Starting phenix.real_space_refine on Sat Aug 23 08:16:20 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u54_41912/08_2025/8u54_41912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u54_41912/08_2025/8u54_41912.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.65 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8u54_41912/08_2025/8u54_41912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u54_41912/08_2025/8u54_41912.map" model { file = "/net/cci-nas-00/data/ceres_data/8u54_41912/08_2025/8u54_41912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u54_41912/08_2025/8u54_41912.cif" } resolution = 2.65 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= 0.028 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 66 5.16 5 C 7130 2.51 5 N 1690 2.21 5 O 1859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/phenix-2.0-5787/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 10745 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 5353 Number of conformers: 1 Conformer: "" Number of residues, atoms: 679, 5353 Classifications: {'peptide': 679} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 655} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "B" Number of atoms: 5364 Number of conformers: 1 Conformer: "" Number of residues, atoms: 680, 5364 Classifications: {'peptide': 680} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 22, 'TRANS': 656} Chain breaks: 3 Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 3 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Chain: "B" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.13, per 1000 atoms: 0.20 Number of scatterers: 10745 At special positions: 0 Unit cell: (94.18, 120.772, 93.072, 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 66 16.00 O 1859 8.00 N 1690 7.00 C 7130 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Links applied NAG-ASN " NAG A 901 " - " ASN A 309 " " NAG B 901 " - " ASN B 309 " Time building additional restraints: 0.78 Conformation dependent library (CDL) restraints added in 357.8 milliseconds Enol-peptide restraints added in 238.4 nanoseconds 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2534 Finding SS restraints... Secondary structure from input PDB file: 62 helices and 2 sheets defined 84.6% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.21 Creating SS restraints... Processing helix chain 'A' and resid 38 through 40 No H-bonds generated for 'chain 'A' and resid 38 through 40' Processing helix chain 'A' and resid 41 through 62 Processing helix chain 'A' and resid 66 through 80 removed outlier: 4.033A pdb=" N GLY A 72 " --> pdb=" O THR A 68 " (cutoff:3.500A) removed outlier: 3.956A pdb=" N LEU A 73 " --> pdb=" O GLN A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 80 through 93 Processing helix chain 'A' and resid 99 through 125 removed outlier: 3.556A pdb=" N LEU A 103 " --> pdb=" O ASP A 99 " (cutoff:3.500A) Processing helix chain 'A' and resid 129 through 143 Proline residue: A 138 - end of helix Processing helix chain 'A' and resid 149 through 159 removed outlier: 3.570A pdb=" N ILE A 153 " --> pdb=" O LEU A 149 " (cutoff:3.500A) Processing helix chain 'A' and resid 164 through 197 removed outlier: 3.921A pdb=" N TYR A 168 " --> pdb=" O GLU A 164 " (cutoff:3.500A) removed outlier: 3.909A pdb=" N ILE A 169 " --> pdb=" O TYR A 165 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N TYR A 170 " --> pdb=" O LEU A 166 " (cutoff:3.500A) Proline residue: A 174 - end of helix Proline residue: A 182 - end of helix Processing helix chain 'A' and resid 202 through 217 removed outlier: 3.539A pdb=" N ILE A 206 " --> pdb=" O ASN A 202 " (cutoff:3.500A) Processing helix chain 'A' and resid 217 through 233 Processing helix chain 'A' and resid 241 through 264 removed outlier: 3.619A pdb=" N SER A 251 " --> pdb=" O GLY A 247 " (cutoff:3.500A) removed outlier: 4.040A pdb=" N SER A 253 " --> pdb=" O GLY A 249 " (cutoff:3.500A) removed outlier: 4.857A pdb=" N GLY A 254 " --> pdb=" O ASN A 250 " (cutoff:3.500A) Processing helix chain 'A' and resid 272 through 288 Processing helix chain 'A' and resid 288 through 302 Processing helix chain 'A' and resid 306 through 322 Processing helix chain 'A' and resid 326 through 337 removed outlier: 4.085A pdb=" N ALA A 330 " --> pdb=" O ALA A 326 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 367 removed outlier: 3.702A pdb=" N ALA A 355 " --> pdb=" O THR A 351 " (cutoff:3.500A) Proline residue: A 356 - end of helix Processing helix chain 'A' and resid 368 through 370 No H-bonds generated for 'chain 'A' and resid 368 through 370' Processing helix chain 'A' and resid 371 through 404 Processing helix chain 'A' and resid 405 through 409 Processing helix chain 'A' and resid 411 through 436 removed outlier: 3.699A pdb=" N PHE A 434 " --> pdb=" O MET A 430 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 473 Processing helix chain 'A' and resid 480 through 503 Proline residue: A 492 - end of helix Processing helix chain 'A' and resid 511 through 515 Processing helix chain 'A' and resid 516 through 549 Processing helix chain 'A' and resid 644 through 682 Processing helix chain 'A' and resid 686 through 712 removed outlier: 5.649A pdb=" N GLY A 704 " --> pdb=" O ASN A 700 " (cutoff:3.500A) removed outlier: 5.158A pdb=" N PHE A 705 " --> pdb=" O PHE A 701 " (cutoff:3.500A) Processing helix chain 'A' and resid 714 through 720 Processing helix chain 'A' and resid 744 through 757 removed outlier: 3.555A pdb=" N TYR A 757 " --> pdb=" O GLN A 753 " (cutoff:3.500A) Processing helix chain 'A' and resid 757 through 767 removed outlier: 4.770A pdb=" N LEU A 761 " --> pdb=" O TYR A 757 " (cutoff:3.500A) Processing helix chain 'A' and resid 783 through 793 Processing helix chain 'A' and resid 798 through 812 Processing helix chain 'B' and resid 38 through 40 No H-bonds generated for 'chain 'B' and resid 38 through 40' Processing helix chain 'B' and resid 41 through 62 Processing helix chain 'B' and resid 66 through 80 removed outlier: 4.031A pdb=" N GLY B 72 " --> pdb=" O THR B 68 " (cutoff:3.500A) removed outlier: 3.955A pdb=" N LEU B 73 " --> pdb=" O GLN B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 80 through 93 Processing helix chain 'B' and resid 99 through 125 removed outlier: 3.568A pdb=" N LEU B 103 " --> pdb=" O ASP B 99 " (cutoff:3.500A) Processing helix chain 'B' and resid 129 through 143 Proline residue: B 138 - end of helix Processing helix chain 'B' and resid 149 through 159 removed outlier: 3.578A pdb=" N ILE B 153 " --> pdb=" O LEU B 149 " (cutoff:3.500A) Processing helix chain 'B' and resid 164 through 197 removed outlier: 3.917A pdb=" N TYR B 168 " --> pdb=" O GLU B 164 " (cutoff:3.500A) removed outlier: 3.913A pdb=" N ILE B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 4.102A pdb=" N TYR B 170 " --> pdb=" O LEU B 166 " (cutoff:3.500A) Proline residue: B 174 - end of helix Proline residue: B 182 - end of helix Processing helix chain 'B' and resid 202 through 217 removed outlier: 3.544A pdb=" N ILE B 206 " --> pdb=" O ASN B 202 " (cutoff:3.500A) Processing helix chain 'B' and resid 217 through 233 Processing helix chain 'B' and resid 241 through 264 removed outlier: 3.585A pdb=" N SER B 251 " --> pdb=" O GLY B 247 " (cutoff:3.500A) removed outlier: 4.032A pdb=" N SER B 253 " --> pdb=" O GLY B 249 " (cutoff:3.500A) removed outlier: 4.858A pdb=" N GLY B 254 " --> pdb=" O ASN B 250 " (cutoff:3.500A) Processing helix chain 'B' and resid 272 through 288 Processing helix chain 'B' and resid 288 through 302 Processing helix chain 'B' and resid 306 through 322 Processing helix chain 'B' and resid 326 through 337 removed outlier: 4.081A pdb=" N ALA B 330 " --> pdb=" O ALA B 326 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 367 removed outlier: 3.689A pdb=" N ALA B 355 " --> pdb=" O THR B 351 " (cutoff:3.500A) Proline residue: B 356 - end of helix Processing helix chain 'B' and resid 368 through 370 No H-bonds generated for 'chain 'B' and resid 368 through 370' Processing helix chain 'B' and resid 371 through 404 Processing helix chain 'B' and resid 405 through 409 Processing helix chain 'B' and resid 411 through 436 removed outlier: 3.698A pdb=" N PHE B 434 " --> pdb=" O MET B 430 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 473 Processing helix chain 'B' and resid 480 through 503 Proline residue: B 492 - end of helix Processing helix chain 'B' and resid 511 through 515 Processing helix chain 'B' and resid 516 through 549 Processing helix chain 'B' and resid 644 through 682 Processing helix chain 'B' and resid 686 through 712 removed outlier: 5.664A pdb=" N GLY B 704 " --> pdb=" O ASN B 700 " (cutoff:3.500A) removed outlier: 5.161A pdb=" N PHE B 705 " --> pdb=" O PHE B 701 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 Processing helix chain 'B' and resid 744 through 757 removed outlier: 3.534A pdb=" N TYR B 757 " --> pdb=" O GLN B 753 " (cutoff:3.500A) Processing helix chain 'B' and resid 757 through 767 removed outlier: 4.768A pdb=" N LEU B 761 " --> pdb=" O TYR B 757 " (cutoff:3.500A) Processing helix chain 'B' and resid 783 through 793 Processing helix chain 'B' and resid 798 through 812 Processing sheet with id=AA1, first strand: chain 'A' and resid 780 through 782 Processing sheet with id=AA2, first strand: chain 'B' and resid 780 through 782 852 hydrogen bonds defined for protein. 2532 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: 1.35 Time building geometry restraints manager: 1.06 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.30: 1643 1.30 - 1.43: 2943 1.43 - 1.56: 6307 1.56 - 1.68: 0 1.68 - 1.81: 102 Bond restraints: 10995 Sorted by residual: bond pdb=" C ASN B 309 " pdb=" O ASN B 309 " ideal model delta sigma weight residual 1.236 1.176 0.059 1.29e-02 6.01e+03 2.12e+01 bond pdb=" CA SER B 306 " pdb=" CB SER B 306 " ideal model delta sigma weight residual 1.528 1.466 0.062 1.58e-02 4.01e+03 1.53e+01 bond pdb=" C ASN B 309 " pdb=" N HIS B 310 " ideal model delta sigma weight residual 1.335 1.304 0.031 1.36e-02 5.41e+03 5.06e+00 bond pdb=" C VAL B 308 " pdb=" N ASN B 309 " ideal model delta sigma weight residual 1.335 1.306 0.029 1.38e-02 5.25e+03 4.51e+00 bond pdb=" CB CYS B 696 " pdb=" SG CYS B 696 " ideal model delta sigma weight residual 1.808 1.740 0.068 3.30e-02 9.18e+02 4.24e+00 ... (remaining 10990 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.47: 14046 1.47 - 2.94: 703 2.94 - 4.41: 130 4.41 - 5.88: 39 5.88 - 7.36: 8 Bond angle restraints: 14926 Sorted by residual: angle pdb=" CA ASN B 309 " pdb=" CB ASN B 309 " pdb=" CG ASN B 309 " ideal model delta sigma weight residual 112.60 117.54 -4.94 1.00e+00 1.00e+00 2.44e+01 angle pdb=" C ILE B 388 " pdb=" N VAL B 389 " pdb=" CA VAL B 389 " ideal model delta sigma weight residual 120.29 114.54 5.75 1.72e+00 3.38e-01 1.12e+01 angle pdb=" C ILE A 388 " pdb=" N VAL A 389 " pdb=" CA VAL A 389 " ideal model delta sigma weight residual 120.29 114.57 5.72 1.72e+00 3.38e-01 1.11e+01 angle pdb=" CA TYR B 451 " pdb=" CB TYR B 451 " pdb=" CG TYR B 451 " ideal model delta sigma weight residual 113.90 108.07 5.83 1.80e+00 3.09e-01 1.05e+01 angle pdb=" CA ASN B 309 " pdb=" C ASN B 309 " pdb=" N HIS B 310 " ideal model delta sigma weight residual 118.14 122.35 -4.21 1.31e+00 5.83e-01 1.03e+01 ... (remaining 14921 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.28: 5906 16.28 - 32.55: 458 32.55 - 48.83: 76 48.83 - 65.10: 17 65.10 - 81.38: 3 Dihedral angle restraints: 6460 sinusoidal: 2523 harmonic: 3937 Sorted by residual: dihedral pdb=" CA GLY B 266 " pdb=" C GLY B 266 " pdb=" N LYS B 267 " pdb=" CA LYS B 267 " ideal model delta harmonic sigma weight residual -180.00 -154.79 -25.21 0 5.00e+00 4.00e-02 2.54e+01 dihedral pdb=" CA GLY A 266 " pdb=" C GLY A 266 " pdb=" N LYS A 267 " pdb=" CA LYS A 267 " ideal model delta harmonic sigma weight residual -180.00 -155.41 -24.59 0 5.00e+00 4.00e-02 2.42e+01 dihedral pdb=" CA SER B 36 " pdb=" C SER B 36 " pdb=" N MET B 37 " pdb=" CA MET B 37 " ideal model delta harmonic sigma weight residual 180.00 156.84 23.16 0 5.00e+00 4.00e-02 2.15e+01 ... (remaining 6457 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 1101 0.038 - 0.076: 484 0.076 - 0.114: 149 0.114 - 0.152: 30 0.152 - 0.191: 5 Chirality restraints: 1769 Sorted by residual: chirality pdb=" CA TYR B 451 " pdb=" N TYR B 451 " pdb=" C TYR B 451 " pdb=" CB TYR B 451 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.08e-01 chirality pdb=" CA TYR A 451 " pdb=" N TYR A 451 " pdb=" C TYR A 451 " pdb=" CB TYR A 451 " both_signs ideal model delta sigma weight residual False 2.51 2.33 0.19 2.00e-01 2.50e+01 8.57e-01 chirality pdb=" CA PHE B 50 " pdb=" N PHE B 50 " pdb=" C PHE B 50 " pdb=" CB PHE B 50 " both_signs ideal model delta sigma weight residual False 2.51 2.35 0.16 2.00e-01 2.50e+01 6.20e-01 ... (remaining 1766 not shown) Planarity restraints: 1824 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASN B 309 " 0.012 2.00e-02 2.50e+03 2.44e-02 5.96e+00 pdb=" C ASN B 309 " -0.042 2.00e-02 2.50e+03 pdb=" O ASN B 309 " 0.015 2.00e-02 2.50e+03 pdb=" N HIS B 310 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR B 320 " 0.033 2.00e-02 2.50e+03 1.70e-02 5.75e+00 pdb=" CG TYR B 320 " -0.027 2.00e-02 2.50e+03 pdb=" CD1 TYR B 320 " -0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR B 320 " -0.007 2.00e-02 2.50e+03 pdb=" CE1 TYR B 320 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR B 320 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR B 320 " 0.003 2.00e-02 2.50e+03 pdb=" OH TYR B 320 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 320 " -0.032 2.00e-02 2.50e+03 1.65e-02 5.42e+00 pdb=" CG TYR A 320 " 0.026 2.00e-02 2.50e+03 pdb=" CD1 TYR A 320 " 0.014 2.00e-02 2.50e+03 pdb=" CD2 TYR A 320 " 0.006 2.00e-02 2.50e+03 pdb=" CE1 TYR A 320 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR A 320 " 0.005 2.00e-02 2.50e+03 pdb=" CZ TYR A 320 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR A 320 " -0.015 2.00e-02 2.50e+03 ... (remaining 1821 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 1796 2.76 - 3.29: 11297 3.29 - 3.83: 18792 3.83 - 4.36: 23026 4.36 - 4.90: 37963 Nonbonded interactions: 92874 Sorted by model distance: nonbonded pdb=" OG SER B 306 " pdb=" C8 NAG B 901 " model vdw 2.221 3.460 nonbonded pdb=" OD1 ASP A 99 " pdb=" OG SER A 101 " model vdw 2.321 3.040 nonbonded pdb=" OD1 ASP B 99 " pdb=" OG SER B 101 " model vdw 2.348 3.040 nonbonded pdb=" O PRO A 238 " pdb=" N TYR A 240 " model vdw 2.374 3.120 nonbonded pdb=" O PRO B 238 " pdb=" N TYR B 240 " model vdw 2.425 3.120 ... (remaining 92869 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = (chain 'B' and (resid 34 through 769 or resid 779 through 901)) } 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: 1.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.140 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 9.410 Find NCS groups from input model: 0.160 Set up NCS constraints: 0.010 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:6.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.660 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6842 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 : 0.006 0.068 10997 Z= 0.289 Angle : 0.794 7.356 14932 Z= 0.447 Chirality : 0.047 0.191 1769 Planarity : 0.006 0.054 1822 Dihedral : 12.072 81.377 3926 Min Nonbonded Distance : 2.221 Molprobity Statistics. All-atom Clashscore : 3.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Rotamer: Outliers : 0.17 % Allowed : 3.55 % Favored : 96.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: -1.34 (0.21), residues: 1343 helix: -0.75 (0.14), residues: 1058 sheet: None (None), residues: 0 loop : -0.70 (0.39), residues: 285 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.001 ARG B 808 TYR 0.033 0.003 TYR B 320 PHE 0.031 0.004 PHE A 711 TRP 0.015 0.002 TRP B 396 HIS 0.011 0.002 HIS B 310 Details of bonding type rmsd covalent geometry : bond 0.00632 (10995) covalent geometry : angle 0.78908 (14926) hydrogen bonds : bond 0.10250 ( 852) hydrogen bonds : angle 6.03352 ( 2532) link_NAG-ASN : bond 0.00878 ( 2) link_NAG-ASN : angle 4.56490 ( 6) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 388 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 386 time to evaluate : 0.319 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 5 residues processed: 388 average time/residue: 0.2973 time to fit residues: 130.8442 Evaluate side-chains 200 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 195 time to evaluate : 0.247 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 342 ILE Chi-restraints excluded: chain A residue 400 ILE Chi-restraints excluded: chain B residue 342 ILE Chi-restraints excluded: chain B residue 400 ILE Chi-restraints excluded: chain B residue 807 ASP Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 10.0000 chunk 10 optimal weight: 0.6980 chunk 66 optimal weight: 0.7980 chunk 130 optimal weight: 0.6980 chunk 124 optimal weight: 0.9980 chunk 103 optimal weight: 0.7980 chunk 77 optimal weight: 0.1980 chunk 122 optimal weight: 1.9990 chunk 91 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 198 ASN A 310 HIS ** A 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 380 GLN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN ** B 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4209 r_free = 0.4209 target = 0.126823 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.085935 restraints weight = 26025.502| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.03 r_work: 0.3354 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.3354 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7516 moved from start: 0.4285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 10997 Z= 0.193 Angle : 0.791 14.362 14932 Z= 0.386 Chirality : 0.046 0.225 1769 Planarity : 0.005 0.052 1822 Dihedral : 5.260 46.605 1492 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 14.98 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.94 % Favored : 97.92 % Rotamer: Outliers : 5.92 % Allowed : 15.64 % Favored : 78.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 0.84 (0.23), residues: 1343 helix: 0.88 (0.15), residues: 1050 sheet: None (None), residues: 0 loop : -0.28 (0.42), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 213 TYR 0.023 0.002 TYR A 689 PHE 0.021 0.002 PHE A 50 TRP 0.013 0.002 TRP B 489 HIS 0.009 0.002 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00409 (10995) covalent geometry : angle 0.79018 (14926) hydrogen bonds : bond 0.05463 ( 852) hydrogen bonds : angle 5.05434 ( 2532) link_NAG-ASN : bond 0.00424 ( 2) link_NAG-ASN : angle 1.59071 ( 6) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 278 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 70 poor density : 208 time to evaluate : 0.257 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8237 (OUTLIER) cc_final: 0.7697 (mmm-85) REVERT: A 278 VAL cc_start: 0.8618 (t) cc_final: 0.8322 (p) REVERT: A 288 LEU cc_start: 0.8702 (OUTLIER) cc_final: 0.8500 (tp) REVERT: A 301 LEU cc_start: 0.8755 (OUTLIER) cc_final: 0.8514 (tp) REVERT: A 316 TYR cc_start: 0.8343 (t80) cc_final: 0.8042 (t80) REVERT: A 667 ILE cc_start: 0.9155 (mt) cc_final: 0.8911 (mm) REVERT: A 752 GLN cc_start: 0.9178 (tp-100) cc_final: 0.8844 (tp-100) REVERT: B 41 ARG cc_start: 0.8116 (OUTLIER) cc_final: 0.7653 (mmm-85) REVERT: B 278 VAL cc_start: 0.8626 (t) cc_final: 0.8349 (p) REVERT: B 301 LEU cc_start: 0.8701 (OUTLIER) cc_final: 0.8442 (tp) REVERT: B 316 TYR cc_start: 0.8490 (t80) cc_final: 0.8133 (t80) REVERT: B 512 SER cc_start: 0.9138 (p) cc_final: 0.8875 (p) REVERT: B 521 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9269 (tpp) REVERT: B 752 GLN cc_start: 0.9187 (tp-100) cc_final: 0.8822 (tp-100) outliers start: 70 outliers final: 20 residues processed: 252 average time/residue: 0.3038 time to fit residues: 86.4802 Evaluate side-chains 194 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 168 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 142 THR Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 288 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 354 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 489 TRP Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 804 ILE Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 521 MET Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 804 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 0.0970 chunk 15 optimal weight: 0.9980 chunk 115 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 96 optimal weight: 0.0980 chunk 11 optimal weight: 0.0050 chunk 132 optimal weight: 7.9990 chunk 4 optimal weight: 0.7980 chunk 47 optimal weight: 0.2980 chunk 18 optimal weight: 0.6980 chunk 61 optimal weight: 6.9990 overall best weight: 0.2392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS B 672 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4225 r_free = 0.4225 target = 0.127473 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3698 r_free = 0.3698 target = 0.088887 restraints weight = 25710.531| |-----------------------------------------------------------------------------| r_work (start): 0.3586 rms_B_bonded: 2.94 r_work: 0.3419 rms_B_bonded: 3.88 restraints_weight: 0.5000 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7592 moved from start: 0.5139 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 10997 Z= 0.148 Angle : 0.704 11.032 14932 Z= 0.342 Chirality : 0.044 0.188 1769 Planarity : 0.004 0.048 1822 Dihedral : 4.637 17.575 1482 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.07 % Allowed : 18.60 % Favored : 76.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.52 (0.23), residues: 1343 helix: 1.38 (0.15), residues: 1062 sheet: None (None), residues: 0 loop : -0.19 (0.44), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 213 TYR 0.022 0.002 TYR A 689 PHE 0.016 0.002 PHE A 695 TRP 0.024 0.001 TRP A 460 HIS 0.008 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00308 (10995) covalent geometry : angle 0.70414 (14926) hydrogen bonds : bond 0.04980 ( 852) hydrogen bonds : angle 4.79319 ( 2532) link_NAG-ASN : bond 0.00484 ( 2) link_NAG-ASN : angle 1.17807 ( 6) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 245 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 185 time to evaluate : 0.401 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 297 MET cc_start: 0.9103 (mmm) cc_final: 0.8664 (mtp) REVERT: A 316 TYR cc_start: 0.8648 (t80) cc_final: 0.8408 (t80) REVERT: A 347 MET cc_start: 0.8670 (tmm) cc_final: 0.8455 (tmm) REVERT: A 540 MET cc_start: 0.8346 (tpp) cc_final: 0.8104 (tpp) REVERT: A 695 PHE cc_start: 0.8261 (m-80) cc_final: 0.7993 (m-80) REVERT: A 752 GLN cc_start: 0.9227 (tp-100) cc_final: 0.8801 (tp-100) REVERT: B 221 PHE cc_start: 0.7759 (OUTLIER) cc_final: 0.6648 (t80) REVERT: B 224 PHE cc_start: 0.8052 (m-80) cc_final: 0.7848 (m-80) REVERT: B 316 TYR cc_start: 0.8595 (t80) cc_final: 0.8280 (t80) REVERT: B 364 LEU cc_start: 0.8649 (OUTLIER) cc_final: 0.8413 (mt) REVERT: B 429 MET cc_start: 0.8741 (tpt) cc_final: 0.8534 (tpt) REVERT: B 430 MET cc_start: 0.7802 (mtm) cc_final: 0.7402 (mpp) REVERT: B 460 TRP cc_start: 0.8776 (m100) cc_final: 0.8500 (m100) REVERT: B 752 GLN cc_start: 0.9199 (tp-100) cc_final: 0.8945 (tp-100) outliers start: 60 outliers final: 15 residues processed: 224 average time/residue: 0.2623 time to fit residues: 67.6011 Evaluate side-chains 170 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 153 time to evaluate : 0.281 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 115 PHE Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 395 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 364 LEU Chi-restraints excluded: chain B residue 690 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.5980 chunk 133 optimal weight: 3.9990 chunk 130 optimal weight: 3.9990 chunk 119 optimal weight: 7.9990 chunk 59 optimal weight: 7.9990 chunk 134 optimal weight: 5.9990 chunk 113 optimal weight: 7.9990 chunk 87 optimal weight: 2.9990 chunk 39 optimal weight: 0.8980 chunk 56 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 overall best weight: 2.0986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 672 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4202 r_free = 0.4202 target = 0.124980 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3562 r_free = 0.3562 target = 0.080978 restraints weight = 26643.659| |-----------------------------------------------------------------------------| r_work (start): 0.3433 rms_B_bonded: 3.05 r_work: 0.3266 rms_B_bonded: 3.94 restraints_weight: 0.5000 r_work (final): 0.3266 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 moved from start: 0.7638 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.059 10997 Z= 0.291 Angle : 0.827 11.061 14932 Z= 0.402 Chirality : 0.049 0.240 1769 Planarity : 0.005 0.048 1822 Dihedral : 4.812 19.564 1482 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 5.58 % Allowed : 18.01 % Favored : 76.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.33 (0.23), residues: 1343 helix: 1.23 (0.15), residues: 1056 sheet: None (None), residues: 0 loop : -0.17 (0.43), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG B 825 TYR 0.024 0.002 TYR A 689 PHE 0.026 0.002 PHE A 221 TRP 0.033 0.002 TRP A 460 HIS 0.006 0.002 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00659 (10995) covalent geometry : angle 0.82646 (14926) hydrogen bonds : bond 0.05642 ( 852) hydrogen bonds : angle 4.88962 ( 2532) link_NAG-ASN : bond 0.00207 ( 2) link_NAG-ASN : angle 1.53122 ( 6) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 232 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 66 poor density : 166 time to evaluate : 0.392 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 198 ASN cc_start: 0.9092 (m110) cc_final: 0.8725 (p0) REVERT: A 221 PHE cc_start: 0.8524 (OUTLIER) cc_final: 0.7852 (t80) REVERT: A 297 MET cc_start: 0.9325 (mmm) cc_final: 0.9081 (mmt) REVERT: A 383 SER cc_start: 0.8871 (m) cc_final: 0.8556 (p) REVERT: A 540 MET cc_start: 0.8535 (tpp) cc_final: 0.8288 (tpp) REVERT: A 695 PHE cc_start: 0.8323 (m-80) cc_final: 0.8037 (m-10) REVERT: A 752 GLN cc_start: 0.9273 (tp-100) cc_final: 0.9014 (tp-100) REVERT: B 149 LEU cc_start: 0.9397 (OUTLIER) cc_final: 0.9178 (tm) REVERT: B 198 ASN cc_start: 0.9096 (m110) cc_final: 0.8731 (p0) REVERT: B 211 LEU cc_start: 0.9374 (OUTLIER) cc_final: 0.9131 (mp) REVERT: B 297 MET cc_start: 0.9183 (tpp) cc_final: 0.8967 (mmt) REVERT: B 383 SER cc_start: 0.8806 (m) cc_final: 0.8451 (p) REVERT: B 430 MET cc_start: 0.8329 (mtm) cc_final: 0.7888 (mpp) REVERT: B 468 LEU cc_start: 0.9524 (pp) cc_final: 0.9111 (mm) REVERT: B 489 TRP cc_start: 0.7239 (m100) cc_final: 0.6491 (m100) REVERT: B 695 PHE cc_start: 0.8387 (m-10) cc_final: 0.8052 (m-80) REVERT: B 752 GLN cc_start: 0.9284 (tp-100) cc_final: 0.9029 (tp-100) outliers start: 66 outliers final: 20 residues processed: 214 average time/residue: 0.2652 time to fit residues: 65.8012 Evaluate side-chains 154 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 131 time to evaluate : 0.338 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 93 LEU Chi-restraints excluded: chain B residue 149 LEU Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 211 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 322 VAL Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 665 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 111 optimal weight: 0.5980 chunk 96 optimal weight: 0.9980 chunk 84 optimal weight: 0.9980 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.5980 chunk 119 optimal weight: 5.9990 chunk 92 optimal weight: 0.5980 chunk 90 optimal weight: 0.4980 chunk 68 optimal weight: 0.5980 chunk 130 optimal weight: 0.8980 chunk 6 optimal weight: 1.9990 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 230 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.127560 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3626 r_free = 0.3626 target = 0.084741 restraints weight = 26494.813| |-----------------------------------------------------------------------------| r_work (start): 0.3502 rms_B_bonded: 3.10 r_work: 0.3336 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3336 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7872 moved from start: 0.7951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10997 Z= 0.162 Angle : 0.752 12.543 14932 Z= 0.354 Chirality : 0.044 0.229 1769 Planarity : 0.004 0.046 1822 Dihedral : 4.586 18.063 1482 Min Nonbonded Distance : 2.528 Molprobity Statistics. All-atom Clashscore : 14.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 4.23 % Allowed : 21.05 % Favored : 74.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.68 (0.23), residues: 1343 helix: 1.52 (0.15), residues: 1059 sheet: None (None), residues: 0 loop : -0.25 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 825 TYR 0.020 0.002 TYR B 689 PHE 0.023 0.002 PHE A 699 TRP 0.034 0.002 TRP A 460 HIS 0.010 0.001 HIS B 716 Details of bonding type rmsd covalent geometry : bond 0.00351 (10995) covalent geometry : angle 0.75185 (14926) hydrogen bonds : bond 0.04985 ( 852) hydrogen bonds : angle 4.58944 ( 2532) link_NAG-ASN : bond 0.00313 ( 2) link_NAG-ASN : angle 1.01808 ( 6) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 50 poor density : 152 time to evaluate : 0.316 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9081 (tm) cc_final: 0.8843 (tp) REVERT: A 221 PHE cc_start: 0.8158 (OUTLIER) cc_final: 0.7347 (t80) REVERT: A 297 MET cc_start: 0.9277 (mmm) cc_final: 0.8979 (mmt) REVERT: A 383 SER cc_start: 0.8779 (m) cc_final: 0.8399 (p) REVERT: A 415 THR cc_start: 0.8679 (OUTLIER) cc_final: 0.8276 (p) REVERT: A 695 PHE cc_start: 0.8361 (m-10) cc_final: 0.8067 (m-10) REVERT: A 752 GLN cc_start: 0.9267 (tp-100) cc_final: 0.8943 (tp-100) REVERT: A 795 LEU cc_start: 0.9092 (OUTLIER) cc_final: 0.8850 (tm) REVERT: B 103 LEU cc_start: 0.9111 (tm) cc_final: 0.8831 (tp) REVERT: B 221 PHE cc_start: 0.7960 (OUTLIER) cc_final: 0.7366 (t80) REVERT: B 224 PHE cc_start: 0.8723 (m-80) cc_final: 0.8260 (m-10) REVERT: B 297 MET cc_start: 0.9209 (tpp) cc_final: 0.8957 (mmt) REVERT: B 369 THR cc_start: 0.9379 (OUTLIER) cc_final: 0.9097 (p) REVERT: B 383 SER cc_start: 0.8712 (m) cc_final: 0.8286 (p) REVERT: B 430 MET cc_start: 0.8314 (mtm) cc_final: 0.8100 (mtm) REVERT: B 695 PHE cc_start: 0.8254 (m-10) cc_final: 0.7928 (m-10) REVERT: B 752 GLN cc_start: 0.9293 (tp-100) cc_final: 0.9007 (tp-100) outliers start: 50 outliers final: 18 residues processed: 189 average time/residue: 0.2519 time to fit residues: 55.0804 Evaluate side-chains 151 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 128 time to evaluate : 0.280 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 795 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 379 ILE Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 665 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 93 optimal weight: 2.9990 chunk 17 optimal weight: 0.0770 chunk 115 optimal weight: 0.9980 chunk 85 optimal weight: 1.9990 chunk 122 optimal weight: 6.9990 chunk 20 optimal weight: 0.5980 chunk 128 optimal weight: 0.2980 chunk 10 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 53 optimal weight: 5.9990 chunk 45 optimal weight: 2.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 816 GLN B 143 GLN B 230 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4244 r_free = 0.4244 target = 0.128136 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3637 r_free = 0.3637 target = 0.085108 restraints weight = 26587.742| |-----------------------------------------------------------------------------| r_work (start): 0.3508 rms_B_bonded: 3.14 r_work: 0.3340 rms_B_bonded: 4.00 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7861 moved from start: 0.8233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10997 Z= 0.155 Angle : 0.736 12.502 14932 Z= 0.346 Chirality : 0.045 0.269 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.518 23.335 1482 Min Nonbonded Distance : 2.550 Molprobity Statistics. All-atom Clashscore : 14.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 3.80 % Allowed : 22.82 % Favored : 73.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.92 (0.23), residues: 1343 helix: 1.68 (0.15), residues: 1057 sheet: None (None), residues: 0 loop : -0.11 (0.43), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 825 TYR 0.018 0.001 TYR A 689 PHE 0.022 0.002 PHE A 699 TRP 0.028 0.001 TRP A 460 HIS 0.008 0.001 HIS B 716 Details of bonding type rmsd covalent geometry : bond 0.00343 (10995) covalent geometry : angle 0.73576 (14926) hydrogen bonds : bond 0.04765 ( 852) hydrogen bonds : angle 4.53381 ( 2532) link_NAG-ASN : bond 0.00275 ( 2) link_NAG-ASN : angle 0.94322 ( 6) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 183 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 45 poor density : 138 time to evaluate : 0.304 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8760 (OUTLIER) cc_final: 0.8449 (mtm-85) REVERT: A 221 PHE cc_start: 0.8022 (OUTLIER) cc_final: 0.7334 (t80) REVERT: A 224 PHE cc_start: 0.8733 (m-80) cc_final: 0.8504 (m-10) REVERT: A 297 MET cc_start: 0.9318 (mmm) cc_final: 0.8989 (mmt) REVERT: A 347 MET cc_start: 0.9272 (tmt) cc_final: 0.8935 (tmm) REVERT: A 369 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9042 (p) REVERT: A 383 SER cc_start: 0.8755 (m) cc_final: 0.8391 (p) REVERT: A 695 PHE cc_start: 0.8397 (m-10) cc_final: 0.8117 (m-10) REVERT: A 752 GLN cc_start: 0.9260 (tp-100) cc_final: 0.8880 (tp-100) REVERT: B 221 PHE cc_start: 0.7870 (t80) cc_final: 0.7367 (t80) REVERT: B 352 PHE cc_start: 0.6744 (t80) cc_final: 0.6486 (t80) REVERT: B 369 THR cc_start: 0.9350 (OUTLIER) cc_final: 0.9070 (p) REVERT: B 383 SER cc_start: 0.8742 (m) cc_final: 0.8374 (p) REVERT: B 468 LEU cc_start: 0.9327 (pp) cc_final: 0.9113 (mm) REVERT: B 695 PHE cc_start: 0.8252 (m-10) cc_final: 0.7927 (m-10) outliers start: 45 outliers final: 10 residues processed: 176 average time/residue: 0.2878 time to fit residues: 57.5194 Evaluate side-chains 145 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 131 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 300 LEU Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 665 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 27 optimal weight: 4.9990 chunk 103 optimal weight: 0.8980 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 0.5980 chunk 58 optimal weight: 2.9990 chunk 87 optimal weight: 0.9990 chunk 124 optimal weight: 0.6980 chunk 83 optimal weight: 0.8980 chunk 21 optimal weight: 1.9990 chunk 114 optimal weight: 6.9990 chunk 108 optimal weight: 2.9990 overall best weight: 0.8182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4241 r_free = 0.4241 target = 0.127956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084962 restraints weight = 26368.469| |-----------------------------------------------------------------------------| r_work (start): 0.3496 rms_B_bonded: 3.11 r_work: 0.3328 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7893 moved from start: 0.8470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10997 Z= 0.169 Angle : 0.756 12.439 14932 Z= 0.355 Chirality : 0.045 0.264 1769 Planarity : 0.004 0.042 1822 Dihedral : 4.498 23.958 1482 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 3.04 % Allowed : 23.08 % Favored : 73.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.88 (0.23), residues: 1343 helix: 1.62 (0.16), residues: 1060 sheet: None (None), residues: 0 loop : -0.04 (0.43), residues: 283 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG B 825 TYR 0.018 0.001 TYR B 451 PHE 0.021 0.002 PHE A 699 TRP 0.028 0.001 TRP A 460 HIS 0.007 0.001 HIS B 716 Details of bonding type rmsd covalent geometry : bond 0.00384 (10995) covalent geometry : angle 0.75610 (14926) hydrogen bonds : bond 0.04776 ( 852) hydrogen bonds : angle 4.57063 ( 2532) link_NAG-ASN : bond 0.00219 ( 2) link_NAG-ASN : angle 0.95665 ( 6) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 175 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 139 time to evaluate : 0.440 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8761 (OUTLIER) cc_final: 0.8417 (mtm-85) REVERT: A 221 PHE cc_start: 0.8062 (OUTLIER) cc_final: 0.7335 (t80) REVERT: A 224 PHE cc_start: 0.8753 (m-80) cc_final: 0.8494 (m-10) REVERT: A 297 MET cc_start: 0.9318 (mmm) cc_final: 0.8981 (mmt) REVERT: A 347 MET cc_start: 0.9281 (tmt) cc_final: 0.8931 (tmm) REVERT: A 369 THR cc_start: 0.9362 (OUTLIER) cc_final: 0.9038 (p) REVERT: A 383 SER cc_start: 0.8781 (m) cc_final: 0.8384 (p) REVERT: A 695 PHE cc_start: 0.8332 (m-10) cc_final: 0.8015 (m-10) REVERT: A 752 GLN cc_start: 0.9282 (tp-100) cc_final: 0.8910 (tp-100) REVERT: A 758 HIS cc_start: 0.9222 (m90) cc_final: 0.9021 (m90) REVERT: A 808 ARG cc_start: 0.9270 (mtt90) cc_final: 0.9067 (ttp-110) REVERT: A 830 PHE cc_start: 0.8982 (m-80) cc_final: 0.8759 (t80) REVERT: B 41 ARG cc_start: 0.8744 (OUTLIER) cc_final: 0.8410 (mtm-85) REVERT: B 221 PHE cc_start: 0.8015 (t80) cc_final: 0.7489 (t80) REVERT: B 224 PHE cc_start: 0.8739 (m-80) cc_final: 0.8432 (m-10) REVERT: B 297 MET cc_start: 0.8585 (mmt) cc_final: 0.8215 (ttm) REVERT: B 369 THR cc_start: 0.9246 (OUTLIER) cc_final: 0.9015 (p) REVERT: B 383 SER cc_start: 0.8748 (m) cc_final: 0.8375 (p) REVERT: B 394 LEU cc_start: 0.9408 (OUTLIER) cc_final: 0.9166 (pp) REVERT: B 695 PHE cc_start: 0.8256 (m-10) cc_final: 0.7969 (m-10) REVERT: B 760 ASP cc_start: 0.9142 (m-30) cc_final: 0.8911 (OUTLIER) outliers start: 36 outliers final: 18 residues processed: 171 average time/residue: 0.3039 time to fit residues: 59.0920 Evaluate side-chains 152 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 129 time to evaluate : 0.439 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 394 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 112 optimal weight: 1.9990 chunk 52 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 109 optimal weight: 5.9990 chunk 55 optimal weight: 0.9980 chunk 26 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 107 optimal weight: 5.9990 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 chunk 76 optimal weight: 0.0040 overall best weight: 0.7192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4242 r_free = 0.4242 target = 0.128199 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.085304 restraints weight = 26389.879| |-----------------------------------------------------------------------------| r_work (start): 0.3505 rms_B_bonded: 3.14 r_work: 0.3333 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.8665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10997 Z= 0.164 Angle : 0.784 12.763 14932 Z= 0.364 Chirality : 0.046 0.283 1769 Planarity : 0.004 0.044 1822 Dihedral : 4.470 23.855 1482 Min Nonbonded Distance : 2.530 Molprobity Statistics. All-atom Clashscore : 14.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 3.04 % Allowed : 24.68 % Favored : 72.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.97 (0.23), residues: 1343 helix: 1.67 (0.16), residues: 1061 sheet: None (None), residues: 0 loop : 0.11 (0.43), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 825 TYR 0.018 0.001 TYR B 451 PHE 0.023 0.002 PHE A 699 TRP 0.013 0.001 TRP A 460 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00370 (10995) covalent geometry : angle 0.78432 (14926) hydrogen bonds : bond 0.04739 ( 852) hydrogen bonds : angle 4.59703 ( 2532) link_NAG-ASN : bond 0.00267 ( 2) link_NAG-ASN : angle 0.91743 ( 6) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 176 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 36 poor density : 140 time to evaluate : 0.404 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8753 (OUTLIER) cc_final: 0.8411 (mtm-85) REVERT: A 221 PHE cc_start: 0.8090 (OUTLIER) cc_final: 0.7420 (t80) REVERT: A 224 PHE cc_start: 0.8789 (m-80) cc_final: 0.8515 (m-10) REVERT: A 232 ILE cc_start: 0.8986 (OUTLIER) cc_final: 0.8775 (tp) REVERT: A 297 MET cc_start: 0.9311 (mmm) cc_final: 0.8999 (mmt) REVERT: A 347 MET cc_start: 0.9280 (tmt) cc_final: 0.8943 (tmm) REVERT: A 369 THR cc_start: 0.9370 (OUTLIER) cc_final: 0.9054 (p) REVERT: A 370 MET cc_start: 0.8058 (ptt) cc_final: 0.7760 (ptp) REVERT: A 383 SER cc_start: 0.8771 (m) cc_final: 0.8482 (p) REVERT: A 430 MET cc_start: 0.8444 (mtm) cc_final: 0.8131 (mpt) REVERT: A 695 PHE cc_start: 0.8320 (m-10) cc_final: 0.8044 (m-10) REVERT: A 752 GLN cc_start: 0.9295 (tp-100) cc_final: 0.9007 (tp-100) REVERT: A 758 HIS cc_start: 0.9239 (m90) cc_final: 0.9024 (m90) REVERT: A 830 PHE cc_start: 0.8986 (m-80) cc_final: 0.8781 (t80) REVERT: B 221 PHE cc_start: 0.7996 (t80) cc_final: 0.7496 (t80) REVERT: B 297 MET cc_start: 0.8558 (mmt) cc_final: 0.8172 (ttm) REVERT: B 347 MET cc_start: 0.9248 (tmt) cc_final: 0.8917 (tmm) REVERT: B 369 THR cc_start: 0.9305 (OUTLIER) cc_final: 0.9053 (p) REVERT: B 370 MET cc_start: 0.7717 (ptm) cc_final: 0.7454 (ptm) REVERT: B 383 SER cc_start: 0.8764 (m) cc_final: 0.8391 (p) REVERT: B 695 PHE cc_start: 0.8239 (m-10) cc_final: 0.7901 (m-10) REVERT: B 760 ASP cc_start: 0.9141 (m-30) cc_final: 0.8915 (OUTLIER) outliers start: 36 outliers final: 18 residues processed: 172 average time/residue: 0.3058 time to fit residues: 59.5077 Evaluate side-chains 151 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 129 time to evaluate : 0.408 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 221 PHE Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 423 SER Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 93 optimal weight: 0.7980 chunk 49 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 chunk 55 optimal weight: 10.0000 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 1.9990 chunk 128 optimal weight: 0.8980 chunk 99 optimal weight: 0.6980 chunk 126 optimal weight: 5.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4248 r_free = 0.4248 target = 0.128534 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.085648 restraints weight = 26298.744| |-----------------------------------------------------------------------------| r_work (start): 0.3512 rms_B_bonded: 3.13 r_work: 0.3343 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3343 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.8850 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 10997 Z= 0.162 Angle : 0.802 12.868 14932 Z= 0.373 Chirality : 0.047 0.295 1769 Planarity : 0.004 0.044 1822 Dihedral : 4.501 24.632 1482 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 14.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.28 % Allowed : 25.36 % Favored : 72.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.96 (0.23), residues: 1343 helix: 1.64 (0.16), residues: 1063 sheet: None (None), residues: 0 loop : 0.14 (0.43), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.015 0.000 ARG B 825 TYR 0.018 0.001 TYR B 451 PHE 0.027 0.002 PHE A 699 TRP 0.017 0.001 TRP A 460 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00361 (10995) covalent geometry : angle 0.80190 (14926) hydrogen bonds : bond 0.04704 ( 852) hydrogen bonds : angle 4.57877 ( 2532) link_NAG-ASN : bond 0.00276 ( 2) link_NAG-ASN : angle 0.89015 ( 6) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 163 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 136 time to evaluate : 0.286 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.8378 (mtm-85) REVERT: A 221 PHE cc_start: 0.7976 (t80) cc_final: 0.7372 (t80) REVERT: A 224 PHE cc_start: 0.8787 (m-80) cc_final: 0.8505 (m-10) REVERT: A 232 ILE cc_start: 0.9031 (OUTLIER) cc_final: 0.8829 (tp) REVERT: A 297 MET cc_start: 0.9275 (mmm) cc_final: 0.8955 (mmt) REVERT: A 369 THR cc_start: 0.9323 (OUTLIER) cc_final: 0.9020 (p) REVERT: A 383 SER cc_start: 0.8840 (m) cc_final: 0.8576 (p) REVERT: A 695 PHE cc_start: 0.8218 (m-10) cc_final: 0.7921 (m-10) REVERT: A 752 GLN cc_start: 0.9287 (tp-100) cc_final: 0.9011 (tp-100) REVERT: A 758 HIS cc_start: 0.9285 (m90) cc_final: 0.9084 (m90) REVERT: B 221 PHE cc_start: 0.8001 (t80) cc_final: 0.7524 (t80) REVERT: B 297 MET cc_start: 0.8536 (mmt) cc_final: 0.7990 (mtp) REVERT: B 347 MET cc_start: 0.9240 (tmt) cc_final: 0.8939 (tmm) REVERT: B 369 THR cc_start: 0.9232 (OUTLIER) cc_final: 0.8966 (p) REVERT: B 370 MET cc_start: 0.7716 (ptm) cc_final: 0.7435 (ptm) REVERT: B 383 SER cc_start: 0.8746 (m) cc_final: 0.8330 (p) REVERT: B 695 PHE cc_start: 0.8240 (m-10) cc_final: 0.7978 (m-10) REVERT: B 748 LYS cc_start: 0.9477 (mmmm) cc_final: 0.9260 (mtpt) REVERT: B 760 ASP cc_start: 0.9140 (m-30) cc_final: 0.8925 (OUTLIER) outliers start: 27 outliers final: 20 residues processed: 161 average time/residue: 0.3068 time to fit residues: 55.9925 Evaluate side-chains 147 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 124 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 103 LEU Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 232 ILE Chi-restraints excluded: chain A residue 280 ILE Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 369 THR Chi-restraints excluded: chain B residue 423 SER Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 118 optimal weight: 5.9990 chunk 81 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 chunk 80 optimal weight: 0.0870 chunk 33 optimal weight: 0.6980 chunk 44 optimal weight: 9.9990 chunk 14 optimal weight: 0.0670 chunk 46 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 47 optimal weight: 0.8980 chunk 25 optimal weight: 0.5980 overall best weight: 0.4496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 143 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4254 r_free = 0.4254 target = 0.128510 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3669 r_free = 0.3669 target = 0.086338 restraints weight = 26355.371| |-----------------------------------------------------------------------------| r_work (start): 0.3535 rms_B_bonded: 3.15 r_work: 0.3369 rms_B_bonded: 4.03 restraints_weight: 0.5000 r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.9026 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 10997 Z= 0.154 Angle : 0.825 13.947 14932 Z= 0.381 Chirality : 0.048 0.312 1769 Planarity : 0.004 0.044 1822 Dihedral : 4.527 25.101 1482 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 14.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.86 % Allowed : 26.71 % Favored : 71.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.95 (0.23), residues: 1343 helix: 1.65 (0.16), residues: 1061 sheet: None (None), residues: 0 loop : 0.11 (0.43), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 825 TYR 0.019 0.001 TYR B 451 PHE 0.025 0.002 PHE A 699 TRP 0.013 0.001 TRP A 679 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00337 (10995) covalent geometry : angle 0.82531 (14926) hydrogen bonds : bond 0.04650 ( 852) hydrogen bonds : angle 4.56953 ( 2532) link_NAG-ASN : bond 0.00344 ( 2) link_NAG-ASN : angle 0.83072 ( 6) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2686 Ramachandran restraints generated. 1343 Oldfield, 0 Emsley, 1343 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 144 time to evaluate : 0.414 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 41 ARG cc_start: 0.8725 (OUTLIER) cc_final: 0.8407 (mtm-85) REVERT: A 221 PHE cc_start: 0.7904 (t80) cc_final: 0.7461 (t80) REVERT: A 224 PHE cc_start: 0.8788 (m-80) cc_final: 0.8513 (m-10) REVERT: A 297 MET cc_start: 0.9284 (mmm) cc_final: 0.8951 (mmt) REVERT: A 369 THR cc_start: 0.9230 (OUTLIER) cc_final: 0.8969 (p) REVERT: A 383 SER cc_start: 0.8846 (m) cc_final: 0.8550 (p) REVERT: A 415 THR cc_start: 0.8647 (m) cc_final: 0.8327 (t) REVERT: A 445 LEU cc_start: 0.9511 (pt) cc_final: 0.9244 (OUTLIER) REVERT: A 695 PHE cc_start: 0.8243 (m-10) cc_final: 0.7983 (m-10) REVERT: A 752 GLN cc_start: 0.9313 (tp-100) cc_final: 0.9008 (tp-100) REVERT: A 758 HIS cc_start: 0.9298 (m90) cc_final: 0.8936 (m90) REVERT: B 221 PHE cc_start: 0.7875 (t80) cc_final: 0.7425 (t80) REVERT: B 297 MET cc_start: 0.8537 (mmt) cc_final: 0.8202 (ttm) REVERT: B 347 MET cc_start: 0.9194 (tmt) cc_final: 0.8979 (tmm) REVERT: B 369 THR cc_start: 0.9236 (OUTLIER) cc_final: 0.8981 (p) REVERT: B 383 SER cc_start: 0.8765 (m) cc_final: 0.8307 (p) REVERT: B 695 PHE cc_start: 0.8249 (m-10) cc_final: 0.7914 (m-10) REVERT: B 748 LYS cc_start: 0.9473 (mmmm) cc_final: 0.9264 (mtpt) REVERT: B 760 ASP cc_start: 0.9132 (m-30) cc_final: 0.8927 (OUTLIER) outliers start: 22 outliers final: 17 residues processed: 162 average time/residue: 0.3028 time to fit residues: 55.7753 Evaluate side-chains 149 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 131 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 41 ARG Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 178 MET Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 223 VAL Chi-restraints excluded: chain A residue 282 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 112 SER Chi-restraints excluded: chain B residue 143 GLN Chi-restraints excluded: chain B residue 179 MET Chi-restraints excluded: chain B residue 215 LEU Chi-restraints excluded: chain B residue 223 VAL Chi-restraints excluded: chain B residue 369 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 88 optimal weight: 1.9990 chunk 19 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 113 optimal weight: 0.9980 chunk 16 optimal weight: 0.0170 chunk 61 optimal weight: 6.9990 chunk 55 optimal weight: 8.9990 chunk 31 optimal weight: 3.9990 chunk 86 optimal weight: 1.9990 chunk 75 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 overall best weight: 0.7622 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4238 r_free = 0.4238 target = 0.127737 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.085000 restraints weight = 26398.790| |-----------------------------------------------------------------------------| r_work (start): 0.3513 rms_B_bonded: 3.16 r_work: 0.3340 rms_B_bonded: 4.05 restraints_weight: 0.5000 r_work (final): 0.3340 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7899 moved from start: 0.9190 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.050 10997 Z= 0.169 Angle : 0.842 14.052 14932 Z= 0.390 Chirality : 0.047 0.304 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.524 25.768 1482 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 1.86 % Allowed : 26.88 % Favored : 71.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % 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: 2.00 (0.23), residues: 1343 helix: 1.70 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : 0.05 (0.42), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 825 TYR 0.019 0.001 TYR B 451 PHE 0.030 0.002 PHE A 699 TRP 0.021 0.001 TRP A 679 HIS 0.005 0.001 HIS B 505 Details of bonding type rmsd covalent geometry : bond 0.00384 (10995) covalent geometry : angle 0.84224 (14926) hydrogen bonds : bond 0.04658 ( 852) hydrogen bonds : angle 4.57806 ( 2532) link_NAG-ASN : bond 0.00227 ( 2) link_NAG-ASN : angle 0.90188 ( 6) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3846.07 seconds wall clock time: 66 minutes 18.97 seconds (3978.97 seconds total)