sheet: 0.04 (0.33), residues: 266 loop : -0.97 (0.23), residues: 780 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 0.016 0.001 PHE F 492 TYR 0.028 0.001 TYR E 216 ARG 0.005 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03365 ( 424) hydrogen bonds : angle 4.19112 ( 1200) SS BOND : bond 0.00285 ( 14) SS BOND : angle 0.79234 ( 28) covalent geometry : bond 0.00281 (11229) covalent geometry : angle 0.58355 (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 196 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 161 time to evaluate : 1.373 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8739 (OUTLIER) cc_final: 0.8430 (pp) REVERT: A 281 ASP cc_start: 0.9244 (t70) cc_final: 0.8520 (t0) REVERT: A 529 PHE cc_start: 0.8493 (OUTLIER) cc_final: 0.8015 (t80) REVERT: A 554 PHE cc_start: 0.6049 (t80) cc_final: 0.5829 (t80) REVERT: A 593 ILE cc_start: 0.7290 (OUTLIER) cc_final: 0.6711 (tp) REVERT: A 771 LEU cc_start: 0.9013 (tt) cc_final: 0.8508 (mp) REVERT: A 812 TRP cc_start: 0.7317 (OUTLIER) cc_final: 0.6555 (t-100) REVERT: C 128 GLN cc_start: 0.8215 (mp10) cc_final: 0.7949 (mm-40) REVERT: C 132 ASP cc_start: 0.8812 (t0) cc_final: 0.8378 (t0) REVERT: C 169 ASN cc_start: 0.9271 (m-40) cc_final: 0.8953 (m110) REVERT: F 500 LYS cc_start: 0.7832 (pttm) cc_final: 0.7489 (pttm) REVERT: F 504 TYR cc_start: 0.8335 (m-80) cc_final: 0.8075 (m-80) REVERT: B 132 PHE cc_start: 0.8189 (m-80) cc_final: 0.7922 (m-80) REVERT: B 139 MET cc_start: 0.8508 (mmm) cc_final: 0.8238 (tpp) REVERT: E 114 ASP cc_start: 0.7713 (m-30) cc_final: 0.6901 (t0) REVERT: E 148 GLN cc_start: 0.9041 (tt0) cc_final: 0.8633 (tt0) REVERT: D 75 LEU cc_start: 0.7459 (OUTLIER) cc_final: 0.7216 (pt) REVERT: D 90 MET cc_start: 0.8540 (ptp) cc_final: 0.8317 (pmm) REVERT: D 99 GLU cc_start: 0.8666 (pm20) cc_final: 0.8295 (pm20) REVERT: D 121 ARG cc_start: 0.8253 (ttp80) cc_final: 0.7976 (ttp80) outliers start: 35 outliers final: 26 residues processed: 187 average time/residue: 0.2357 time to fit residues: 62.8531 Evaluate side-chains 184 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 153 time to evaluate : 1.242 ------------------------------------------------------------------------------- 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 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 761 CYS 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 450 SER 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 520 CYS 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 Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 112 optimal weight: 3.9990 chunk 55 optimal weight: 1.9990 chunk 62 optimal weight: 5.9990 chunk 127 optimal weight: 0.8980 chunk 89 optimal weight: 10.0000 chunk 99 optimal weight: 4.9990 chunk 35 optimal weight: 0.3980 chunk 116 optimal weight: 8.9990 chunk 67 optimal weight: 0.6980 chunk 109 optimal weight: 0.2980 chunk 61 optimal weight: 0.8980 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 E 128 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3831 r_free = 0.3831 target = 0.110005 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3308 r_free = 0.3308 target = 0.077591 restraints weight = 24816.567| |-----------------------------------------------------------------------------| r_work (start): 0.3266 rms_B_bonded: 4.02 r_work: 0.3099 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3099 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7786 moved from start: 0.1533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11243 Z= 0.128 Angle : 0.592 11.601 15255 Z= 0.288 Chirality : 0.042 0.163 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.227 55.077 1530 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 6.27 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.78 % Favored : 94.08 % Rotamer: Outliers : 3.24 % Allowed : 12.96 % Favored : 83.80 % 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: 0.16 (0.23), residues: 1401 helix: 2.40 (0.28), residues: 355 sheet: 0.01 (0.33), residues: 268 loop : -0.98 (0.23), residues: 778 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 0.014 0.001 PHE C 222 TYR 0.041 0.001 TYR E 216 ARG 0.005 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03411 ( 424) hydrogen bonds : angle 4.17133 ( 1200) SS BOND : bond 0.00270 ( 14) SS BOND : angle 0.73992 ( 28) covalent geometry : bond 0.00295 (11229) covalent geometry : angle 0.59124 (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 195 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 156 time to evaluate : 1.219 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8740 (OUTLIER) cc_final: 0.8432 (pp) REVERT: A 281 ASP cc_start: 0.9253 (t70) cc_final: 0.8536 (t0) REVERT: A 529 PHE cc_start: 0.8491 (OUTLIER) cc_final: 0.8017 (t80) REVERT: A 554 PHE cc_start: 0.5909 (t80) cc_final: 0.5669 (t80) REVERT: A 593 ILE cc_start: 0.7306 (OUTLIER) cc_final: 0.6698 (tp) REVERT: A 771 LEU cc_start: 0.9033 (tt) cc_final: 0.8529 (mp) REVERT: A 812 TRP cc_start: 0.7240 (OUTLIER) cc_final: 0.6527 (t-100) REVERT: C 132 ASP cc_start: 0.8807 (t0) cc_final: 0.8358 (t0) REVERT: C 169 ASN cc_start: 0.9282 (m-40) cc_final: 0.8979 (m110) REVERT: F 500 LYS cc_start: 0.7823 (pttm) cc_final: 0.7460 (pttm) REVERT: F 504 TYR cc_start: 0.8290 (m-80) cc_final: 0.7988 (m-80) REVERT: B 139 MET cc_start: 0.8607 (mmm) cc_final: 0.8304 (tpp) REVERT: E 114 ASP cc_start: 0.7709 (m-30) cc_final: 0.6873 (t0) REVERT: E 148 GLN cc_start: 0.9051 (tt0) cc_final: 0.8612 (tt0) REVERT: E 192 MET cc_start: 0.8655 (mmm) cc_final: 0.8443 (mmm) REVERT: D 75 LEU cc_start: 0.7453 (OUTLIER) cc_final: 0.7247 (pt) REVERT: D 90 MET cc_start: 0.8563 (ptp) cc_final: 0.8336 (pmm) REVERT: D 99 GLU cc_start: 0.8753 (pm20) cc_final: 0.8370 (pm20) REVERT: D 121 ARG cc_start: 0.8257 (ttp80) cc_final: 0.7957 (ttp80) REVERT: D 139 MET cc_start: 0.4472 (tpp) cc_final: 0.4167 (tpp) outliers start: 39 outliers final: 27 residues processed: 187 average time/residue: 0.2616 time to fit residues: 69.3679 Evaluate side-chains 180 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 148 time to evaluate : 1.341 ------------------------------------------------------------------------------- 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 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 761 CYS 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 520 CYS Chi-restraints excluded: chain E residue 76 THR 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 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: 0.0570 chunk 59 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 132 optimal weight: 6.9990 chunk 67 optimal weight: 2.9990 chunk 24 optimal weight: 0.6980 chunk 22 optimal weight: 1.9990 chunk 133 optimal weight: 1.9990 chunk 129 optimal weight: 10.0000 chunk 43 optimal weight: 0.9980 overall best weight: 0.9502 ------------------------------------------------------------------------------- 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 D 120 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3783 r_free = 0.3783 target = 0.109057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3254 r_free = 0.3254 target = 0.077065 restraints weight = 24933.583| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 4.07 r_work: 0.3056 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3056 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7503 moved from start: 0.1683 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 11243 Z= 0.164 Angle : 0.612 12.044 15255 Z= 0.300 Chirality : 0.043 0.149 1731 Planarity : 0.003 0.042 1954 Dihedral : 5.373 54.613 1530 Min Nonbonded Distance : 2.509 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.78 % Favored : 94.08 % Rotamer: Outliers : 3.49 % Allowed : 13.12 % Favored : 83.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.09 (0.23), residues: 1401 helix: 2.33 (0.27), residues: 354 sheet: -0.08 (0.33), residues: 268 loop : -1.00 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.003 0.001 HIS A 658 PHE 0.017 0.001 PHE C 222 TYR 0.024 0.001 TYR E 216 ARG 0.006 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03603 ( 424) hydrogen bonds : angle 4.26283 ( 1200) SS BOND : bond 0.00331 ( 14) SS BOND : angle 0.83589 ( 28) covalent geometry : bond 0.00383 (11229) covalent geometry : angle 0.61190 (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 199 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 157 time to evaluate : 1.246 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 101 LEU cc_start: 0.8724 (OUTLIER) cc_final: 0.8465 (pp) REVERT: A 281 ASP cc_start: 0.9222 (t70) cc_final: 0.8498 (t0) REVERT: A 529 PHE cc_start: 0.8279 (OUTLIER) cc_final: 0.7836 (t80) REVERT: A 554 PHE cc_start: 0.5654 (t80) cc_final: 0.5441 (t80) REVERT: A 593 ILE cc_start: 0.7095 (OUTLIER) cc_final: 0.6601 (tp) REVERT: A 771 LEU cc_start: 0.9027 (tt) cc_final: 0.8496 (mp) REVERT: A 812 TRP cc_start: 0.7264 (OUTLIER) cc_final: 0.6613 (t-100) REVERT: C 132 ASP cc_start: 0.8769 (t0) cc_final: 0.8324 (t0) REVERT: C 169 ASN cc_start: 0.9259 (m-40) cc_final: 0.8949 (m110) REVERT: C 208 ARG cc_start: 0.8127 (tmm-80) cc_final: 0.7592 (tpt170) REVERT: F 500 LYS cc_start: 0.7897 (pttm) cc_final: 0.7597 (pttm) REVERT: F 504 TYR cc_start: 0.8112 (m-80) cc_final: 0.7890 (m-80) REVERT: B 45 SER cc_start: 0.9066 (t) cc_final: 0.8705 (p) REVERT: B 139 MET cc_start: 0.8476 (mmm) cc_final: 0.8163 (tpp) REVERT: E 114 ASP cc_start: 0.7630 (m-30) cc_final: 0.6853 (t0) REVERT: E 148 GLN cc_start: 0.8927 (tt0) cc_final: 0.8495 (tt0) REVERT: D 99 GLU cc_start: 0.8717 (pm20) cc_final: 0.8385 (pm20) REVERT: D 121 ARG cc_start: 0.8288 (ttp80) cc_final: 0.8026 (ttp80) REVERT: D 139 MET cc_start: 0.4509 (tpp) cc_final: 0.4224 (tpp) outliers start: 42 outliers final: 31 residues processed: 188 average time/residue: 0.2509 time to fit residues: 67.6151 Evaluate side-chains 189 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.320 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 55 LEU 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 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 761 CYS 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 487 SER 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 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 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 118 optimal weight: 2.9990 chunk 41 optimal weight: 0.8980 chunk 1 optimal weight: 0.0980 chunk 57 optimal weight: 6.9990 chunk 0 optimal weight: 0.9980 chunk 113 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 121 optimal weight: 0.6980 chunk 24 optimal weight: 0.7980 chunk 52 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 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 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3793 r_free = 0.3793 target = 0.109835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.078009 restraints weight = 25106.852| |-----------------------------------------------------------------------------| r_work (start): 0.3238 rms_B_bonded: 4.06 r_work: 0.3074 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7527 moved from start: 0.1753 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 11243 Z= 0.131 Angle : 0.609 12.376 15255 Z= 0.297 Chirality : 0.042 0.162 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.243 53.143 1528 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.64 % Favored : 94.22 % Rotamer: Outliers : 3.32 % Allowed : 13.62 % Favored : 83.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.08 (0.23), residues: 1401 helix: 2.33 (0.27), residues: 354 sheet: -0.09 (0.33), residues: 268 loop : -1.01 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.002 0.001 HIS B 76 PHE 0.020 0.001 PHE F 492 TYR 0.045 0.001 TYR E 216 ARG 0.006 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03458 ( 424) hydrogen bonds : angle 4.21440 ( 1200) SS BOND : bond 0.00290 ( 14) SS BOND : angle 1.44559 ( 28) covalent geometry : bond 0.00304 (11229) covalent geometry : angle 0.60599 (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 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 153 time to evaluate : 1.515 Fit side-chains REVERT: A 92 ASP cc_start: 0.8554 (t70) cc_final: 0.8215 (t70) REVERT: A 101 LEU cc_start: 0.8636 (OUTLIER) cc_final: 0.8332 (pp) REVERT: A 281 ASP cc_start: 0.9224 (t70) cc_final: 0.8498 (t0) REVERT: A 529 PHE cc_start: 0.8278 (OUTLIER) cc_final: 0.7847 (t80) REVERT: A 554 PHE cc_start: 0.5671 (t80) cc_final: 0.5461 (t80) REVERT: A 593 ILE cc_start: 0.6986 (OUTLIER) cc_final: 0.6480 (tp) REVERT: A 771 LEU cc_start: 0.9032 (tt) cc_final: 0.8510 (mp) REVERT: A 812 TRP cc_start: 0.7157 (OUTLIER) cc_final: 0.6591 (t-100) REVERT: C 87 ARG cc_start: 0.8621 (mtp-110) cc_final: 0.8336 (mtm110) REVERT: C 132 ASP cc_start: 0.8795 (t0) cc_final: 0.8360 (t0) REVERT: C 169 ASN cc_start: 0.9254 (m-40) cc_final: 0.8932 (m110) REVERT: C 208 ARG cc_start: 0.8133 (tmm-80) cc_final: 0.7610 (tpt170) REVERT: F 500 LYS cc_start: 0.7867 (pttm) cc_final: 0.7550 (pttm) REVERT: F 504 TYR cc_start: 0.8190 (m-80) cc_final: 0.7950 (m-80) REVERT: B 45 SER cc_start: 0.9162 (t) cc_final: 0.8822 (p) REVERT: B 139 MET cc_start: 0.8489 (mmm) cc_final: 0.8183 (tpp) REVERT: E 114 ASP cc_start: 0.7630 (m-30) cc_final: 0.6923 (t0) REVERT: E 148 GLN cc_start: 0.8967 (tt0) cc_final: 0.8526 (tt0) REVERT: D 90 MET cc_start: 0.8583 (ptp) cc_final: 0.8377 (pmm) REVERT: D 99 GLU cc_start: 0.8851 (pm20) cc_final: 0.8522 (pm20) REVERT: D 112 LYS cc_start: 0.8658 (mptt) cc_final: 0.8402 (mppt) REVERT: D 121 ARG cc_start: 0.8304 (ttp80) cc_final: 0.7765 (ttp80) REVERT: D 123 ARG cc_start: 0.9000 (ttm110) cc_final: 0.8422 (ptt-90) REVERT: D 139 MET cc_start: 0.4702 (tpp) cc_final: 0.4379 (tpp) outliers start: 40 outliers final: 34 residues processed: 183 average time/residue: 0.2411 time to fit residues: 63.3604 Evaluate side-chains 188 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 150 time to evaluate : 1.353 ------------------------------------------------------------------------------- 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 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 761 CYS 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 C residue 112 GLU Chi-restraints excluded: chain F residue 445 LEU Chi-restraints excluded: chain F residue 450 SER 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 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 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 50 optimal weight: 1.9990 chunk 83 optimal weight: 0.9980 chunk 135 optimal weight: 9.9990 chunk 69 optimal weight: 5.9990 chunk 107 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 11 optimal weight: 0.9980 chunk 9 optimal weight: 0.6980 chunk 67 optimal weight: 0.8980 chunk 10 optimal weight: 0.3980 chunk 49 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3790 r_free = 0.3790 target = 0.109575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.077818 restraints weight = 24841.159| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 4.02 r_work: 0.3071 rms_B_bonded: 4.36 restraints_weight: 0.5000 r_work (final): 0.3071 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7535 moved from start: 0.1804 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 11243 Z= 0.142 Angle : 0.619 12.571 15255 Z= 0.301 Chirality : 0.042 0.158 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.255 52.450 1528 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.64 % Favored : 94.22 % Rotamer: Outliers : 3.07 % Allowed : 14.20 % Favored : 82.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (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: 2.32 (0.27), residues: 354 sheet: -0.11 (0.33), residues: 268 loop : -1.02 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.002 0.001 HIS B 76 PHE 0.023 0.001 PHE C 222 TYR 0.007 0.001 TYR E 116 ARG 0.006 0.000 ARG D 123 Details of bonding type rmsd hydrogen bonds : bond 0.03483 ( 424) hydrogen bonds : angle 4.25272 ( 1200) SS BOND : bond 0.00301 ( 14) SS BOND : angle 1.22436 ( 28) covalent geometry : bond 0.00331 (11229) covalent geometry : angle 0.61685 (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 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 149 time to evaluate : 1.249 Fit side-chains revert: symmetry clash REVERT: A 92 ASP cc_start: 0.8587 (t70) cc_final: 0.8246 (t70) REVERT: A 101 LEU cc_start: 0.8656 (OUTLIER) cc_final: 0.8406 (pp) REVERT: A 281 ASP cc_start: 0.9222 (t70) cc_final: 0.8494 (t0) REVERT: A 529 PHE cc_start: 0.8298 (OUTLIER) cc_final: 0.7861 (t80) REVERT: A 554 PHE cc_start: 0.5706 (t80) cc_final: 0.5482 (t80) REVERT: A 593 ILE cc_start: 0.6994 (OUTLIER) cc_final: 0.6493 (tp) REVERT: A 771 LEU cc_start: 0.9031 (tt) cc_final: 0.8511 (mp) REVERT: A 812 TRP cc_start: 0.7189 (OUTLIER) cc_final: 0.6602 (t-100) REVERT: C 132 ASP cc_start: 0.8798 (t0) cc_final: 0.8358 (t0) REVERT: C 169 ASN cc_start: 0.9260 (m-40) cc_final: 0.8982 (m110) REVERT: C 208 ARG cc_start: 0.8128 (tmm-80) cc_final: 0.7594 (tpt170) REVERT: F 500 LYS cc_start: 0.8024 (pttm) cc_final: 0.7722 (pttm) REVERT: F 504 TYR cc_start: 0.8205 (m-80) cc_final: 0.7969 (m-80) REVERT: B 45 SER cc_start: 0.9159 (t) cc_final: 0.8819 (p) REVERT: B 139 MET cc_start: 0.8534 (mmm) cc_final: 0.8236 (tpp) REVERT: E 114 ASP cc_start: 0.7765 (m-30) cc_final: 0.6897 (t0) REVERT: E 148 GLN cc_start: 0.8977 (tt0) cc_final: 0.8541 (tt0) REVERT: D 90 MET cc_start: 0.8583 (ptp) cc_final: 0.8374 (pmm) REVERT: D 99 GLU cc_start: 0.8850 (pm20) cc_final: 0.8532 (pm20) REVERT: D 112 LYS cc_start: 0.8661 (mptt) cc_final: 0.8395 (mppt) REVERT: D 121 ARG cc_start: 0.8284 (ttp80) cc_final: 0.7756 (ttp80) REVERT: D 123 ARG cc_start: 0.9004 (ttm110) cc_final: 0.8449 (ptt-90) REVERT: D 139 MET cc_start: 0.5150 (tpp) cc_final: 0.4838 (tpp) outliers start: 37 outliers final: 30 residues processed: 177 average time/residue: 0.2294 time to fit residues: 58.0142 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 : 1.431 ------------------------------------------------------------------------------- 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 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 761 CYS 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 F residue 450 SER 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 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 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 79 optimal weight: 2.9990 chunk 26 optimal weight: 2.9990 chunk 105 optimal weight: 0.6980 chunk 61 optimal weight: 0.0570 chunk 108 optimal weight: 0.9990 chunk 115 optimal weight: 0.4980 chunk 20 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 136 optimal weight: 2.9990 chunk 35 optimal weight: 1.9990 overall best weight: 0.6300 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3795 r_free = 0.3795 target = 0.109968 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.078057 restraints weight = 25052.109| |-----------------------------------------------------------------------------| r_work (start): 0.3236 rms_B_bonded: 4.10 r_work: 0.3076 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3076 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.1826 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= 0.131 Angle : 0.621 12.601 15255 Z= 0.302 Chirality : 0.042 0.161 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.201 52.112 1528 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.78 % Favored : 94.08 % Rotamer: Outliers : 2.82 % Allowed : 14.53 % Favored : 82.64 % 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: 0.06 (0.23), residues: 1401 helix: 2.34 (0.28), residues: 354 sheet: -0.11 (0.33), residues: 268 loop : -1.03 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 159 HIS 0.002 0.000 HIS B 76 PHE 0.026 0.001 PHE C 222 TYR 0.010 0.001 TYR E 216 ARG 0.006 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03424 ( 424) hydrogen bonds : angle 4.24596 ( 1200) SS BOND : bond 0.00276 ( 14) SS BOND : angle 1.10780 ( 28) covalent geometry : bond 0.00305 (11229) covalent geometry : angle 0.61951 (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 185 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 151 time to evaluate : 1.217 Fit side-chains revert: symmetry clash REVERT: A 92 ASP cc_start: 0.8566 (t70) cc_final: 0.8197 (t70) REVERT: A 101 LEU cc_start: 0.8599 (OUTLIER) cc_final: 0.8291 (pp) REVERT: A 281 ASP cc_start: 0.9227 (t70) cc_final: 0.8502 (t0) REVERT: A 529 PHE cc_start: 0.8249 (OUTLIER) cc_final: 0.7823 (t80) REVERT: A 554 PHE cc_start: 0.5669 (t80) cc_final: 0.5444 (t80) REVERT: A 593 ILE cc_start: 0.6895 (OUTLIER) cc_final: 0.6378 (tp) REVERT: A 771 LEU cc_start: 0.9010 (tt) cc_final: 0.8461 (mp) REVERT: A 812 TRP cc_start: 0.7230 (OUTLIER) cc_final: 0.6699 (t-100) REVERT: C 132 ASP cc_start: 0.8781 (t0) cc_final: 0.8336 (t0) REVERT: C 169 ASN cc_start: 0.9316 (m-40) cc_final: 0.9072 (m110) REVERT: C 208 ARG cc_start: 0.8081 (tmm-80) cc_final: 0.7582 (tpt170) REVERT: F 500 LYS cc_start: 0.7980 (pttm) cc_final: 0.7777 (pttm) REVERT: B 45 SER cc_start: 0.9139 (t) cc_final: 0.8802 (p) REVERT: B 139 MET cc_start: 0.8542 (mmm) cc_final: 0.8249 (tpp) REVERT: E 114 ASP cc_start: 0.7868 (m-30) cc_final: 0.7001 (t0) REVERT: E 148 GLN cc_start: 0.8945 (tt0) cc_final: 0.8476 (tt0) REVERT: D 90 MET cc_start: 0.8597 (ptp) cc_final: 0.8391 (pmm) REVERT: D 99 GLU cc_start: 0.8903 (pm20) cc_final: 0.8568 (pm20) REVERT: D 112 LYS cc_start: 0.8681 (mptt) cc_final: 0.8418 (mppt) REVERT: D 121 ARG cc_start: 0.8309 (ttp80) cc_final: 0.7765 (ttp80) REVERT: D 123 ARG cc_start: 0.8990 (ttm110) cc_final: 0.8421 (ptt-90) REVERT: D 139 MET cc_start: 0.5079 (tpp) cc_final: 0.4780 (tpp) outliers start: 34 outliers final: 30 residues processed: 177 average time/residue: 0.2228 time to fit residues: 56.2102 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 : 1.195 ------------------------------------------------------------------------------- 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 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 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 761 CYS 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 487 SER 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 D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 117 optimal weight: 0.1980 chunk 123 optimal weight: 0.9980 chunk 30 optimal weight: 1.9990 chunk 65 optimal weight: 0.9990 chunk 42 optimal weight: 3.9990 chunk 90 optimal weight: 7.9990 chunk 97 optimal weight: 0.5980 chunk 110 optimal weight: 7.9990 chunk 135 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 154 GLN ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 ASN C 148 GLN C 206 GLN F 506 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3792 r_free = 0.3792 target = 0.109730 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.077613 restraints weight = 24949.232| |-----------------------------------------------------------------------------| r_work (start): 0.3226 rms_B_bonded: 4.09 r_work: 0.3062 rms_B_bonded: 4.42 restraints_weight: 0.5000 r_work (final): 0.3062 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7559 moved from start: 0.1889 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= 0.145 Angle : 0.631 13.047 15255 Z= 0.306 Chirality : 0.042 0.144 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.249 52.423 1528 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 2.91 % Allowed : 14.53 % Favored : 82.56 % 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: 2.29 (0.28), residues: 354 sheet: -0.16 (0.33), residues: 268 loop : -1.04 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.002 0.001 HIS B 76 PHE 0.029 0.001 PHE C 222 TYR 0.028 0.001 TYR E 216 ARG 0.007 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03496 ( 424) hydrogen bonds : angle 4.27029 ( 1200) SS BOND : bond 0.00305 ( 14) SS BOND : angle 1.21049 ( 28) covalent geometry : bond 0.00340 (11229) covalent geometry : angle 0.62897 (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 189 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 154 time to evaluate : 1.356 Fit side-chains revert: symmetry clash REVERT: A 92 ASP cc_start: 0.8678 (t70) cc_final: 0.8314 (t70) REVERT: A 101 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8432 (pp) REVERT: A 281 ASP cc_start: 0.9214 (t70) cc_final: 0.8487 (t0) REVERT: A 529 PHE cc_start: 0.8290 (OUTLIER) cc_final: 0.7858 (t80) REVERT: A 554 PHE cc_start: 0.5707 (t80) cc_final: 0.5484 (t80) REVERT: A 593 ILE cc_start: 0.6956 (OUTLIER) cc_final: 0.6450 (tp) REVERT: A 771 LEU cc_start: 0.8998 (tt) cc_final: 0.8451 (mp) REVERT: A 812 TRP cc_start: 0.7228 (OUTLIER) cc_final: 0.6673 (t-100) REVERT: C 132 ASP cc_start: 0.8759 (t0) cc_final: 0.8297 (t0) REVERT: C 169 ASN cc_start: 0.9331 (m-40) cc_final: 0.9089 (m110) REVERT: C 208 ARG cc_start: 0.8131 (tmm-80) cc_final: 0.7632 (tpt170) REVERT: F 500 LYS cc_start: 0.8101 (pttm) cc_final: 0.7877 (pttm) REVERT: B 45 SER cc_start: 0.9158 (t) cc_final: 0.8827 (p) REVERT: B 139 MET cc_start: 0.8589 (mmm) cc_final: 0.8315 (tpp) REVERT: E 114 ASP cc_start: 0.7944 (m-30) cc_final: 0.7069 (t0) REVERT: E 148 GLN cc_start: 0.8981 (tt0) cc_final: 0.8506 (tt0) REVERT: D 90 MET cc_start: 0.8585 (ptp) cc_final: 0.8350 (pmm) REVERT: D 99 GLU cc_start: 0.8887 (pm20) cc_final: 0.8557 (pm20) REVERT: D 121 ARG cc_start: 0.8274 (ttp80) cc_final: 0.7629 (ttp80) REVERT: D 123 ARG cc_start: 0.8999 (ttm110) cc_final: 0.8434 (ptt-90) REVERT: D 139 MET cc_start: 0.5183 (tpp) cc_final: 0.4875 (tpp) outliers start: 35 outliers final: 30 residues processed: 180 average time/residue: 0.2333 time to fit residues: 60.0790 Evaluate side-chains 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 34 poor density : 152 time to evaluate : 1.331 ------------------------------------------------------------------------------- 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 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 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 761 CYS 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 487 SER 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 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 Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 13 optimal weight: 0.9980 chunk 34 optimal weight: 0.7980 chunk 86 optimal weight: 0.6980 chunk 0 optimal weight: 10.0000 chunk 47 optimal weight: 0.9980 chunk 135 optimal weight: 7.9990 chunk 50 optimal weight: 0.8980 chunk 78 optimal weight: 0.7980 chunk 118 optimal weight: 3.9990 chunk 19 optimal weight: 0.5980 chunk 107 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 258 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** 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 = 0.3788 r_free = 0.3788 target = 0.109476 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.077648 restraints weight = 24726.057| |-----------------------------------------------------------------------------| r_work (start): 0.3228 rms_B_bonded: 4.05 r_work: 0.3063 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3063 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7561 moved from start: 0.1925 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 11243 Z= 0.144 Angle : 0.630 12.930 15255 Z= 0.306 Chirality : 0.042 0.158 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.242 52.519 1528 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 2.74 % Allowed : 14.70 % Favored : 82.56 % 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: 2.30 (0.28), residues: 354 sheet: -0.14 (0.33), residues: 268 loop : -1.05 (0.22), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 159 HIS 0.002 0.001 HIS B 76 PHE 0.029 0.001 PHE C 222 TYR 0.044 0.001 TYR E 216 ARG 0.007 0.000 ARG D 64 Details of bonding type rmsd hydrogen bonds : bond 0.03494 ( 424) hydrogen bonds : angle 4.25906 ( 1200) SS BOND : bond 0.00300 ( 14) SS BOND : angle 1.19799 ( 28) covalent geometry : bond 0.00338 (11229) covalent geometry : angle 0.62898 (15227) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6868.59 seconds wall clock time: 120 minutes 16.86 seconds (7216.86 seconds total)