Starting phenix.real_space_refine on Sat Nov 16 09:48:42 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u54_41912/11_2024/8u54_41912.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u54_41912/11_2024/8u54_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u54_41912/11_2024/8u54_41912.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u54_41912/11_2024/8u54_41912.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u54_41912/11_2024/8u54_41912.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8u54_41912/11_2024/8u54_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): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/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: 7.38, per 1000 atoms: 0.69 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: 2.61 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: 1.03 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: 3.45 Time building geometry restraints manager: 3.04 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 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: 1.890 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: 0.430 Check model and map are aligned: 0.080 Set scattering table: 0.100 Process input model: 27.440 Find NCS groups from input model: 0.430 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:12.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 43.200 ------------------------------------------------------------------------------- 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 10995 Z= 0.405 Angle : 0.789 7.356 14926 Z= 0.446 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 *********************** 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 : 1.219 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: 0.7426 time to fit residues: 326.1574 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 : 1.205 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7458 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 10995 Z= 0.309 Angle : 0.817 14.247 14926 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 *********************** 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 : 1.313 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: 0.7369 (OUTLIER) cc_final: 0.6950 (mmm-85) REVERT: A 752 GLN cc_start: 0.8062 (tp-100) cc_final: 0.7781 (tp-100) REVERT: A 758 HIS cc_start: 0.6936 (OUTLIER) cc_final: 0.6453 (m90) REVERT: B 41 ARG cc_start: 0.7421 (OUTLIER) cc_final: 0.7081 (mmm-85) REVERT: B 316 TYR cc_start: 0.7606 (t80) cc_final: 0.7398 (t80) REVERT: B 748 LYS cc_start: 0.9184 (mmmt) cc_final: 0.8976 (mmmm) REVERT: B 752 GLN cc_start: 0.8007 (tp-100) cc_final: 0.7758 (tp-100) REVERT: B 758 HIS cc_start: 0.6853 (OUTLIER) cc_final: 0.6354 (m90) outliers start: 69 outliers final: 19 residues processed: 250 average time/residue: 0.7279 time to fit residues: 205.8397 Evaluate side-chains 186 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 163 time to evaluate : 1.294 ------------------------------------------------------------------------------- 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 354 SER Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 451 TYR Chi-restraints excluded: chain A residue 489 TRP Chi-restraints excluded: chain A residue 665 LEU Chi-restraints excluded: chain A residue 758 HIS Chi-restraints excluded: chain B residue 41 ARG Chi-restraints excluded: chain B residue 78 SER Chi-restraints excluded: chain B residue 142 THR Chi-restraints excluded: chain B residue 209 LEU Chi-restraints excluded: chain B residue 279 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 665 LEU Chi-restraints excluded: chain B residue 758 HIS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 68 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 102 optimal weight: 0.9980 chunk 83 optimal weight: 5.9990 chunk 33 optimal weight: 0.5980 chunk 122 optimal weight: 7.9990 chunk 132 optimal weight: 7.9990 chunk 109 optimal weight: 1.9990 chunk 121 optimal weight: 1.9990 chunk 41 optimal weight: 0.6980 chunk 98 optimal weight: 0.7980 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 310 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7673 moved from start: 0.5909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 10995 Z= 0.249 Angle : 0.727 10.195 14926 Z= 0.354 Chirality : 0.044 0.147 1769 Planarity : 0.004 0.049 1822 Dihedral : 4.674 17.698 1482 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 13.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 5.33 % Allowed : 18.09 % Favored : 76.58 % 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: 1.46 (0.23), residues: 1343 helix: 1.31 (0.15), residues: 1066 sheet: None (None), residues: 0 loop : -0.11 (0.44), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP A 460 HIS 0.015 0.002 HIS B 310 PHE 0.018 0.002 PHE A 221 TYR 0.025 0.002 TYR A 689 ARG 0.006 0.001 ARG A 825 *********************** 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 231 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 63 poor density : 168 time to evaluate : 1.213 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 290 LEU cc_start: 0.8873 (OUTLIER) cc_final: 0.8628 (tp) REVERT: B 221 PHE cc_start: 0.7560 (OUTLIER) cc_final: 0.6608 (t80) REVERT: B 290 LEU cc_start: 0.8907 (OUTLIER) cc_final: 0.8609 (tp) REVERT: B 489 TRP cc_start: 0.6091 (m100) cc_final: 0.5669 (m-10) REVERT: B 540 MET cc_start: 0.7969 (tpp) cc_final: 0.7751 (tpp) REVERT: B 748 LYS cc_start: 0.9127 (mmmt) cc_final: 0.8869 (mmmm) outliers start: 63 outliers final: 17 residues processed: 208 average time/residue: 0.7098 time to fit residues: 167.8606 Evaluate side-chains 160 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 140 time to evaluate : 1.231 ------------------------------------------------------------------------------- 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 290 LEU Chi-restraints excluded: chain A residue 388 ILE 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 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 290 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 121 optimal weight: 4.9990 chunk 92 optimal weight: 0.3980 chunk 63 optimal weight: 5.9990 chunk 13 optimal weight: 0.9980 chunk 58 optimal weight: 2.9990 chunk 82 optimal weight: 0.9980 chunk 123 optimal weight: 1.9990 chunk 130 optimal weight: 0.9980 chunk 64 optimal weight: 1.9990 chunk 116 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 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 181 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 422 GLN ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 380 GLN ** B 412 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7770 moved from start: 0.6909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 10995 Z= 0.239 Angle : 0.730 12.107 14926 Z= 0.350 Chirality : 0.045 0.281 1769 Planarity : 0.004 0.045 1822 Dihedral : 4.587 17.337 1482 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 13.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.90 % Allowed : 18.51 % Favored : 76.58 % 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: 1.80 (0.23), residues: 1343 helix: 1.61 (0.15), residues: 1057 sheet: None (None), residues: 0 loop : -0.23 (0.43), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP A 460 HIS 0.007 0.001 HIS B 505 PHE 0.018 0.002 PHE A 695 TYR 0.025 0.002 TYR A 689 ARG 0.005 0.000 ARG B 825 *********************** 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 214 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 58 poor density : 156 time to evaluate : 1.266 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 748 LYS cc_start: 0.9216 (mmmt) cc_final: 0.9000 (mmmm) REVERT: B 221 PHE cc_start: 0.7462 (OUTLIER) cc_final: 0.6686 (t80) REVERT: B 281 LEU cc_start: 0.8763 (OUTLIER) cc_final: 0.8534 (mt) REVERT: B 290 LEU cc_start: 0.8906 (OUTLIER) cc_final: 0.8685 (tp) outliers start: 58 outliers final: 14 residues processed: 198 average time/residue: 0.6904 time to fit residues: 157.1961 Evaluate side-chains 149 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 132 time to evaluate : 1.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 118 CYS Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 393 SER Chi-restraints excluded: chain A residue 423 SER 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 290 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 108 optimal weight: 0.5980 chunk 74 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 97 optimal weight: 2.9990 chunk 53 optimal weight: 1.9990 chunk 111 optimal weight: 2.9990 chunk 90 optimal weight: 1.9990 chunk 0 optimal weight: 0.5980 chunk 66 optimal weight: 6.9990 chunk 117 optimal weight: 7.9990 chunk 32 optimal weight: 0.9990 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 230 ASN ** A 422 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 672 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 816 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 230 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7795 moved from start: 0.7535 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 10995 Z= 0.227 Angle : 0.714 12.135 14926 Z= 0.344 Chirality : 0.044 0.244 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.486 17.293 1482 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 4.14 % Allowed : 20.29 % Favored : 75.57 % 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: 1.90 (0.23), residues: 1343 helix: 1.63 (0.15), residues: 1065 sheet: None (None), residues: 0 loop : -0.01 (0.44), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP B 460 HIS 0.006 0.001 HIS B 505 PHE 0.016 0.002 PHE B 221 TYR 0.041 0.002 TYR A 455 ARG 0.002 0.000 ARG B 213 *********************** 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 196 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 49 poor density : 147 time to evaluate : 1.420 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7168 (t80) cc_final: 0.6592 (t80) REVERT: A 415 THR cc_start: 0.8497 (OUTLIER) cc_final: 0.8144 (p) REVERT: B 221 PHE cc_start: 0.7328 (OUTLIER) cc_final: 0.6676 (t80) REVERT: B 281 LEU cc_start: 0.8795 (OUTLIER) cc_final: 0.8592 (mt) REVERT: B 290 LEU cc_start: 0.8844 (OUTLIER) cc_final: 0.8609 (tp) REVERT: B 540 MET cc_start: 0.8096 (tpp) cc_final: 0.7854 (tpp) outliers start: 49 outliers final: 18 residues processed: 185 average time/residue: 0.6876 time to fit residues: 145.4833 Evaluate side-chains 150 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 128 time to evaluate : 1.287 ------------------------------------------------------------------------------- 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 212 LEU Chi-restraints excluded: chain A residue 271 LEU Chi-restraints excluded: chain A residue 414 LEU 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 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 280 ILE Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 461 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 43 optimal weight: 0.5980 chunk 117 optimal weight: 8.9990 chunk 25 optimal weight: 0.6980 chunk 76 optimal weight: 0.3980 chunk 32 optimal weight: 1.9990 chunk 130 optimal weight: 8.9990 chunk 108 optimal weight: 0.9980 chunk 60 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 68 optimal weight: 0.9980 chunk 125 optimal weight: 6.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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** ** A 816 GLN ** 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7807 moved from start: 0.7889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 10995 Z= 0.229 Angle : 0.735 12.940 14926 Z= 0.351 Chirality : 0.044 0.232 1769 Planarity : 0.004 0.041 1822 Dihedral : 4.469 18.021 1482 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 14.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % Rotamer: Outliers : 3.38 % Allowed : 21.98 % Favored : 74.64 % 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: 1.96 (0.23), residues: 1343 helix: 1.67 (0.15), residues: 1063 sheet: None (None), residues: 0 loop : 0.02 (0.43), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 460 HIS 0.006 0.001 HIS B 505 PHE 0.023 0.002 PHE B 695 TYR 0.030 0.002 TYR A 455 ARG 0.003 0.000 ARG B 825 *********************** 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 186 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 40 poor density : 146 time to evaluate : 1.283 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7116 (t80) cc_final: 0.6697 (t80) REVERT: A 748 LYS cc_start: 0.9191 (mmmt) cc_final: 0.8964 (mmmm) REVERT: A 758 HIS cc_start: 0.7239 (OUTLIER) cc_final: 0.6485 (m90) REVERT: B 221 PHE cc_start: 0.7340 (OUTLIER) cc_final: 0.6776 (t80) REVERT: B 290 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8637 (tp) REVERT: B 758 HIS cc_start: 0.7472 (OUTLIER) cc_final: 0.6821 (m90) outliers start: 40 outliers final: 16 residues processed: 178 average time/residue: 0.6914 time to fit residues: 140.3317 Evaluate side-chains 158 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 138 time to evaluate : 1.265 ------------------------------------------------------------------------------- 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 289 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 423 SER Chi-restraints excluded: chain A residue 758 HIS 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 215 LEU Chi-restraints excluded: chain B residue 221 PHE Chi-restraints excluded: chain B residue 271 LEU Chi-restraints excluded: chain B residue 280 ILE Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 758 HIS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 14 optimal weight: 0.5980 chunk 74 optimal weight: 0.9990 chunk 95 optimal weight: 0.9980 chunk 73 optimal weight: 0.9990 chunk 109 optimal weight: 0.9990 chunk 72 optimal weight: 0.7980 chunk 130 optimal weight: 0.9990 chunk 81 optimal weight: 0.8980 chunk 79 optimal weight: 0.6980 chunk 60 optimal weight: 0.8980 chunk 80 optimal weight: 0.9980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.8303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 10995 Z= 0.237 Angle : 0.752 12.599 14926 Z= 0.357 Chirality : 0.045 0.231 1769 Planarity : 0.004 0.041 1822 Dihedral : 4.487 18.442 1482 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.16 % Favored : 97.84 % Rotamer: Outliers : 3.21 % Allowed : 22.99 % Favored : 73.80 % 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: 1.84 (0.23), residues: 1343 helix: 1.57 (0.15), residues: 1061 sheet: None (None), residues: 0 loop : 0.07 (0.43), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP A 460 HIS 0.005 0.001 HIS B 505 PHE 0.020 0.002 PHE A 699 TYR 0.027 0.002 TYR A 455 ARG 0.003 0.000 ARG A 808 *********************** 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 183 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 38 poor density : 145 time to evaluate : 1.302 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7144 (t80) cc_final: 0.6760 (t80) REVERT: A 758 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.6760 (m90) REVERT: B 221 PHE cc_start: 0.7282 (t80) cc_final: 0.6808 (t80) REVERT: B 290 LEU cc_start: 0.8856 (OUTLIER) cc_final: 0.8647 (tp) REVERT: B 758 HIS cc_start: 0.7512 (OUTLIER) cc_final: 0.6965 (m90) outliers start: 38 outliers final: 14 residues processed: 169 average time/residue: 0.7047 time to fit residues: 135.8984 Evaluate side-chains 146 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 129 time to evaluate : 1.197 ------------------------------------------------------------------------------- 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 280 ILE Chi-restraints excluded: chain A residue 289 VAL Chi-restraints excluded: chain A residue 388 ILE Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 758 HIS 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 284 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 758 HIS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 51 optimal weight: 5.9990 chunk 77 optimal weight: 0.9990 chunk 39 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 chunk 82 optimal weight: 0.5980 chunk 88 optimal weight: 0.5980 chunk 64 optimal weight: 7.9990 chunk 12 optimal weight: 0.6980 chunk 102 optimal weight: 0.7980 chunk 118 optimal weight: 6.9990 chunk 124 optimal weight: 0.3980 overall best weight: 0.6180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 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 143 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7808 moved from start: 0.8581 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.047 10995 Z= 0.220 Angle : 0.771 12.846 14926 Z= 0.362 Chirality : 0.046 0.334 1769 Planarity : 0.004 0.042 1822 Dihedral : 4.520 18.693 1482 Min Nonbonded Distance : 2.544 Molprobity Statistics. All-atom Clashscore : 14.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.08 % Favored : 97.92 % Rotamer: Outliers : 2.62 % Allowed : 23.84 % 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: 1.90 (0.23), residues: 1343 helix: 1.62 (0.15), residues: 1064 sheet: None (None), residues: 0 loop : 0.05 (0.43), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP B 679 HIS 0.005 0.001 HIS B 505 PHE 0.031 0.002 PHE A 695 TYR 0.026 0.002 TYR A 455 ARG 0.007 0.000 ARG B 825 *********************** 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 173 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 142 time to evaluate : 1.580 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7193 (t80) cc_final: 0.6849 (t80) REVERT: A 758 HIS cc_start: 0.7513 (OUTLIER) cc_final: 0.6814 (m90) REVERT: B 221 PHE cc_start: 0.7253 (t80) cc_final: 0.7006 (t80) REVERT: B 290 LEU cc_start: 0.8779 (OUTLIER) cc_final: 0.8569 (tp) REVERT: B 758 HIS cc_start: 0.7518 (OUTLIER) cc_final: 0.6977 (m90) outliers start: 31 outliers final: 13 residues processed: 164 average time/residue: 0.7304 time to fit residues: 137.5460 Evaluate side-chains 142 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 126 time to evaluate : 1.286 ------------------------------------------------------------------------------- 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 280 ILE Chi-restraints excluded: chain A residue 284 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 758 HIS 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 388 ILE Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 758 HIS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 113 optimal weight: 10.0000 chunk 121 optimal weight: 0.8980 chunk 124 optimal weight: 0.9980 chunk 72 optimal weight: 1.9990 chunk 52 optimal weight: 8.9990 chunk 95 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 109 optimal weight: 1.9990 chunk 114 optimal weight: 10.0000 chunk 120 optimal weight: 5.9990 chunk 79 optimal weight: 0.5980 overall best weight: 1.2984 ------------------------------------------------------------------------------- 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 752 GLN B 143 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.8823 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.047 10995 Z= 0.301 Angle : 0.826 13.890 14926 Z= 0.387 Chirality : 0.049 0.406 1769 Planarity : 0.004 0.042 1822 Dihedral : 4.592 18.862 1482 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 15.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.46 % Favored : 97.54 % Rotamer: Outliers : 2.20 % Allowed : 25.27 % Favored : 72.53 % 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: 1.86 (0.23), residues: 1343 helix: 1.55 (0.15), residues: 1066 sheet: None (None), residues: 0 loop : 0.22 (0.44), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 460 HIS 0.005 0.001 HIS B 505 PHE 0.024 0.002 PHE A 699 TYR 0.025 0.002 TYR A 455 ARG 0.003 0.000 ARG B 825 *********************** 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: 26 poor density : 129 time to evaluate : 1.226 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7218 (t80) cc_final: 0.6798 (t80) REVERT: A 429 MET cc_start: 0.8143 (tpt) cc_final: 0.7808 (tpt) REVERT: A 758 HIS cc_start: 0.7575 (OUTLIER) cc_final: 0.6990 (m90) REVERT: B 221 PHE cc_start: 0.7301 (t80) cc_final: 0.6964 (t80) REVERT: B 290 LEU cc_start: 0.8862 (OUTLIER) cc_final: 0.8659 (tp) REVERT: B 670 PHE cc_start: 0.7533 (OUTLIER) cc_final: 0.7301 (t80) outliers start: 26 outliers final: 11 residues processed: 149 average time/residue: 0.7378 time to fit residues: 125.4535 Evaluate side-chains 131 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 117 time to evaluate : 1.351 ------------------------------------------------------------------------------- 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 284 THR Chi-restraints excluded: chain A residue 424 ILE Chi-restraints excluded: chain A residue 445 LEU Chi-restraints excluded: chain A residue 758 HIS 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 670 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 128 optimal weight: 2.9990 chunk 78 optimal weight: 0.8980 chunk 60 optimal weight: 0.7980 chunk 89 optimal weight: 0.5980 chunk 134 optimal weight: 8.9990 chunk 123 optimal weight: 3.9990 chunk 107 optimal weight: 0.0020 chunk 11 optimal weight: 0.7980 chunk 82 optimal weight: 0.9980 chunk 65 optimal weight: 9.9990 chunk 85 optimal weight: 0.6980 overall best weight: 0.5788 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7825 moved from start: 0.8982 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 10995 Z= 0.220 Angle : 0.830 14.007 14926 Z= 0.384 Chirality : 0.048 0.355 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.574 23.077 1482 Min Nonbonded Distance : 2.487 Molprobity Statistics. All-atom Clashscore : 14.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.23 % Favored : 97.77 % Rotamer: Outliers : 1.27 % Allowed : 26.12 % Favored : 72.61 % 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: 1.90 (0.23), residues: 1343 helix: 1.60 (0.15), residues: 1066 sheet: None (None), residues: 0 loop : 0.13 (0.44), residues: 277 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 679 HIS 0.005 0.001 HIS B 505 PHE 0.024 0.002 PHE A 224 TYR 0.025 0.001 TYR A 455 ARG 0.009 0.000 ARG A 825 ********************** 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 145 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 130 time to evaluate : 1.335 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 221 PHE cc_start: 0.7086 (t80) cc_final: 0.6879 (t80) REVERT: A 758 HIS cc_start: 0.7601 (OUTLIER) cc_final: 0.7033 (m90) REVERT: B 221 PHE cc_start: 0.7205 (t80) cc_final: 0.6973 (t80) REVERT: B 290 LEU cc_start: 0.8809 (OUTLIER) cc_final: 0.8607 (tp) REVERT: B 670 PHE cc_start: 0.7498 (OUTLIER) cc_final: 0.7255 (t80) REVERT: B 807 ASP cc_start: 0.8217 (t0) cc_final: 0.7992 (t0) outliers start: 15 outliers final: 8 residues processed: 144 average time/residue: 0.7819 time to fit residues: 127.2713 Evaluate side-chains 132 residues out of total 1185 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 121 time to evaluate : 1.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 78 SER Chi-restraints excluded: chain A residue 209 LEU Chi-restraints excluded: chain A residue 758 HIS 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 284 THR Chi-restraints excluded: chain B residue 290 LEU Chi-restraints excluded: chain B residue 423 SER Chi-restraints excluded: chain B residue 670 PHE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 135 random chunks: chunk 114 optimal weight: 8.9990 chunk 32 optimal weight: 0.0170 chunk 98 optimal weight: 0.9990 chunk 15 optimal weight: 0.6980 chunk 29 optimal weight: 0.3980 chunk 107 optimal weight: 0.0770 chunk 44 optimal weight: 8.9990 chunk 110 optimal weight: 0.8980 chunk 13 optimal weight: 0.9980 chunk 19 optimal weight: 1.9990 chunk 94 optimal weight: 1.9990 overall best weight: 0.4176 ------------------------------------------------------------------------------- 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 = 0.4268 r_free = 0.4268 target = 0.130032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.087970 restraints weight = 26255.899| |-----------------------------------------------------------------------------| r_work (start): 0.3561 rms_B_bonded: 3.11 r_work: 0.3397 rms_B_bonded: 4.02 restraints_weight: 0.5000 r_work (final): 0.3397 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7914 moved from start: 0.9221 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 10995 Z= 0.211 Angle : 0.854 14.047 14926 Z= 0.391 Chirality : 0.048 0.388 1769 Planarity : 0.004 0.043 1822 Dihedral : 4.589 25.150 1482 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 14.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 1.27 % Allowed : 26.71 % Favored : 72.02 % 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: 2.06 (0.23), residues: 1343 helix: 1.70 (0.16), residues: 1067 sheet: None (None), residues: 0 loop : 0.23 (0.44), residues: 276 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP B 679 HIS 0.005 0.001 HIS A 505 PHE 0.022 0.002 PHE B 699 TYR 0.025 0.002 TYR A 455 ARG 0.007 0.000 ARG A 41 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3665.62 seconds wall clock time: 66 minutes 58.40 seconds (4018.40 seconds total)