Starting phenix.real_space_refine on Mon Jun 9 16:52:30 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8u54_41912/06_2025/8u54_41912.cif Found real_map, /net/cci-nas-00/data/ceres_data/8u54_41912/06_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_41912/06_2025/8u54_41912.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8u54_41912/06_2025/8u54_41912.map" model { file = "/net/cci-nas-00/data/ceres_data/8u54_41912/06_2025/8u54_41912.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8u54_41912/06_2025/8u54_41912.cif" } resolution = 2.65 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.028 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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/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: 7.09, per 1000 atoms: 0.66 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: 2.68 Conformation dependent library (CDL) restraints added in 1.5 seconds 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: 0.92 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: 3.17 Time building geometry restraints manager: 3.17 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 834 or resid 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: 1.640 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.440 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 26.670 Find NCS groups from input model: 0.560 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.290 ------------------------------------------------------------------------------- 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (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 TRP 0.015 0.002 TRP B 396 HIS 0.011 0.002 HIS B 310 PHE 0.031 0.004 PHE A 711 TYR 0.033 0.003 TYR B 320 ARG 0.003 0.001 ARG B 808 Details of bonding type rmsd link_NAG-ASN : bond 0.00878 ( 2) link_NAG-ASN : angle 4.56490 ( 6) hydrogen bonds : bond 0.10250 ( 852) hydrogen bonds : angle 6.03352 ( 2532) covalent geometry : bond 0.00632 (10995) covalent geometry : angle 0.78908 (14926) *********************** 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 : 1.101 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: 0.7087 time to fit residues: 310.5347 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 : 0.939 ------------------------------------------------------------------------------- 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 113 optimal weight: 7.9990 chunk 102 optimal weight: 0.9990 chunk 56 optimal weight: 0.7980 chunk 34 optimal weight: 0.9990 chunk 69 optimal weight: 0.5980 chunk 54 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 40 optimal weight: 9.9990 chunk 64 optimal weight: 5.9990 chunk 78 optimal weight: 0.9990 chunk 122 optimal weight: 3.9990 overall best weight: 0.8786 ------------------------------------------------------------------------------- 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 337 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 672 ASN ** 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 = 0.4199 r_free = 0.4199 target = 0.126006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.084722 restraints weight = 25620.402| |-----------------------------------------------------------------------------| r_work (start): 0.3503 rms_B_bonded: 2.98 r_work: 0.3335 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.3335 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7584 moved from start: 0.4371 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 10997 Z= 0.216 Angle : 0.818 14.247 14932 Z= 0.402 Chirality : 0.047 0.222 1769 Planarity : 0.005 0.052 1822 Dihedral : 5.311 46.551 1492 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 15.21 Ramachandran Plot: Outliers : 0.15 % Allowed : 1.94 % Favored : 97.92 % Rotamer: Outliers : 5.83 % Allowed : 15.72 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.76 (0.23), residues: 1343 helix: 0.81 (0.15), residues: 1054 sheet: None (None), residues: 0 loop : -0.28 (0.42), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 489 HIS 0.009 0.002 HIS B 505 PHE 0.021 0.002 PHE A 50 TYR 0.025 0.002 TYR A 689 ARG 0.008 0.001 ARG A 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00375 ( 2) link_NAG-ASN : angle 1.83142 ( 6) hydrogen bonds : bond 0.05688 ( 852) hydrogen bonds : angle 5.09730 ( 2532) covalent geometry : bond 0.00485 (10995) covalent geometry : angle 0.81709 (14926) *********************** 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 276 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 69 poor density : 207 time to evaluate : 1.147 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: A 41 ARG cc_start: 0.8300 (OUTLIER) cc_final: 0.7776 (mmm-85) REVERT: A 198 ASN cc_start: 0.9026 (m110) cc_final: 0.8814 (p0) REVERT: A 278 VAL cc_start: 0.8700 (t) cc_final: 0.8392 (p) REVERT: A 297 MET cc_start: 0.9076 (mmm) cc_final: 0.8790 (mmm) REVERT: A 301 LEU cc_start: 0.8817 (OUTLIER) cc_final: 0.8574 (tp) REVERT: A 316 TYR cc_start: 0.8589 (t80) cc_final: 0.8347 (t80) REVERT: A 667 ILE cc_start: 0.9165 (mt) cc_final: 0.8920 (mm) REVERT: A 752 GLN cc_start: 0.9106 (tp-100) cc_final: 0.8721 (tp-100) REVERT: B 41 ARG cc_start: 0.8263 (OUTLIER) cc_final: 0.7813 (mmm-85) REVERT: B 278 VAL cc_start: 0.8740 (t) cc_final: 0.8457 (p) REVERT: B 288 LEU cc_start: 0.8802 (OUTLIER) cc_final: 0.8576 (tp) REVERT: B 293 LEU cc_start: 0.8859 (OUTLIER) cc_final: 0.8622 (tp) REVERT: B 301 LEU cc_start: 0.8835 (OUTLIER) cc_final: 0.8556 (tp) REVERT: B 316 TYR cc_start: 0.8705 (t80) cc_final: 0.8403 (t80) REVERT: B 460 TRP cc_start: 0.8933 (m100) cc_final: 0.8711 (m100) REVERT: B 512 SER cc_start: 0.9134 (p) cc_final: 0.8885 (p) REVERT: B 521 MET cc_start: 0.9483 (OUTLIER) cc_final: 0.9253 (tpp) REVERT: B 667 ILE cc_start: 0.9140 (mt) cc_final: 0.8884 (mm) REVERT: B 752 GLN cc_start: 0.9139 (tp-100) cc_final: 0.8757 (tp-100) outliers start: 69 outliers final: 19 residues processed: 250 average time/residue: 0.8607 time to fit residues: 245.3926 Evaluate side-chains 192 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 166 time to evaluate : 1.645 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain A residue 292 LEU Chi-restraints excluded: chain A residue 293 LEU Chi-restraints excluded: chain A residue 300 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 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 288 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 293 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 Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 37 optimal weight: 6.9990 chunk 6 optimal weight: 0.9980 chunk 16 optimal weight: 0.0870 chunk 48 optimal weight: 0.8980 chunk 22 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 131 optimal weight: 8.9990 chunk 44 optimal weight: 4.9990 chunk 133 optimal weight: 6.9990 chunk 4 optimal weight: 0.6980 chunk 70 optimal weight: 1.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4226 r_free = 0.4226 target = 0.126988 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3653 r_free = 0.3653 target = 0.086037 restraints weight = 26310.364| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.03 r_work: 0.3352 rms_B_bonded: 3.93 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7740 moved from start: 0.5853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.061 10997 Z= 0.171 Angle : 0.716 10.275 14932 Z= 0.349 Chirality : 0.043 0.151 1769 Planarity : 0.004 0.049 1822 Dihedral : 4.626 17.770 1482 Min Nonbonded Distance : 2.522 Molprobity Statistics. All-atom Clashscore : 13.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.49 % Allowed : 18.01 % Favored : 76.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.54 (0.23), residues: 1343 helix: 1.37 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -0.11 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP A 460 HIS 0.008 0.002 HIS B 505 PHE 0.018 0.002 PHE A 221 TYR 0.025 0.002 TYR A 689 ARG 0.005 0.001 ARG A 213 Details of bonding type rmsd link_NAG-ASN : bond 0.00104 ( 2) link_NAG-ASN : angle 1.43801 ( 6) hydrogen bonds : bond 0.04997 ( 852) hydrogen bonds : angle 4.78636 ( 2532) covalent geometry : bond 0.00380 (10995) covalent geometry : angle 0.71517 (14926) *********************** 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 246 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 65 poor density : 181 time to evaluate : 1.227 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 224 PHE cc_start: 0.8314 (m-80) cc_final: 0.8021 (m-10) REVERT: A 290 LEU cc_start: 0.9287 (OUTLIER) cc_final: 0.8998 (tp) REVERT: A 297 MET cc_start: 0.9197 (mmm) cc_final: 0.8863 (mmt) REVERT: A 301 LEU cc_start: 0.8967 (OUTLIER) cc_final: 0.8760 (tp) REVERT: A 430 MET cc_start: 0.8218 (mtm) cc_final: 0.7921 (mpp) REVERT: A 540 MET cc_start: 0.8404 (tpp) cc_final: 0.8165 (tpp) REVERT: A 695 PHE cc_start: 0.8331 (m-80) cc_final: 0.8038 (m-80) REVERT: A 752 GLN cc_start: 0.9250 (tp-100) cc_final: 0.8985 (tp-100) REVERT: B 198 ASN cc_start: 0.9080 (m-40) cc_final: 0.8790 (p0) REVERT: B 221 PHE cc_start: 0.8186 (OUTLIER) cc_final: 0.6980 (t80) REVERT: B 224 PHE cc_start: 0.8269 (m-80) cc_final: 0.8040 (m-80) REVERT: B 288 LEU cc_start: 0.8827 (tm) cc_final: 0.8527 (tt) REVERT: B 290 LEU cc_start: 0.9174 (OUTLIER) cc_final: 0.8881 (tp) REVERT: B 301 LEU cc_start: 0.9010 (OUTLIER) cc_final: 0.8749 (tp) REVERT: B 430 MET cc_start: 0.7948 (mtm) cc_final: 0.7574 (mpp) REVERT: B 489 TRP cc_start: 0.7176 (m100) cc_final: 0.6505 (m-10) REVERT: B 695 PHE cc_start: 0.8094 (m-80) cc_final: 0.7822 (m-80) REVERT: B 705 PHE cc_start: 0.8183 (m-80) cc_final: 0.7978 (m-80) REVERT: B 752 GLN cc_start: 0.9247 (tp-100) cc_final: 0.8985 (tp-100) outliers start: 65 outliers final: 17 residues processed: 222 average time/residue: 0.7384 time to fit residues: 188.1988 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 : 1.361 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 91 VAL Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 215 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 LEU 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 91 VAL Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 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 301 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 665 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 48 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 71 optimal weight: 0.0980 chunk 36 optimal weight: 0.7980 chunk 69 optimal weight: 1.9990 chunk 116 optimal weight: 3.9990 chunk 108 optimal weight: 0.9990 chunk 26 optimal weight: 2.9990 chunk 70 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 52 optimal weight: 3.9990 overall best weight: 0.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 198 ASN B 380 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4234 r_free = 0.4234 target = 0.127506 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3640 r_free = 0.3640 target = 0.085258 restraints weight = 26044.656| |-----------------------------------------------------------------------------| r_work (start): 0.3526 rms_B_bonded: 3.06 r_work: 0.3352 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.3352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7867 moved from start: 0.6609 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10997 Z= 0.162 Angle : 0.706 11.812 14932 Z= 0.337 Chirality : 0.044 0.308 1769 Planarity : 0.004 0.045 1822 Dihedral : 4.527 17.156 1482 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 4.40 % Allowed : 18.68 % Favored : 76.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.85 (0.23), residues: 1343 helix: 1.64 (0.15), residues: 1059 sheet: None (None), residues: 0 loop : -0.18 (0.43), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.002 TRP A 460 HIS 0.007 0.001 HIS B 505 PHE 0.019 0.002 PHE B 699 TYR 0.022 0.002 TYR A 689 ARG 0.003 0.000 ARG B 825 Details of bonding type rmsd link_NAG-ASN : bond 0.00240 ( 2) link_NAG-ASN : angle 1.13089 ( 6) hydrogen bonds : bond 0.04841 ( 852) hydrogen bonds : angle 4.62298 ( 2532) covalent geometry : bond 0.00356 (10995) covalent geometry : angle 0.70619 (14926) *********************** 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 208 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 52 poor density : 156 time to evaluate : 1.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 178 MET cc_start: 0.9234 (mtt) cc_final: 0.8998 (mpp) REVERT: A 281 LEU cc_start: 0.9364 (OUTLIER) cc_final: 0.9110 (mt) REVERT: A 290 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9016 (tp) REVERT: A 297 MET cc_start: 0.9256 (mmm) cc_final: 0.8905 (mmt) REVERT: A 301 LEU cc_start: 0.9080 (OUTLIER) cc_final: 0.8821 (OUTLIER) REVERT: A 695 PHE cc_start: 0.8380 (m-10) cc_final: 0.8101 (m-80) REVERT: A 705 PHE cc_start: 0.8254 (m-80) cc_final: 0.8024 (m-10) REVERT: A 748 LYS cc_start: 0.9531 (mmmt) cc_final: 0.9317 (mmmm) REVERT: A 752 GLN cc_start: 0.9266 (tp-100) cc_final: 0.8978 (tp-100) REVERT: B 221 PHE cc_start: 0.8089 (OUTLIER) cc_final: 0.7078 (t80) REVERT: B 281 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9123 (mt) REVERT: B 288 LEU cc_start: 0.8807 (tm) cc_final: 0.8571 (tt) REVERT: B 290 LEU cc_start: 0.9194 (OUTLIER) cc_final: 0.8955 (tp) REVERT: B 301 LEU cc_start: 0.9083 (OUTLIER) cc_final: 0.8873 (tp) REVERT: B 370 MET cc_start: 0.6738 (ptm) cc_final: 0.6411 (ptm) REVERT: B 430 MET cc_start: 0.8218 (mtm) cc_final: 0.7923 (mpp) REVERT: B 460 TRP cc_start: 0.8778 (m100) cc_final: 0.8557 (m100) REVERT: B 695 PHE cc_start: 0.8202 (m-80) cc_final: 0.8000 (m-80) REVERT: B 705 PHE cc_start: 0.8323 (m-80) cc_final: 0.8079 (m-10) REVERT: B 752 GLN cc_start: 0.9279 (tp-100) cc_final: 0.9008 (tp-100) outliers start: 52 outliers final: 16 residues processed: 198 average time/residue: 0.7080 time to fit residues: 159.5372 Evaluate side-chains 155 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 133 time to evaluate : 1.221 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 279 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 78 SER 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 281 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 301 LEU Chi-restraints excluded: chain B residue 423 SER Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 123 optimal weight: 0.6980 chunk 90 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 16 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 61 optimal weight: 8.9990 chunk 68 optimal weight: 0.3980 chunk 81 optimal weight: 0.5980 chunk 58 optimal weight: 3.9990 chunk 20 optimal weight: 1.9990 chunk 133 optimal weight: 4.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 230 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** 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 = 0.4235 r_free = 0.4235 target = 0.127141 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3633 r_free = 0.3633 target = 0.084393 restraints weight = 26205.719| |-----------------------------------------------------------------------------| r_work (start): 0.3511 rms_B_bonded: 3.08 r_work: 0.3337 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.3337 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7926 moved from start: 0.7294 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= 0.171 Angle : 0.704 12.446 14932 Z= 0.338 Chirality : 0.044 0.249 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.476 17.960 1482 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 14.15 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.94 (0.23), residues: 1343 helix: 1.69 (0.16), residues: 1064 sheet: None (None), residues: 0 loop : -0.11 (0.44), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 460 HIS 0.006 0.001 HIS B 505 PHE 0.017 0.002 PHE A 699 TYR 0.021 0.002 TYR A 689 ARG 0.003 0.000 ARG B 759 Details of bonding type rmsd link_NAG-ASN : bond 0.00205 ( 2) link_NAG-ASN : angle 1.09517 ( 6) hydrogen bonds : bond 0.04811 ( 852) hydrogen bonds : angle 4.51897 ( 2532) covalent geometry : bond 0.00384 (10995) covalent geometry : angle 0.70333 (14926) *********************** 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 201 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 60 poor density : 141 time to evaluate : 1.252 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9263 (OUTLIER) cc_final: 0.9024 (mt) REVERT: A 281 LEU cc_start: 0.9382 (OUTLIER) cc_final: 0.9128 (mt) REVERT: A 290 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9138 (tp) REVERT: A 297 MET cc_start: 0.9264 (mmm) cc_final: 0.8873 (mmt) REVERT: A 415 THR cc_start: 0.8539 (OUTLIER) cc_final: 0.8095 (p) REVERT: A 540 MET cc_start: 0.8375 (tpp) cc_final: 0.8130 (tpp) REVERT: A 695 PHE cc_start: 0.8427 (m-10) cc_final: 0.8150 (m-10) REVERT: A 752 GLN cc_start: 0.9295 (tp-100) cc_final: 0.9001 (tp-100) REVERT: B 221 PHE cc_start: 0.8124 (OUTLIER) cc_final: 0.7136 (t80) REVERT: B 281 LEU cc_start: 0.9387 (OUTLIER) cc_final: 0.9157 (mt) REVERT: B 288 LEU cc_start: 0.8762 (tm) cc_final: 0.8533 (tt) REVERT: B 290 LEU cc_start: 0.9311 (OUTLIER) cc_final: 0.9058 (tp) REVERT: B 297 MET cc_start: 0.9186 (tpp) cc_final: 0.8963 (mmt) REVERT: B 370 MET cc_start: 0.7201 (ptm) cc_final: 0.6961 (ptm) REVERT: B 430 MET cc_start: 0.8253 (mtm) cc_final: 0.7963 (mpp) REVERT: B 695 PHE cc_start: 0.8390 (m-10) cc_final: 0.8155 (m-10) REVERT: B 752 GLN cc_start: 0.9305 (tp-100) cc_final: 0.9009 (tp-100) outliers start: 60 outliers final: 22 residues processed: 191 average time/residue: 0.7344 time to fit residues: 161.5200 Evaluate side-chains 153 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 29 poor density : 124 time to evaluate : 1.089 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 209 LEU Chi-restraints excluded: chain A residue 211 LEU Chi-restraints excluded: chain A residue 212 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 461 THR Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 103 LEU Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 393 SER Chi-restraints excluded: chain B residue 423 SER Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 61 optimal weight: 0.4980 chunk 131 optimal weight: 8.9990 chunk 110 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 62 optimal weight: 0.9980 chunk 76 optimal weight: 0.6980 chunk 96 optimal weight: 0.0770 chunk 111 optimal weight: 10.0000 chunk 86 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 116 optimal weight: 1.9990 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 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4252 r_free = 0.4252 target = 0.128469 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3658 r_free = 0.3658 target = 0.086122 restraints weight = 26502.902| |-----------------------------------------------------------------------------| r_work (start): 0.3527 rms_B_bonded: 3.10 r_work: 0.3361 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.7705 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 10997 Z= 0.152 Angle : 0.715 12.611 14932 Z= 0.339 Chirality : 0.044 0.244 1769 Planarity : 0.004 0.041 1822 Dihedral : 4.468 21.450 1482 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 14.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.86 % Favored : 98.14 % Rotamer: Outliers : 3.80 % Allowed : 20.46 % Favored : 75.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.23), residues: 1343 helix: 1.74 (0.16), residues: 1065 sheet: None (None), residues: 0 loop : -0.09 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.002 TRP B 460 HIS 0.006 0.001 HIS B 505 PHE 0.020 0.002 PHE A 699 TYR 0.018 0.001 TYR A 689 ARG 0.003 0.000 ARG B 825 Details of bonding type rmsd link_NAG-ASN : bond 0.00311 ( 2) link_NAG-ASN : angle 0.98574 ( 6) hydrogen bonds : bond 0.04680 ( 852) hydrogen bonds : angle 4.44304 ( 2532) covalent geometry : bond 0.00334 (10995) covalent geometry : angle 0.71505 (14926) *********************** 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 : 1.436 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7922 (t80) cc_final: 0.7268 (t80) REVERT: A 281 LEU cc_start: 0.9365 (OUTLIER) cc_final: 0.9123 (mt) REVERT: A 290 LEU cc_start: 0.9329 (OUTLIER) cc_final: 0.9090 (tp) REVERT: A 297 MET cc_start: 0.9192 (mmm) cc_final: 0.8873 (mmt) REVERT: A 301 LEU cc_start: 0.9131 (OUTLIER) cc_final: 0.8827 (tp) REVERT: A 369 THR cc_start: 0.9403 (OUTLIER) cc_final: 0.9033 (p) REVERT: A 430 MET cc_start: 0.8409 (mtm) cc_final: 0.8195 (mpp) REVERT: A 540 MET cc_start: 0.8447 (tpp) cc_final: 0.8203 (tpp) REVERT: A 695 PHE cc_start: 0.8421 (m-10) cc_final: 0.8119 (m-10) REVERT: A 752 GLN cc_start: 0.9271 (tp-100) cc_final: 0.8963 (tp-100) REVERT: B 103 LEU cc_start: 0.9221 (mt) cc_final: 0.8809 (tp) REVERT: B 221 PHE cc_start: 0.7994 (OUTLIER) cc_final: 0.7158 (t80) REVERT: B 281 LEU cc_start: 0.9413 (OUTLIER) cc_final: 0.9201 (mt) REVERT: B 290 LEU cc_start: 0.9305 (OUTLIER) cc_final: 0.9041 (tp) REVERT: B 297 MET cc_start: 0.9201 (tpp) cc_final: 0.8953 (mmt) REVERT: B 352 PHE cc_start: 0.6796 (t80) cc_final: 0.6502 (t80) REVERT: B 370 MET cc_start: 0.7335 (ptm) cc_final: 0.7093 (ptm) REVERT: B 521 MET cc_start: 0.9440 (ttm) cc_final: 0.9016 (ptm) REVERT: B 695 PHE cc_start: 0.8344 (m-10) cc_final: 0.8087 (m-10) REVERT: B 752 GLN cc_start: 0.9305 (tp-100) cc_final: 0.9011 (tp-100) outliers start: 45 outliers final: 11 residues processed: 173 average time/residue: 0.9235 time to fit residues: 186.1770 Evaluate side-chains 145 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 127 time to evaluate : 1.149 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 423 SER Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 7 optimal weight: 0.8980 chunk 64 optimal weight: 3.9990 chunk 119 optimal weight: 0.9990 chunk 115 optimal weight: 2.9990 chunk 86 optimal weight: 0.7980 chunk 123 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 33 optimal weight: 0.8980 chunk 44 optimal weight: 7.9990 chunk 45 optimal weight: 2.9990 chunk 88 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** 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 = 0.4248 r_free = 0.4248 target = 0.127975 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3634 r_free = 0.3634 target = 0.084893 restraints weight = 26569.053| |-----------------------------------------------------------------------------| r_work (start): 0.3499 rms_B_bonded: 3.12 r_work: 0.3333 rms_B_bonded: 3.98 restraints_weight: 0.5000 r_work (final): 0.3333 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7876 moved from start: 0.8039 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= 0.167 Angle : 0.738 13.075 14932 Z= 0.347 Chirality : 0.045 0.236 1769 Planarity : 0.004 0.040 1822 Dihedral : 4.433 23.095 1482 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.21 % Allowed : 22.23 % Favored : 74.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.02 (0.23), residues: 1343 helix: 1.73 (0.16), residues: 1066 sheet: None (None), residues: 0 loop : -0.08 (0.44), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.002 TRP B 460 HIS 0.005 0.001 HIS B 505 PHE 0.020 0.002 PHE A 699 TYR 0.019 0.001 TYR B 451 ARG 0.003 0.000 ARG B 825 Details of bonding type rmsd link_NAG-ASN : bond 0.00202 ( 2) link_NAG-ASN : angle 1.01648 ( 6) hydrogen bonds : bond 0.04671 ( 852) hydrogen bonds : angle 4.48199 ( 2532) covalent geometry : bond 0.00377 (10995) covalent geometry : angle 0.73801 (14926) *********************** 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 177 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 139 time to evaluate : 1.635 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8208 (m-10) cc_final: 0.7968 (m-10) REVERT: A 221 PHE cc_start: 0.7907 (t80) cc_final: 0.7307 (t80) REVERT: A 281 LEU cc_start: 0.9342 (OUTLIER) cc_final: 0.9120 (mt) REVERT: A 290 LEU cc_start: 0.9331 (OUTLIER) cc_final: 0.9086 (tp) REVERT: A 297 MET cc_start: 0.9236 (mmm) cc_final: 0.8854 (mmt) REVERT: A 369 THR cc_start: 0.9439 (OUTLIER) cc_final: 0.9081 (p) REVERT: A 383 SER cc_start: 0.8765 (m) cc_final: 0.8389 (p) REVERT: A 695 PHE cc_start: 0.8393 (m-10) cc_final: 0.8070 (m-10) REVERT: A 752 GLN cc_start: 0.9271 (tp-100) cc_final: 0.8890 (tp-100) REVERT: B 103 LEU cc_start: 0.9197 (mt) cc_final: 0.8923 (tp) REVERT: B 221 PHE cc_start: 0.7999 (t80) cc_final: 0.7214 (t80) REVERT: B 281 LEU cc_start: 0.9343 (OUTLIER) cc_final: 0.9140 (mt) REVERT: B 290 LEU cc_start: 0.9317 (OUTLIER) cc_final: 0.9060 (tp) REVERT: B 297 MET cc_start: 0.9256 (tpp) cc_final: 0.9042 (mmt) REVERT: B 370 MET cc_start: 0.7397 (ptm) cc_final: 0.7188 (ptm) REVERT: B 383 SER cc_start: 0.8626 (m) cc_final: 0.8253 (p) REVERT: B 394 LEU cc_start: 0.9393 (mt) cc_final: 0.9169 (pp) REVERT: B 695 PHE cc_start: 0.8332 (m-10) cc_final: 0.8019 (m-10) REVERT: B 752 GLN cc_start: 0.9346 (tp-100) cc_final: 0.9073 (tp-100) outliers start: 38 outliers final: 15 residues processed: 170 average time/residue: 0.7050 time to fit residues: 138.1397 Evaluate side-chains 153 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 133 time to evaluate : 1.436 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER 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 271 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 388 ILE Chi-restraints excluded: chain B residue 461 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 50 optimal weight: 8.9990 chunk 124 optimal weight: 0.5980 chunk 109 optimal weight: 0.9980 chunk 111 optimal weight: 3.9990 chunk 25 optimal weight: 0.8980 chunk 89 optimal weight: 0.5980 chunk 130 optimal weight: 5.9990 chunk 4 optimal weight: 0.6980 chunk 131 optimal weight: 4.9990 chunk 114 optimal weight: 10.0000 chunk 63 optimal weight: 9.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 412 HIS ** 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 = 0.4248 r_free = 0.4248 target = 0.128502 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.086137 restraints weight = 26352.853| |-----------------------------------------------------------------------------| r_work (start): 0.3518 rms_B_bonded: 3.05 r_work: 0.3350 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3350 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7934 moved from start: 0.8336 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= 0.162 Angle : 0.762 12.783 14932 Z= 0.356 Chirality : 0.045 0.287 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.454 22.906 1482 Min Nonbonded Distance : 2.548 Molprobity Statistics. All-atom Clashscore : 14.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.54 % Allowed : 23.08 % Favored : 74.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.23), residues: 1343 helix: 1.71 (0.16), residues: 1065 sheet: None (None), residues: 0 loop : -0.04 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.001 TRP B 460 HIS 0.005 0.001 HIS B 505 PHE 0.024 0.002 PHE A 699 TYR 0.018 0.001 TYR B 451 ARG 0.003 0.000 ARG B 825 Details of bonding type rmsd link_NAG-ASN : bond 0.00250 ( 2) link_NAG-ASN : angle 0.97728 ( 6) hydrogen bonds : bond 0.04674 ( 852) hydrogen bonds : angle 4.54794 ( 2532) covalent geometry : bond 0.00364 (10995) covalent geometry : angle 0.76192 (14926) *********************** 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 165 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 135 time to evaluate : 1.115 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 95 PHE cc_start: 0.8211 (m-10) cc_final: 0.7956 (m-10) REVERT: A 221 PHE cc_start: 0.7926 (t80) cc_final: 0.7324 (t80) REVERT: A 281 LEU cc_start: 0.9367 (OUTLIER) cc_final: 0.9164 (mt) REVERT: A 290 LEU cc_start: 0.9337 (OUTLIER) cc_final: 0.9105 (tp) REVERT: A 297 MET cc_start: 0.9248 (mmm) cc_final: 0.8889 (mmt) REVERT: A 369 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9052 (p) REVERT: A 383 SER cc_start: 0.8722 (m) cc_final: 0.8391 (p) REVERT: A 521 MET cc_start: 0.9202 (OUTLIER) cc_final: 0.8875 (ptt) REVERT: A 695 PHE cc_start: 0.8370 (m-10) cc_final: 0.8094 (m-10) REVERT: A 752 GLN cc_start: 0.9280 (tp-100) cc_final: 0.8980 (tp-100) REVERT: B 103 LEU cc_start: 0.9200 (mt) cc_final: 0.8971 (tp) REVERT: B 221 PHE cc_start: 0.8050 (t80) cc_final: 0.7413 (t80) REVERT: B 224 PHE cc_start: 0.8549 (m-80) cc_final: 0.8234 (m-10) REVERT: B 290 LEU cc_start: 0.9344 (OUTLIER) cc_final: 0.9092 (tp) REVERT: B 297 MET cc_start: 0.9200 (tpp) cc_final: 0.8937 (mmt) REVERT: B 383 SER cc_start: 0.8666 (m) cc_final: 0.8256 (p) REVERT: B 394 LEU cc_start: 0.9395 (mt) cc_final: 0.9174 (pp) REVERT: B 695 PHE cc_start: 0.8306 (m-10) cc_final: 0.8033 (m-10) outliers start: 30 outliers final: 11 residues processed: 158 average time/residue: 0.7087 time to fit residues: 127.0542 Evaluate side-chains 140 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 124 time to evaluate : 1.087 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 281 LEU Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 521 MET Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 212 LEU Chi-restraints excluded: chain B residue 290 LEU 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 77 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 102 optimal weight: 0.9980 chunk 4 optimal weight: 1.9990 chunk 85 optimal weight: 0.9980 chunk 41 optimal weight: 0.8980 chunk 13 optimal weight: 0.6980 chunk 74 optimal weight: 0.7980 chunk 23 optimal weight: 0.8980 chunk 116 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4247 r_free = 0.4247 target = 0.128482 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3645 r_free = 0.3645 target = 0.085940 restraints weight = 26366.268| |-----------------------------------------------------------------------------| r_work (start): 0.3504 rms_B_bonded: 3.05 r_work: 0.3332 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3332 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7891 moved from start: 0.8596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10997 Z= 0.169 Angle : 0.775 12.945 14932 Z= 0.364 Chirality : 0.046 0.292 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.440 23.872 1482 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.03 % Allowed : 24.26 % Favored : 73.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.97 (0.23), residues: 1343 helix: 1.66 (0.16), residues: 1070 sheet: None (None), residues: 0 loop : 0.10 (0.44), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP B 460 HIS 0.005 0.001 HIS B 505 PHE 0.027 0.002 PHE A 699 TYR 0.019 0.001 TYR B 451 ARG 0.007 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00222 ( 2) link_NAG-ASN : angle 0.95989 ( 6) hydrogen bonds : bond 0.04686 ( 852) hydrogen bonds : angle 4.56106 ( 2532) covalent geometry : bond 0.00379 (10995) covalent geometry : angle 0.77466 (14926) *********************** 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 155 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 131 time to evaluate : 1.792 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 103 LEU cc_start: 0.9142 (mt) cc_final: 0.8913 (tp) REVERT: A 221 PHE cc_start: 0.8039 (t80) cc_final: 0.7462 (t80) REVERT: A 290 LEU cc_start: 0.9319 (OUTLIER) cc_final: 0.9105 (tp) REVERT: A 297 MET cc_start: 0.9273 (mmm) cc_final: 0.8908 (mmt) REVERT: A 369 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9059 (p) REVERT: A 383 SER cc_start: 0.8705 (m) cc_final: 0.8362 (p) REVERT: A 430 MET cc_start: 0.8398 (mtm) cc_final: 0.8055 (mpt) REVERT: A 695 PHE cc_start: 0.8325 (m-10) cc_final: 0.8011 (m-10) REVERT: A 752 GLN cc_start: 0.9291 (tp-100) cc_final: 0.8993 (tp-100) REVERT: B 221 PHE cc_start: 0.8083 (t80) cc_final: 0.7476 (t80) REVERT: B 290 LEU cc_start: 0.9334 (OUTLIER) cc_final: 0.9092 (tp) REVERT: B 297 MET cc_start: 0.9261 (tpp) cc_final: 0.9025 (mmt) REVERT: B 383 SER cc_start: 0.8661 (m) cc_final: 0.8248 (p) REVERT: B 394 LEU cc_start: 0.9417 (mt) cc_final: 0.9166 (pp) REVERT: B 430 MET cc_start: 0.8452 (mtm) cc_final: 0.7990 (mpt) REVERT: B 680 LEU cc_start: 0.8997 (mt) cc_final: 0.8787 (mt) REVERT: B 695 PHE cc_start: 0.8190 (m-10) cc_final: 0.7959 (m-10) REVERT: B 760 ASP cc_start: 0.9086 (m-30) cc_final: 0.8761 (p0) outliers start: 24 outliers final: 12 residues processed: 152 average time/residue: 0.9276 time to fit residues: 160.8522 Evaluate side-chains 138 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 123 time to evaluate : 1.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER 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 284 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 290 LEU 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 74 optimal weight: 0.9990 chunk 47 optimal weight: 9.9990 chunk 4 optimal weight: 1.9990 chunk 108 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 89 optimal weight: 0.6980 chunk 59 optimal weight: 3.9990 chunk 50 optimal weight: 4.9990 chunk 90 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 1.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4226 r_free = 0.4226 target = 0.127360 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3612 r_free = 0.3612 target = 0.084320 restraints weight = 26546.559| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 3.06 r_work: 0.3304 rms_B_bonded: 3.97 restraints_weight: 0.5000 r_work (final): 0.3304 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7910 moved from start: 0.8876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 10997 Z= 0.191 Angle : 0.812 12.912 14932 Z= 0.381 Chirality : 0.047 0.306 1769 Planarity : 0.004 0.042 1822 Dihedral : 4.527 23.010 1482 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 14.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.38 % Favored : 97.62 % Rotamer: Outliers : 1.78 % Allowed : 24.68 % Favored : 73.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.92 (0.23), residues: 1343 helix: 1.59 (0.16), residues: 1069 sheet: None (None), residues: 0 loop : 0.20 (0.45), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 460 HIS 0.005 0.001 HIS B 505 PHE 0.025 0.002 PHE B 699 TYR 0.017 0.002 TYR B 451 ARG 0.007 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00139 ( 2) link_NAG-ASN : angle 1.00737 ( 6) hydrogen bonds : bond 0.04805 ( 852) hydrogen bonds : angle 4.62869 ( 2532) covalent geometry : bond 0.00435 (10995) covalent geometry : angle 0.81191 (14926) ********************** 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 152 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 131 time to evaluate : 2.340 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.8087 (t80) cc_final: 0.7449 (t80) REVERT: A 232 ILE cc_start: 0.9086 (OUTLIER) cc_final: 0.8828 (tp) REVERT: A 290 LEU cc_start: 0.9376 (OUTLIER) cc_final: 0.9167 (tp) REVERT: A 297 MET cc_start: 0.9261 (mmm) cc_final: 0.8932 (mmt) REVERT: A 369 THR cc_start: 0.9387 (OUTLIER) cc_final: 0.9081 (p) REVERT: A 383 SER cc_start: 0.8748 (m) cc_final: 0.8391 (p) REVERT: A 430 MET cc_start: 0.8337 (mtm) cc_final: 0.7984 (mpt) REVERT: A 445 LEU cc_start: 0.9510 (pt) cc_final: 0.9193 (OUTLIER) REVERT: A 695 PHE cc_start: 0.8273 (m-10) cc_final: 0.7961 (m-10) REVERT: A 752 GLN cc_start: 0.9307 (tp-100) cc_final: 0.8997 (tp-100) REVERT: A 760 ASP cc_start: 0.9099 (m-30) cc_final: 0.8787 (p0) REVERT: B 221 PHE cc_start: 0.8062 (t80) cc_final: 0.7362 (t80) REVERT: B 290 LEU cc_start: 0.9345 (OUTLIER) cc_final: 0.9109 (tp) REVERT: B 383 SER cc_start: 0.8736 (m) cc_final: 0.8341 (p) REVERT: B 394 LEU cc_start: 0.9436 (mt) cc_final: 0.9159 (pp) REVERT: B 695 PHE cc_start: 0.8156 (m-10) cc_final: 0.7857 (m-10) REVERT: B 748 LYS cc_start: 0.9471 (mmmm) cc_final: 0.9257 (mtpt) REVERT: B 760 ASP cc_start: 0.9096 (m-30) cc_final: 0.8790 (p0) outliers start: 21 outliers final: 13 residues processed: 150 average time/residue: 1.1118 time to fit residues: 190.0612 Evaluate side-chains 136 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 120 time to evaluate : 3.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER 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 232 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 290 LEU Chi-restraints excluded: chain A residue 301 LEU Chi-restraints excluded: chain A residue 369 THR Chi-restraints excluded: chain A residue 690 VAL Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 118 CYS Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 284 THR Chi-restraints excluded: chain B residue 290 LEU 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 71 optimal weight: 0.9980 chunk 63 optimal weight: 0.9990 chunk 90 optimal weight: 2.9990 chunk 20 optimal weight: 0.2980 chunk 60 optimal weight: 0.9990 chunk 69 optimal weight: 0.7980 chunk 72 optimal weight: 0.7980 chunk 108 optimal weight: 0.9990 chunk 11 optimal weight: 0.0970 chunk 118 optimal weight: 5.9990 chunk 82 optimal weight: 3.9990 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4252 r_free = 0.4252 target = 0.129280 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3649 r_free = 0.3649 target = 0.086575 restraints weight = 26159.497| |-----------------------------------------------------------------------------| r_work (start): 0.3525 rms_B_bonded: 3.06 r_work: 0.3355 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3355 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7937 moved from start: 0.9091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 10997 Z= 0.159 Angle : 0.814 13.992 14932 Z= 0.377 Chirality : 0.047 0.308 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.502 23.935 1482 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 14.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.69 % Allowed : 25.02 % Favored : 73.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.35 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.99 (0.23), residues: 1343 helix: 1.66 (0.16), residues: 1070 sheet: None (None), residues: 0 loop : 0.12 (0.44), residues: 273 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 396 HIS 0.005 0.001 HIS A 505 PHE 0.032 0.002 PHE A 699 TYR 0.018 0.001 TYR B 451 ARG 0.006 0.000 ARG A 41 Details of bonding type rmsd link_NAG-ASN : bond 0.00333 ( 2) link_NAG-ASN : angle 0.88516 ( 6) hydrogen bonds : bond 0.04604 ( 852) hydrogen bonds : angle 4.56460 ( 2532) covalent geometry : bond 0.00350 (10995) covalent geometry : angle 0.81382 (14926) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9615.79 seconds wall clock time: 172 minutes 51.62 seconds (10371.62 seconds total)