Starting phenix.real_space_refine on Wed Sep 17 20:06:50 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8xfs_38308/09_2025/8xfs_38308.cif Found real_map, /net/cci-nas-00/data/ceres_data/8xfs_38308/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8xfs_38308/09_2025/8xfs_38308.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8xfs_38308/09_2025/8xfs_38308.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8xfs_38308/09_2025/8xfs_38308.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8xfs_38308/09_2025/8xfs_38308.map" } resolution = 3.2 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: {'ASP:plan': 1, 'GLU: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: {'ASN:plan1': 1, 'ARG:plan': 1, 'GLN:plan1': 1, 'GLU:plan': 1, 'TYR:plan': 1, 'PHE: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: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU: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: {'ARG:plan': 2, 'GLN:plan1': 1, 'GLU:plan': 1} 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: {'ARG:plan': 1, 'GLN:plan1': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 16 Time building chain proxies: 2.90, per 1000 atoms: 0.26 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: 1.02 Conformation dependent library (CDL) restraints added in 564.0 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.46 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: 1.87 Time building geometry restraints manager: 1.35 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: 12.050 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: 0.190 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 12.100 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.050 ------------------------------------------------------------------------------- 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.23 (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 ARG 0.001 0.000 ARG E 202 TYR 0.008 0.001 TYR C 182 PHE 0.013 0.001 PHE A 255 TRP 0.010 0.001 TRP A 159 HIS 0.002 0.000 HIS A 209 Details of bonding type rmsd covalent geometry : bond 0.00228 (11229) covalent geometry : angle 0.51561 (15227) SS BOND : bond 0.00254 ( 14) SS BOND : angle 0.74315 ( 28) hydrogen bonds : bond 0.06870 ( 424) hydrogen bonds : angle 4.12440 ( 1200) *********************** 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 : 0.500 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: 0.7950 (t80) REVERT: C 132 ASP cc_start: 0.8194 (t0) cc_final: 0.7925 (t0) REVERT: F 518 TYR cc_start: 0.7247 (m-80) cc_final: 0.6847 (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: 0.1176 time to fit residues: 37.1616 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 : 0.604 ------------------------------------------------------------------------------- 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 98 optimal weight: 2.9990 chunk 107 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 130 optimal weight: 7.9990 chunk 124 optimal weight: 0.8980 chunk 103 optimal weight: 0.8980 chunk 77 optimal weight: 4.9990 chunk 122 optimal weight: 4.9990 chunk 91 optimal weight: 7.9990 chunk 55 optimal weight: 0.7980 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 742 GLN A 797 ASN C 108 ASN C 169 ASN C 206 GLN F 501 ASN E 244 GLN D 56 GLN Total number of N/Q/H flips: 10 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3802 r_free = 0.3802 target = 0.108057 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3266 r_free = 0.3266 target = 0.075411 restraints weight = 25110.173| |-----------------------------------------------------------------------------| r_work (start): 0.3224 rms_B_bonded: 4.03 r_work: 0.3055 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7829 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 11243 Z= 0.215 Angle : 0.649 10.483 15255 Z= 0.320 Chirality : 0.044 0.295 1731 Planarity : 0.004 0.044 1954 Dihedral : 5.954 56.809 1540 Min Nonbonded Distance : 2.406 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 2.91 % Allowed : 10.22 % Favored : 86.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.23), residues: 1401 helix: 2.29 (0.27), residues: 357 sheet: -0.05 (0.33), residues: 266 loop : -1.02 (0.23), residues: 778 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG D 123 TYR 0.037 0.002 TYR E 216 PHE 0.018 0.001 PHE A 255 TRP 0.013 0.001 TRP A 159 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00506 (11229) covalent geometry : angle 0.64708 (15227) SS BOND : bond 0.00398 ( 14) SS BOND : angle 1.25711 ( 28) hydrogen bonds : bond 0.03945 ( 424) hydrogen bonds : angle 4.31270 ( 1200) *********************** 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 192 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 157 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 281 ASP cc_start: 0.9237 (t70) cc_final: 0.8545 (t0) REVERT: A 529 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8045 (t80) REVERT: A 593 ILE cc_start: 0.7464 (OUTLIER) cc_final: 0.6858 (tp) REVERT: A 812 TRP cc_start: 0.7345 (OUTLIER) cc_final: 0.6598 (t-100) REVERT: C 132 ASP cc_start: 0.8803 (t0) cc_final: 0.8379 (t0) REVERT: C 169 ASN cc_start: 0.9161 (m-40) cc_final: 0.8871 (m110) REVERT: C 219 MET cc_start: 0.6303 (ppp) cc_final: 0.6014 (ppp) REVERT: F 500 LYS cc_start: 0.7629 (pttm) cc_final: 0.7355 (pttm) REVERT: F 504 TYR cc_start: 0.8387 (m-80) cc_final: 0.8152 (m-80) REVERT: B 139 MET cc_start: 0.8572 (mmm) cc_final: 0.8198 (tpp) REVERT: E 101 MET cc_start: 0.8884 (mmm) cc_final: 0.8594 (mmm) REVERT: E 114 ASP cc_start: 0.7843 (m-30) cc_final: 0.7069 (t0) REVERT: E 192 MET cc_start: 0.8661 (mmm) cc_final: 0.8407 (mmm) REVERT: D 64 ARG cc_start: 0.7924 (ttm110) cc_final: 0.7704 (ttm110) REVERT: D 75 LEU cc_start: 0.7487 (OUTLIER) cc_final: 0.7266 (pt) REVERT: D 121 ARG cc_start: 0.8161 (ttp80) cc_final: 0.7880 (ttp80) REVERT: D 139 MET cc_start: 0.3810 (tpt) cc_final: 0.3281 (tpp) outliers start: 35 outliers final: 22 residues processed: 185 average time/residue: 0.1111 time to fit residues: 29.4264 Evaluate side-chains 176 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 150 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 108 ASN 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 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 136 optimal weight: 3.9990 chunk 82 optimal weight: 3.9990 chunk 58 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 125 optimal weight: 2.9990 chunk 105 optimal weight: 0.0370 chunk 30 optimal weight: 1.9990 chunk 90 optimal weight: 6.9990 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 39 optimal weight: 2.9990 overall best weight: 1.4064 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3790 r_free = 0.3790 target = 0.107254 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.074693 restraints weight = 25133.930| |-----------------------------------------------------------------------------| r_work (start): 0.3208 rms_B_bonded: 4.01 r_work: 0.3039 rms_B_bonded: 4.37 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11243 Z= 0.222 Angle : 0.641 10.693 15255 Z= 0.318 Chirality : 0.044 0.190 1731 Planarity : 0.004 0.044 1954 Dihedral : 5.669 56.501 1530 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 6.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.64 % Favored : 93.22 % Rotamer: Outliers : 3.65 % Allowed : 11.30 % Favored : 85.05 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.08 (0.23), residues: 1401 helix: 2.16 (0.27), residues: 355 sheet: -0.27 (0.33), residues: 272 loop : -1.07 (0.23), residues: 774 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG D 123 TYR 0.033 0.001 TYR E 216 PHE 0.017 0.001 PHE A 255 TRP 0.015 0.001 TRP A 159 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00522 (11229) covalent geometry : angle 0.63909 (15227) SS BOND : bond 0.00442 ( 14) SS BOND : angle 1.23569 ( 28) hydrogen bonds : bond 0.03973 ( 424) hydrogen bonds : angle 4.37255 ( 1200) *********************** 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 197 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 153 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 125 ILE cc_start: 0.8994 (OUTLIER) cc_final: 0.8685 (mp) REVERT: A 281 ASP cc_start: 0.9248 (t70) cc_final: 0.8549 (t0) REVERT: A 529 PHE cc_start: 0.8556 (OUTLIER) cc_final: 0.8079 (t80) REVERT: A 593 ILE cc_start: 0.7500 (OUTLIER) cc_final: 0.6929 (tp) REVERT: A 808 PHE cc_start: 0.7179 (m-80) cc_final: 0.6917 (m-80) REVERT: A 812 TRP cc_start: 0.7407 (OUTLIER) cc_final: 0.6653 (t-100) REVERT: C 132 ASP cc_start: 0.8829 (t0) cc_final: 0.8421 (t0) REVERT: C 169 ASN cc_start: 0.9245 (m-40) cc_final: 0.8965 (m110) REVERT: F 468 LYS cc_start: 0.8684 (ptpp) cc_final: 0.8474 (ptpp) REVERT: E 101 MET cc_start: 0.8956 (mmm) cc_final: 0.8560 (mmm) REVERT: E 114 ASP cc_start: 0.7879 (m-30) cc_final: 0.7085 (t0) REVERT: E 192 MET cc_start: 0.8683 (mmm) cc_final: 0.8366 (mmm) REVERT: D 75 LEU cc_start: 0.7590 (OUTLIER) cc_final: 0.7341 (pt) REVERT: D 139 MET cc_start: 0.3760 (OUTLIER) cc_final: 0.3296 (tpp) outliers start: 44 outliers final: 32 residues processed: 183 average time/residue: 0.1076 time to fit residues: 28.3338 Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 149 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 509 SER Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 135 LEU 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 7 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 43 optimal weight: 0.6980 chunk 136 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 chunk 108 optimal weight: 0.0670 chunk 124 optimal weight: 0.7980 chunk 133 optimal weight: 0.8980 chunk 82 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.5918 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 108 ASN C 206 GLN E 128 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3818 r_free = 0.3818 target = 0.109182 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076686 restraints weight = 25083.387| |-----------------------------------------------------------------------------| r_work (start): 0.3247 rms_B_bonded: 4.02 r_work: 0.3082 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7781 moved from start: 0.1526 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= 0.125 Angle : 0.599 11.444 15255 Z= 0.291 Chirality : 0.042 0.184 1731 Planarity : 0.003 0.044 1954 Dihedral : 5.382 54.846 1530 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 6.36 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.07 % Favored : 93.79 % Rotamer: Outliers : 3.41 % Allowed : 12.87 % Favored : 83.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.01 (0.23), residues: 1401 helix: 2.29 (0.28), residues: 355 sheet: -0.26 (0.33), residues: 270 loop : -1.02 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG D 64 TYR 0.026 0.001 TYR E 216 PHE 0.014 0.001 PHE A 255 TRP 0.012 0.001 TRP A 159 HIS 0.003 0.000 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00289 (11229) covalent geometry : angle 0.59661 (15227) SS BOND : bond 0.00315 ( 14) SS BOND : angle 1.38413 ( 28) hydrogen bonds : bond 0.03480 ( 424) hydrogen bonds : angle 4.25033 ( 1200) *********************** 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 202 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 161 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 125 ILE cc_start: 0.9049 (OUTLIER) cc_final: 0.8783 (mp) REVERT: A 281 ASP cc_start: 0.9249 (t70) cc_final: 0.8535 (t0) REVERT: A 529 PHE cc_start: 0.8500 (OUTLIER) cc_final: 0.8036 (t80) REVERT: A 593 ILE cc_start: 0.7368 (OUTLIER) cc_final: 0.6786 (tp) REVERT: A 771 LEU cc_start: 0.8942 (tt) cc_final: 0.8423 (mp) REVERT: A 812 TRP cc_start: 0.7388 (OUTLIER) cc_final: 0.6652 (t-100) REVERT: C 132 ASP cc_start: 0.8803 (t0) cc_final: 0.8383 (t0) REVERT: C 169 ASN cc_start: 0.9293 (m-40) cc_final: 0.8988 (m110) REVERT: C 208 ARG cc_start: 0.8176 (tmm-80) cc_final: 0.7651 (tpt170) REVERT: F 443 LEU cc_start: 0.8358 (pt) cc_final: 0.8124 (pt) REVERT: F 468 LYS cc_start: 0.8604 (ptpp) cc_final: 0.8319 (ptpp) REVERT: F 500 LYS cc_start: 0.7696 (OUTLIER) cc_final: 0.7424 (pttm) REVERT: B 139 MET cc_start: 0.8595 (mmm) cc_final: 0.8301 (tpp) REVERT: E 101 MET cc_start: 0.8973 (mmm) cc_final: 0.8552 (mmm) REVERT: E 114 ASP cc_start: 0.7769 (m-30) cc_final: 0.6792 (t0) REVERT: E 116 TYR cc_start: 0.8153 (m-80) cc_final: 0.7908 (m-80) REVERT: E 192 MET cc_start: 0.8665 (mmm) cc_final: 0.8381 (mmm) REVERT: D 75 LEU cc_start: 0.7434 (OUTLIER) cc_final: 0.7181 (pt) REVERT: D 121 ARG cc_start: 0.8225 (ttp80) cc_final: 0.7903 (ttp80) REVERT: D 139 MET cc_start: 0.3434 (OUTLIER) cc_final: 0.3062 (tpp) outliers start: 41 outliers final: 27 residues processed: 190 average time/residue: 0.1077 time to fit residues: 29.4553 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 : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 81 LEU 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 500 LYS 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 E residue 189 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 123 optimal weight: 1.9990 chunk 57 optimal weight: 6.9990 chunk 85 optimal weight: 2.9990 chunk 56 optimal weight: 0.8980 chunk 92 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 103 optimal weight: 1.9990 chunk 96 optimal weight: 0.6980 chunk 36 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 105 optimal weight: 1.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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 D 120 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3787 r_free = 0.3787 target = 0.107164 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3250 r_free = 0.3250 target = 0.074627 restraints weight = 25085.180| |-----------------------------------------------------------------------------| r_work (start): 0.3204 rms_B_bonded: 4.02 r_work: 0.3039 rms_B_bonded: 4.34 restraints_weight: 0.5000 r_work (final): 0.3039 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7828 moved from start: 0.1816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.040 11243 Z= 0.213 Angle : 0.651 11.455 15255 Z= 0.320 Chirality : 0.045 0.409 1731 Planarity : 0.004 0.042 1954 Dihedral : 5.659 53.187 1530 Min Nonbonded Distance : 2.499 Molprobity Statistics. All-atom Clashscore : 7.23 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.64 % Favored : 93.22 % Rotamer: Outliers : 4.24 % Allowed : 12.87 % Favored : 82.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.10 (0.23), residues: 1401 helix: 2.14 (0.28), residues: 354 sheet: -0.28 (0.34), residues: 263 loop : -1.07 (0.22), residues: 784 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 123 TYR 0.040 0.002 TYR E 216 PHE 0.021 0.001 PHE F 492 TRP 0.014 0.001 TRP A 159 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00501 (11229) covalent geometry : angle 0.64977 (15227) SS BOND : bond 0.00421 ( 14) SS BOND : angle 1.21723 ( 28) hydrogen bonds : bond 0.03970 ( 424) hydrogen bonds : angle 4.38694 ( 1200) *********************** 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 206 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 51 poor density : 155 time to evaluate : 0.451 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8937 (OUTLIER) cc_final: 0.8655 (m-40) REVERT: A 125 ILE cc_start: 0.9023 (OUTLIER) cc_final: 0.8731 (mp) REVERT: A 281 ASP cc_start: 0.9248 (t70) cc_final: 0.8541 (t0) REVERT: A 529 PHE cc_start: 0.8535 (OUTLIER) cc_final: 0.8082 (t80) REVERT: A 593 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 771 LEU cc_start: 0.8974 (tt) cc_final: 0.8466 (mp) REVERT: A 812 TRP cc_start: 0.7387 (OUTLIER) cc_final: 0.6628 (t-100) REVERT: C 117 GLU cc_start: 0.8389 (pm20) cc_final: 0.8079 (pm20) REVERT: C 132 ASP cc_start: 0.8819 (t0) cc_final: 0.8396 (t0) REVERT: C 169 ASN cc_start: 0.9316 (m-40) cc_final: 0.8999 (m110) REVERT: F 468 LYS cc_start: 0.8669 (ptpp) cc_final: 0.8338 (ptpp) REVERT: B 139 MET cc_start: 0.8625 (mmm) cc_final: 0.8309 (tpp) REVERT: E 101 MET cc_start: 0.8924 (mmm) cc_final: 0.8451 (mmm) REVERT: E 114 ASP cc_start: 0.7916 (m-30) cc_final: 0.7135 (t0) REVERT: E 148 GLN cc_start: 0.9066 (tt0) cc_final: 0.8710 (tt0) REVERT: E 192 MET cc_start: 0.8683 (mmm) cc_final: 0.8390 (mmm) REVERT: D 75 LEU cc_start: 0.7547 (OUTLIER) cc_final: 0.7328 (pt) REVERT: D 99 GLU cc_start: 0.8701 (pm20) cc_final: 0.8315 (pm20) REVERT: D 139 MET cc_start: 0.3253 (OUTLIER) cc_final: 0.2946 (tpp) outliers start: 51 outliers final: 38 residues processed: 190 average time/residue: 0.1108 time to fit residues: 30.1971 Evaluate side-chains 195 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 150 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 645 LEU Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 78 THR Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 108 ASN Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 450 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 500 LYS Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 75 LEU Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 125 PHE Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 124 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 55 optimal weight: 1.9990 chunk 97 optimal weight: 0.8980 chunk 98 optimal weight: 0.6980 chunk 113 optimal weight: 0.9980 chunk 53 optimal weight: 0.6980 chunk 63 optimal weight: 0.3980 chunk 78 optimal weight: 3.9990 chunk 93 optimal weight: 0.5980 chunk 14 optimal weight: 0.5980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3817 r_free = 0.3817 target = 0.109102 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.076749 restraints weight = 25047.235| |-----------------------------------------------------------------------------| r_work (start): 0.3244 rms_B_bonded: 4.03 r_work: 0.3078 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3078 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7789 moved from start: 0.1788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 11243 Z= 0.128 Angle : 0.613 12.045 15255 Z= 0.297 Chirality : 0.043 0.336 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.425 52.509 1530 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.00 % Favored : 93.86 % Rotamer: Outliers : 3.49 % Allowed : 14.37 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.00 (0.23), residues: 1401 helix: 2.26 (0.28), residues: 355 sheet: -0.26 (0.33), residues: 270 loop : -1.01 (0.23), residues: 776 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 123 TYR 0.025 0.001 TYR E 216 PHE 0.014 0.001 PHE A 255 TRP 0.012 0.001 TRP A 159 HIS 0.002 0.000 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00294 (11229) covalent geometry : angle 0.61239 (15227) SS BOND : bond 0.00278 ( 14) SS BOND : angle 0.89857 ( 28) hydrogen bonds : bond 0.03538 ( 424) hydrogen bonds : angle 4.27748 ( 1200) *********************** 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 201 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 42 poor density : 159 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8844 (OUTLIER) cc_final: 0.8532 (m-40) REVERT: A 92 ASP cc_start: 0.8507 (t70) cc_final: 0.8199 (t70) REVERT: A 125 ILE cc_start: 0.8997 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 281 ASP cc_start: 0.9246 (t70) cc_final: 0.8531 (t0) REVERT: A 529 PHE cc_start: 0.8519 (OUTLIER) cc_final: 0.8028 (t80) REVERT: A 593 ILE cc_start: 0.7413 (OUTLIER) cc_final: 0.6840 (tp) REVERT: A 771 LEU cc_start: 0.8977 (tt) cc_final: 0.8445 (mp) REVERT: A 808 PHE cc_start: 0.7114 (m-80) cc_final: 0.6859 (m-80) REVERT: A 812 TRP cc_start: 0.7374 (OUTLIER) cc_final: 0.6690 (t-100) REVERT: C 117 GLU cc_start: 0.8418 (pm20) cc_final: 0.8117 (pm20) REVERT: C 132 ASP cc_start: 0.8842 (t0) cc_final: 0.8425 (t0) REVERT: C 169 ASN cc_start: 0.9305 (m-40) cc_final: 0.8993 (m110) REVERT: C 208 ARG cc_start: 0.8200 (tmm-80) cc_final: 0.7689 (tpt170) REVERT: F 468 LYS cc_start: 0.8659 (ptpp) cc_final: 0.8322 (ptpp) REVERT: B 139 MET cc_start: 0.8635 (mmm) cc_final: 0.8304 (tpp) REVERT: E 101 MET cc_start: 0.8999 (mmm) cc_final: 0.8581 (mmm) REVERT: E 114 ASP cc_start: 0.7962 (m-30) cc_final: 0.6894 (t0) REVERT: E 116 TYR cc_start: 0.8177 (m-80) cc_final: 0.7851 (m-80) REVERT: E 148 GLN cc_start: 0.9079 (tt0) cc_final: 0.8704 (tt0) REVERT: E 192 MET cc_start: 0.8645 (mmm) cc_final: 0.8383 (mmm) REVERT: D 86 ARG cc_start: 0.8340 (tpt90) cc_final: 0.8106 (tpt170) REVERT: D 90 MET cc_start: 0.8554 (pmm) cc_final: 0.8351 (pmm) REVERT: D 99 GLU cc_start: 0.8682 (pm20) cc_final: 0.8335 (pm20) REVERT: D 112 LYS cc_start: 0.8627 (mptt) cc_final: 0.8366 (mppt) REVERT: D 121 ARG cc_start: 0.8279 (ttp80) cc_final: 0.7620 (ttp80) REVERT: D 123 ARG cc_start: 0.9038 (ttm110) cc_final: 0.8418 (ptt-90) REVERT: D 139 MET cc_start: 0.3437 (OUTLIER) cc_final: 0.3081 (tpp) outliers start: 42 outliers final: 33 residues processed: 188 average time/residue: 0.1181 time to fit residues: 31.2448 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 39 poor density : 154 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 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 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 500 LYS Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 36 optimal weight: 2.9990 chunk 6 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 88 optimal weight: 0.2980 chunk 81 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 chunk 84 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 82 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 206 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3799 r_free = 0.3799 target = 0.107894 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3267 r_free = 0.3267 target = 0.075525 restraints weight = 24940.261| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 4.02 r_work: 0.3055 rms_B_bonded: 4.38 restraints_weight: 0.5000 r_work (final): 0.3055 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7830 moved from start: 0.1905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 11243 Z= 0.173 Angle : 0.631 12.083 15255 Z= 0.309 Chirality : 0.043 0.274 1731 Planarity : 0.004 0.042 1954 Dihedral : 5.464 52.981 1528 Min Nonbonded Distance : 2.516 Molprobity Statistics. All-atom Clashscore : 6.96 Ramachandran Plot: Outliers : 0.14 % Allowed : 6.07 % Favored : 93.79 % Rotamer: Outliers : 3.65 % Allowed : 14.20 % Favored : 82.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -0.04 (0.23), residues: 1401 helix: 2.22 (0.28), residues: 354 sheet: -0.25 (0.33), residues: 268 loop : -1.05 (0.23), residues: 779 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG D 64 TYR 0.039 0.001 TYR E 216 PHE 0.017 0.001 PHE A 255 TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS A 658 Details of bonding type rmsd covalent geometry : bond 0.00406 (11229) covalent geometry : angle 0.63024 (15227) SS BOND : bond 0.00363 ( 14) SS BOND : angle 0.96004 ( 28) hydrogen bonds : bond 0.03746 ( 424) hydrogen bonds : angle 4.32275 ( 1200) *********************** 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 200 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 44 poor density : 156 time to evaluate : 0.446 Fit side-chains revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8888 (OUTLIER) cc_final: 0.8578 (m-40) REVERT: A 92 ASP cc_start: 0.8555 (t70) cc_final: 0.8219 (t70) REVERT: A 125 ILE cc_start: 0.9019 (OUTLIER) cc_final: 0.8740 (mp) REVERT: A 281 ASP cc_start: 0.9221 (t70) cc_final: 0.8493 (t0) REVERT: A 529 PHE cc_start: 0.8555 (OUTLIER) cc_final: 0.8047 (t80) REVERT: A 593 ILE cc_start: 0.7465 (OUTLIER) cc_final: 0.6893 (tp) REVERT: A 771 LEU cc_start: 0.8978 (tt) cc_final: 0.8448 (mp) REVERT: A 812 TRP cc_start: 0.7343 (OUTLIER) cc_final: 0.6641 (t-100) REVERT: C 84 ARG cc_start: 0.7133 (mmm160) cc_final: 0.6652 (ttm-80) REVERT: C 117 GLU cc_start: 0.8447 (pm20) cc_final: 0.8116 (pm20) REVERT: C 132 ASP cc_start: 0.8851 (t0) cc_final: 0.8443 (t0) REVERT: C 169 ASN cc_start: 0.9312 (m-40) cc_final: 0.9018 (m110) REVERT: C 208 ARG cc_start: 0.8203 (tmm-80) cc_final: 0.7690 (tpt170) REVERT: F 500 LYS cc_start: 0.7839 (OUTLIER) cc_final: 0.7537 (pttm) REVERT: B 45 SER cc_start: 0.9140 (t) cc_final: 0.8827 (p) REVERT: B 139 MET cc_start: 0.8639 (mmm) cc_final: 0.8300 (tpp) REVERT: E 101 MET cc_start: 0.8946 (mmm) cc_final: 0.8492 (mmm) REVERT: E 114 ASP cc_start: 0.8061 (m-30) cc_final: 0.6964 (t0) REVERT: E 116 TYR cc_start: 0.8242 (m-80) cc_final: 0.7924 (m-80) REVERT: E 148 GLN cc_start: 0.9099 (tt0) cc_final: 0.8707 (tt0) REVERT: E 192 MET cc_start: 0.8646 (mmm) cc_final: 0.8379 (mmm) REVERT: D 86 ARG cc_start: 0.8310 (tpt90) cc_final: 0.8035 (tpt170) REVERT: D 99 GLU cc_start: 0.8709 (pm20) cc_final: 0.8328 (pm20) REVERT: D 121 ARG cc_start: 0.8258 (ttp80) cc_final: 0.7594 (ttp80) REVERT: D 123 ARG cc_start: 0.9043 (ttm110) cc_final: 0.8422 (ptt-90) REVERT: D 139 MET cc_start: 0.3300 (OUTLIER) cc_final: 0.3013 (tpp) outliers start: 44 outliers final: 34 residues processed: 187 average time/residue: 0.1130 time to fit residues: 30.0392 Evaluate side-chains 193 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 41 poor density : 152 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 388 LEU Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 THR Chi-restraints excluded: chain A residue 444 ASN Chi-restraints excluded: chain A residue 464 VAL Chi-restraints excluded: chain A residue 523 THR Chi-restraints excluded: chain A residue 529 PHE Chi-restraints excluded: chain A residue 534 TYR Chi-restraints excluded: chain A residue 541 ILE Chi-restraints excluded: chain A residue 557 LEU Chi-restraints excluded: chain A residue 570 LEU Chi-restraints excluded: chain A residue 575 LEU Chi-restraints excluded: chain A residue 593 ILE Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 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 81 LEU Chi-restraints excluded: chain C residue 82 THR Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 500 LYS Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain B residue 75 LEU Chi-restraints excluded: chain E residue 76 THR Chi-restraints excluded: chain E residue 110 ASN Chi-restraints excluded: chain E residue 157 ASP Chi-restraints excluded: chain E residue 181 VAL Chi-restraints excluded: chain E residue 187 ASP Chi-restraints excluded: chain E residue 189 ILE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 131 optimal weight: 0.0370 chunk 112 optimal weight: 2.9990 chunk 16 optimal weight: 0.1980 chunk 45 optimal weight: 0.0030 chunk 73 optimal weight: 1.9990 chunk 50 optimal weight: 0.9980 chunk 106 optimal weight: 0.7980 chunk 56 optimal weight: 0.6980 chunk 121 optimal weight: 2.9990 chunk 97 optimal weight: 0.9990 chunk 19 optimal weight: 0.9990 overall best weight: 0.3468 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 714 ASN C 206 GLN F 506 GLN 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 = 0.110126 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.078088 restraints weight = 24711.497| |-----------------------------------------------------------------------------| r_work (start): 0.3269 rms_B_bonded: 4.01 r_work: 0.3103 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3103 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7774 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.049 11243 Z= 0.110 Angle : 0.604 12.847 15255 Z= 0.293 Chirality : 0.042 0.255 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.186 52.186 1526 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 6.59 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.64 % Favored : 94.22 % Rotamer: Outliers : 3.07 % Allowed : 15.45 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.23), residues: 1401 helix: 2.32 (0.28), residues: 355 sheet: -0.21 (0.33), residues: 271 loop : -0.98 (0.23), residues: 775 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 64 TYR 0.033 0.001 TYR E 216 PHE 0.012 0.001 PHE A 255 TRP 0.011 0.001 TRP A 159 HIS 0.005 0.000 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00249 (11229) covalent geometry : angle 0.60315 (15227) SS BOND : bond 0.00488 ( 14) SS BOND : angle 0.87549 ( 28) hydrogen bonds : bond 0.03340 ( 424) hydrogen bonds : angle 4.25707 ( 1200) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 37 poor density : 157 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8833 (OUTLIER) cc_final: 0.8511 (m-40) REVERT: A 92 ASP cc_start: 0.8502 (t70) cc_final: 0.8163 (t70) REVERT: A 125 ILE cc_start: 0.9021 (OUTLIER) cc_final: 0.8730 (mp) REVERT: A 281 ASP cc_start: 0.9246 (t70) cc_final: 0.8507 (t0) REVERT: A 529 PHE cc_start: 0.8522 (OUTLIER) cc_final: 0.8033 (t80) REVERT: A 771 LEU cc_start: 0.9004 (tt) cc_final: 0.8434 (mp) REVERT: A 812 TRP cc_start: 0.7340 (OUTLIER) cc_final: 0.6757 (t-100) REVERT: C 117 GLU cc_start: 0.8420 (pm20) cc_final: 0.8096 (pm20) REVERT: C 132 ASP cc_start: 0.8830 (t0) cc_final: 0.8397 (t0) REVERT: C 169 ASN cc_start: 0.9294 (m-40) cc_final: 0.9040 (m110) REVERT: C 208 ARG cc_start: 0.8163 (tmm-80) cc_final: 0.7684 (tpt170) REVERT: F 500 LYS cc_start: 0.7774 (OUTLIER) cc_final: 0.7439 (pttm) REVERT: B 45 SER cc_start: 0.9070 (t) cc_final: 0.8776 (p) REVERT: B 139 MET cc_start: 0.8584 (mmm) cc_final: 0.8259 (tpp) REVERT: E 101 MET cc_start: 0.9011 (mmm) cc_final: 0.8587 (mmm) REVERT: E 114 ASP cc_start: 0.8000 (m-30) cc_final: 0.6900 (t0) REVERT: E 116 TYR cc_start: 0.8218 (m-80) cc_final: 0.7874 (m-80) REVERT: E 148 GLN cc_start: 0.9066 (tt0) cc_final: 0.8693 (tt0) REVERT: E 192 MET cc_start: 0.8641 (mmm) cc_final: 0.8365 (mmm) REVERT: D 86 ARG cc_start: 0.8360 (tpt90) cc_final: 0.8081 (tpt170) REVERT: D 99 GLU cc_start: 0.8734 (pm20) cc_final: 0.8373 (pm20) REVERT: D 121 ARG cc_start: 0.8342 (ttp80) cc_final: 0.7716 (ttp80) REVERT: D 123 ARG cc_start: 0.9009 (ttm110) cc_final: 0.8390 (ptt-90) REVERT: D 139 MET cc_start: 0.3675 (OUTLIER) cc_final: 0.3295 (tpp) outliers start: 37 outliers final: 29 residues processed: 184 average time/residue: 0.1055 time to fit residues: 27.6148 Evaluate side-chains 187 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 152 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 THR 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 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 486 ASP Chi-restraints excluded: chain F residue 500 LYS Chi-restraints excluded: chain F residue 520 CYS Chi-restraints excluded: chain B residue 78 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 E residue 189 ILE Chi-restraints excluded: chain D residue 83 TYR Chi-restraints excluded: chain D residue 111 THR Chi-restraints excluded: chain D residue 115 VAL Chi-restraints excluded: chain D residue 135 LEU Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 22 optimal weight: 2.9990 chunk 60 optimal weight: 0.8980 chunk 123 optimal weight: 2.9990 chunk 75 optimal weight: 6.9990 chunk 74 optimal weight: 0.4980 chunk 86 optimal weight: 0.7980 chunk 94 optimal weight: 0.4980 chunk 65 optimal weight: 6.9990 chunk 127 optimal weight: 0.7980 chunk 46 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 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 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 = 0.3821 r_free = 0.3821 target = 0.109405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3299 r_free = 0.3299 target = 0.077226 restraints weight = 24869.027| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 4.00 r_work: 0.3087 rms_B_bonded: 4.39 restraints_weight: 0.5000 r_work (final): 0.3087 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7783 moved from start: 0.1938 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 11243 Z= 0.132 Angle : 0.612 12.673 15255 Z= 0.297 Chirality : 0.042 0.232 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.215 52.623 1526 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.71 % Favored : 94.15 % Rotamer: Outliers : 2.99 % Allowed : 15.53 % Favored : 81.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.07 (0.23), residues: 1401 helix: 2.37 (0.28), residues: 354 sheet: -0.23 (0.33), residues: 270 loop : -0.98 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG D 64 TYR 0.034 0.001 TYR E 216 PHE 0.015 0.001 PHE A 255 TRP 0.011 0.001 TRP A 159 HIS 0.004 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00309 (11229) covalent geometry : angle 0.61066 (15227) SS BOND : bond 0.00303 ( 14) SS BOND : angle 1.00169 ( 28) hydrogen bonds : bond 0.03436 ( 424) hydrogen bonds : angle 4.26827 ( 1200) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2802 Ramachandran restraints generated. 1401 Oldfield, 0 Emsley, 1401 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 154 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8864 (OUTLIER) cc_final: 0.8545 (m-40) REVERT: A 92 ASP cc_start: 0.8538 (t70) cc_final: 0.8174 (t70) REVERT: A 125 ILE cc_start: 0.9008 (OUTLIER) cc_final: 0.8719 (mp) REVERT: A 281 ASP cc_start: 0.9254 (t70) cc_final: 0.8529 (t0) REVERT: A 529 PHE cc_start: 0.8529 (OUTLIER) cc_final: 0.8054 (t80) REVERT: A 771 LEU cc_start: 0.9002 (tt) cc_final: 0.8439 (mp) REVERT: A 812 TRP cc_start: 0.7318 (OUTLIER) cc_final: 0.6734 (t-100) REVERT: C 84 ARG cc_start: 0.7100 (mmm160) cc_final: 0.6628 (ttm-80) REVERT: C 87 ARG cc_start: 0.8691 (mtp-110) cc_final: 0.8184 (mtm110) REVERT: C 117 GLU cc_start: 0.8449 (pm20) cc_final: 0.8111 (pm20) REVERT: C 132 ASP cc_start: 0.8834 (t0) cc_final: 0.8398 (t0) REVERT: C 169 ASN cc_start: 0.9318 (m-40) cc_final: 0.8886 (m110) REVERT: C 208 ARG cc_start: 0.8185 (tmm-80) cc_final: 0.7685 (tpt170) REVERT: F 500 LYS cc_start: 0.7771 (OUTLIER) cc_final: 0.7469 (pttm) REVERT: B 45 SER cc_start: 0.9183 (t) cc_final: 0.8881 (p) REVERT: B 139 MET cc_start: 0.8654 (mmm) cc_final: 0.8330 (tpp) REVERT: E 101 MET cc_start: 0.8989 (mmm) cc_final: 0.8572 (mmm) REVERT: E 114 ASP cc_start: 0.8036 (m-30) cc_final: 0.6934 (t0) REVERT: E 116 TYR cc_start: 0.8265 (m-80) cc_final: 0.7942 (m-80) REVERT: E 148 GLN cc_start: 0.9073 (tt0) cc_final: 0.8683 (tt0) REVERT: E 192 MET cc_start: 0.8634 (mmm) cc_final: 0.8356 (mmm) REVERT: D 86 ARG cc_start: 0.8367 (tpt90) cc_final: 0.8088 (tpt170) REVERT: D 99 GLU cc_start: 0.8737 (pm20) cc_final: 0.8374 (pm20) REVERT: D 121 ARG cc_start: 0.8324 (ttp80) cc_final: 0.8033 (ttp80) REVERT: D 139 MET cc_start: 0.3623 (OUTLIER) cc_final: 0.3231 (tpp) outliers start: 36 outliers final: 28 residues processed: 180 average time/residue: 0.1011 time to fit residues: 25.6770 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 : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 THR 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 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 486 ASP Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 495 SER Chi-restraints excluded: chain F residue 500 LYS 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 Chi-restraints excluded: chain D residue 139 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 119 optimal weight: 0.4980 chunk 4 optimal weight: 0.0020 chunk 61 optimal weight: 0.5980 chunk 17 optimal weight: 1.9990 chunk 106 optimal weight: 4.9990 chunk 39 optimal weight: 1.9990 chunk 73 optimal weight: 2.9990 chunk 13 optimal weight: 0.4980 chunk 0 optimal weight: 10.0000 chunk 53 optimal weight: 0.9990 chunk 88 optimal weight: 0.9990 overall best weight: 0.5190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 114 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 714 ASN C 148 GLN C 206 GLN ** B 76 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3827 r_free = 0.3827 target = 0.109870 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3307 r_free = 0.3307 target = 0.077697 restraints weight = 25043.354| |-----------------------------------------------------------------------------| r_work (start): 0.3262 rms_B_bonded: 4.03 r_work: 0.3097 rms_B_bonded: 4.41 restraints_weight: 0.5000 r_work (final): 0.3097 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7775 moved from start: 0.1973 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= 0.120 Angle : 0.611 12.479 15255 Z= 0.296 Chirality : 0.042 0.216 1731 Planarity : 0.003 0.043 1954 Dihedral : 4.991 52.508 1524 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.85 % Favored : 94.00 % Rotamer: Outliers : 2.99 % Allowed : 15.70 % Favored : 81.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.09 (0.23), residues: 1401 helix: 2.38 (0.28), residues: 355 sheet: -0.23 (0.33), residues: 266 loop : -0.97 (0.23), residues: 780 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 64 TYR 0.042 0.001 TYR E 216 PHE 0.022 0.001 PHE A 554 TRP 0.011 0.001 TRP A 159 HIS 0.002 0.000 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00278 (11229) covalent geometry : angle 0.60986 (15227) SS BOND : bond 0.00263 ( 14) SS BOND : angle 0.98309 ( 28) hydrogen bonds : bond 0.03345 ( 424) hydrogen bonds : angle 4.24418 ( 1200) ********************** 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 186 residues out of total 1230 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 150 time to evaluate : 0.456 Fit side-chains revert: symmetry clash REVERT: A 91 ASN cc_start: 0.8846 (OUTLIER) cc_final: 0.8563 (m-40) REVERT: A 92 ASP cc_start: 0.8510 (t70) cc_final: 0.8140 (t70) REVERT: A 125 ILE cc_start: 0.9009 (OUTLIER) cc_final: 0.8709 (mp) REVERT: A 281 ASP cc_start: 0.9264 (t70) cc_final: 0.8532 (t0) REVERT: A 529 PHE cc_start: 0.8505 (OUTLIER) cc_final: 0.8036 (t80) REVERT: A 771 LEU cc_start: 0.8990 (tt) cc_final: 0.8435 (mp) REVERT: A 812 TRP cc_start: 0.7328 (OUTLIER) cc_final: 0.6762 (t-100) REVERT: C 84 ARG cc_start: 0.7075 (mmm160) cc_final: 0.6597 (ttm-80) REVERT: C 87 ARG cc_start: 0.8688 (mtp-110) cc_final: 0.8176 (mtm110) REVERT: C 117 GLU cc_start: 0.8471 (pm20) cc_final: 0.8177 (pm20) REVERT: C 132 ASP cc_start: 0.8804 (t0) cc_final: 0.8345 (t0) REVERT: C 169 ASN cc_start: 0.9371 (m-40) cc_final: 0.8954 (m110) REVERT: C 208 ARG cc_start: 0.8176 (tmm-80) cc_final: 0.7682 (tpt170) REVERT: F 500 LYS cc_start: 0.7741 (OUTLIER) cc_final: 0.7424 (pttm) REVERT: B 45 SER cc_start: 0.9159 (t) cc_final: 0.8872 (p) REVERT: B 139 MET cc_start: 0.8649 (mmm) cc_final: 0.8334 (tpp) REVERT: E 101 MET cc_start: 0.9003 (mmm) cc_final: 0.8586 (mmm) REVERT: E 114 ASP cc_start: 0.8032 (m-30) cc_final: 0.6922 (t0) REVERT: E 116 TYR cc_start: 0.8265 (m-80) cc_final: 0.7960 (m-80) REVERT: E 148 GLN cc_start: 0.9067 (tt0) cc_final: 0.8670 (tt0) REVERT: E 192 MET cc_start: 0.8626 (mmm) cc_final: 0.8352 (mmm) REVERT: D 99 GLU cc_start: 0.8767 (pm20) cc_final: 0.8405 (pm20) REVERT: D 121 ARG cc_start: 0.8366 (ttp80) cc_final: 0.8105 (ttp80) REVERT: D 139 MET cc_start: 0.3632 (OUTLIER) cc_final: 0.3239 (tpp) outliers start: 36 outliers final: 28 residues processed: 174 average time/residue: 0.1145 time to fit residues: 28.0614 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 : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 91 ASN Chi-restraints excluded: chain A residue 125 ILE Chi-restraints excluded: chain A residue 396 LEU Chi-restraints excluded: chain A residue 415 ILE Chi-restraints excluded: chain A residue 416 THR 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 575 LEU Chi-restraints excluded: chain A residue 610 ILE Chi-restraints excluded: chain A residue 670 PHE Chi-restraints excluded: chain A residue 707 THR Chi-restraints excluded: chain A residue 788 ILE Chi-restraints excluded: chain A residue 812 TRP Chi-restraints excluded: chain C residue 81 LEU Chi-restraints excluded: chain C residue 112 GLU Chi-restraints excluded: chain F residue 446 SER Chi-restraints excluded: chain F residue 475 THR Chi-restraints excluded: chain F residue 486 ASP Chi-restraints excluded: chain F residue 487 SER Chi-restraints excluded: chain F residue 494 ILE Chi-restraints excluded: chain F residue 500 LYS 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 139 MET Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 140 random chunks: chunk 61 optimal weight: 0.7980 chunk 64 optimal weight: 6.9990 chunk 11 optimal weight: 0.7980 chunk 74 optimal weight: 1.9990 chunk 110 optimal weight: 5.9990 chunk 51 optimal weight: 0.8980 chunk 125 optimal weight: 2.9990 chunk 88 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 68 optimal weight: 1.9990 chunk 132 optimal weight: 0.6980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 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 = 0.3815 r_free = 0.3815 target = 0.108996 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.076721 restraints weight = 25017.450| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 4.01 r_work: 0.3074 rms_B_bonded: 4.40 restraints_weight: 0.5000 r_work (final): 0.3074 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7796 moved from start: 0.2020 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= 0.148 Angle : 0.616 12.430 15255 Z= 0.301 Chirality : 0.042 0.204 1731 Planarity : 0.003 0.043 1954 Dihedral : 5.092 52.856 1523 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 7.14 Ramachandran Plot: Outliers : 0.14 % Allowed : 5.92 % Favored : 93.93 % Rotamer: Outliers : 3.07 % Allowed : 15.37 % Favored : 81.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.04 (0.23), residues: 1401 helix: 2.36 (0.28), residues: 354 sheet: -0.28 (0.33), residues: 270 loop : -1.00 (0.23), residues: 777 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 64 TYR 0.015 0.001 TYR A 352 PHE 0.020 0.001 PHE A 554 TRP 0.013 0.001 TRP A 159 HIS 0.003 0.001 HIS B 76 Details of bonding type rmsd covalent geometry : bond 0.00349 (11229) covalent geometry : angle 0.61535 (15227) SS BOND : bond 0.00314 ( 14) SS BOND : angle 1.03935 ( 28) hydrogen bonds : bond 0.03510 ( 424) hydrogen bonds : angle 4.28293 ( 1200) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3458.17 seconds wall clock time: 60 minutes 0.04 seconds (3600.04 seconds total)