Starting phenix.real_space_refine on Tue Mar 3 19:39:42 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7s0e_24788/03_2026/7s0e_24788.cif Found real_map, /net/cci-nas-00/data/ceres_data/7s0e_24788/03_2026/7s0e_24788.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7s0e_24788/03_2026/7s0e_24788.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7s0e_24788/03_2026/7s0e_24788.map" model { file = "/net/cci-nas-00/data/ceres_data/7s0e_24788/03_2026/7s0e_24788.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7s0e_24788/03_2026/7s0e_24788.cif" } resolution = 4.9 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.009 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 36 5.16 5 C 5234 2.51 5 N 1373 2.21 5 O 1605 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 26 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-5986/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 8248 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 4918 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 639, 4909 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 34, 'TRANS': 604} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 66 Conformer: "B" Number of residues, atoms: 639, 4909 Classifications: {'peptide': 639} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 34, 'TRANS': 604} Chain breaks: 8 Unresolved chain link angles: 2 Unresolved non-hydrogen bonds: 134 Unresolved non-hydrogen angles: 168 Unresolved non-hydrogen dihedrals: 113 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 2, 'ARG:plan': 3, 'PHE:plan': 1, 'ASN:plan1': 4, 'GLU:plan': 2, 'HIS:plan': 1, 'ASP:plan': 1, 'TRP:plan': 1} Unresolved non-hydrogen planarities: 66 bond proxies already assigned to first conformer: 5016 Chain: "H" Number of atoms: 1673 Number of conformers: 1 Conformer: "" Number of residues, atoms: 223, 1673 Classifications: {'peptide': 223} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 211} Chain: "L" Number of atoms: 1657 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} Conformer: "B" Number of residues, atoms: 214, 1654 Classifications: {'peptide': 214} Link IDs: {'PCIS': 2, 'PTRANS': 9, 'TRANS': 202} bond proxies already assigned to first conformer: 1687 Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ASER A 459 " occ=0.60 ... (10 atoms not shown) pdb=" OG BSER A 459 " occ=0.40 Time building chain proxies: 2.86, per 1000 atoms: 0.35 Number of scatterers: 8248 At special positions: 0 Unit cell: (91.245, 109.494, 171.193, 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 36 16.00 O 1605 8.00 N 1373 7.00 C 5234 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=15, symmetry=0 Simple disulfide: pdb=" SG CYS A 15 " - pdb=" SG CYS A 136 " distance=2.03 Simple disulfide: pdb=" SG CYS A 131 " - pdb=" SG CYS A 166 " distance=2.02 Simple disulfide: pdb=" SG CYS A 291 " - pdb=" SG CYS A 301 " distance=2.03 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS A 538 " - pdb=" SG CYS A 590 " distance=2.03 Simple disulfide: pdb=" SG CYS A 617 " - pdb=" SG CYS A 649 " distance=2.03 Simple disulfide: pdb=" SG CYS A 662 " - pdb=" SG CYS A 671 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 148 " - pdb=" SG CYS H 204 " distance=2.05 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG ACYS L 194 " distance=2.03 Simple disulfide: pdb=" SG CYS L 134 " - pdb=" SG BCYS L 194 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.56 Conformation dependent library (CDL) restraints added in 482.0 milliseconds 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2006 Finding SS restraints... Secondary structure from input PDB file: 13 helices and 24 sheets defined 7.4% alpha, 26.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'A' and resid 294 through 304 removed outlier: 3.930A pdb=" N LYS A 300 " --> pdb=" O LEU A 296 " (cutoff:3.500A) Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.697A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 349 through 353 Processing helix chain 'A' and resid 365 through 370 Processing helix chain 'A' and resid 386 through 389 Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 569 through 571 No H-bonds generated for 'chain 'A' and resid 569 through 571' Processing helix chain 'A' and resid 619 through 624 removed outlier: 4.123A pdb=" N ILE A 624 " --> pdb=" O VAL A 620 " (cutoff:3.500A) Processing helix chain 'A' and resid 628 through 634 Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.843A pdb=" N ILE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'L' and resid 121 through 128 Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.538A pdb=" N LYS L 188 " --> pdb=" O ALA L 184 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 29 through 30 Processing sheet with id=AA2, first strand: chain 'A' and resid 48 through 55 removed outlier: 3.876A pdb=" N ASP A 287 " --> pdb=" O LYS A 278 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 84 through 85 removed outlier: 3.696A pdb=" N LEU A 84 " --> pdb=" O PHE A 238 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 225 through 229 removed outlier: 5.395A pdb=" N SER A 205 " --> pdb=" O PRO A 225 " (cutoff:3.500A) removed outlier: 3.800A pdb=" N VAL A 90 " --> pdb=" O PHE A 194 " (cutoff:3.500A) removed outlier: 3.554A pdb=" N ALA A 93 " --> pdb=" O TYR A 266 " (cutoff:3.500A) removed outlier: 3.809A pdb=" N TYR A 266 " --> pdb=" O ALA A 93 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 118 through 121 Processing sheet with id=AA6, first strand: chain 'A' and resid 140 through 145 removed outlier: 7.707A pdb=" N PHE A 140 " --> pdb=" O PHE A 157 " (cutoff:3.500A) removed outlier: 5.926A pdb=" N PHE A 157 " --> pdb=" O PHE A 140 " (cutoff:3.500A) removed outlier: 6.575A pdb=" N GLY A 142 " --> pdb=" O SER A 155 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 324 through 328 removed outlier: 3.579A pdb=" N GLU A 324 " --> pdb=" O CYS A 538 " (cutoff:3.500A) removed outlier: 5.371A pdb=" N ASP A 574 " --> pdb=" O ILE A 587 " (cutoff:3.500A) removed outlier: 3.804A pdb=" N THR A 572 " --> pdb=" O ASP A 568 " (cutoff:3.500A) removed outlier: 7.223A pdb=" N GLY A 566 " --> pdb=" O ASP A 574 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.669A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.848A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 334 through 335 removed outlier: 6.669A pdb=" N ASN A 334 " --> pdb=" O VAL A 362 " (cutoff:3.500A) removed outlier: 6.957A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) removed outlier: 3.628A pdb=" N VAL A 524 " --> pdb=" O PHE A 392 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.577A pdb=" N PHE A 400 " --> pdb=" O VAL A 510 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N VAL A 510 " --> pdb=" O PHE A 400 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 452 through 454 removed outlier: 3.699A pdb=" N GLN A 493 " --> pdb=" O TYR A 453 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'A' and resid 473 through 474 removed outlier: 3.545A pdb=" N TYR A 489 " --> pdb=" O TYR A 473 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'A' and resid 641 through 645 removed outlier: 3.821A pdb=" N ASN A 641 " --> pdb=" O GLY A 652 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'A' and resid 654 through 655 removed outlier: 6.267A pdb=" N GLU A 654 " --> pdb=" O ALA A 694 " (cutoff:3.500A) removed outlier: 8.134A pdb=" N THR A 696 " --> pdb=" O GLU A 654 " (cutoff:3.500A) removed outlier: 6.662A pdb=" N ILE A 670 " --> pdb=" O ILE A 666 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.519A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER H 25 " --> pdb=" O GLN H 3 " (cutoff:3.500A) removed outlier: 3.610A pdb=" N VAL H 5 " --> pdb=" O ALA H 23 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N SER H 71 " --> pdb=" O TYR H 80 " (cutoff:3.500A) Processing sheet with id=AB6, first strand: chain 'H' and resid 11 through 12 removed outlier: 6.837A pdb=" N MET H 34 " --> pdb=" O ALA H 50 " (cutoff:3.500A) removed outlier: 4.680A pdb=" N ALA H 50 " --> pdb=" O MET H 34 " (cutoff:3.500A) removed outlier: 6.671A pdb=" N TRP H 36 " --> pdb=" O VAL H 48 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'H' and resid 128 through 130 removed outlier: 5.038A pdb=" N LYS H 151 " --> pdb=" O LEU H 186 " (cutoff:3.500A) removed outlier: 6.988A pdb=" N LEU H 186 " --> pdb=" O LYS H 151 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'H' and resid 143 through 144 Processing sheet with id=AB9, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.508A pdb=" N THR L 102 " --> pdb=" O TYR L 86 " (cutoff:3.500A) removed outlier: 3.606A pdb=" N VAL L 104 " --> pdb=" O ALA L 84 " (cutoff:3.500A) removed outlier: 4.296A pdb=" N ALA L 84 " --> pdb=" O VAL L 104 " (cutoff:3.500A) Processing sheet with id=AC1, first strand: chain 'L' and resid 19 through 20 Processing sheet with id=AC2, first strand: chain 'L' and resid 23 through 24 removed outlier: 3.928A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.570A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AC3, first strand: chain 'L' and resid 48 through 49 Processing sheet with id=AC4, first strand: chain 'L' and resid 129 through 130 Processing sheet with id=AC5, first strand: chain 'L' and resid 133 through 139 removed outlier: 3.890A pdb=" N SER L 177 " --> pdb=" O CYS L 134 " (cutoff:3.500A) removed outlier: 5.998A pdb=" N TYR L 173 " --> pdb=" O ASN L 138 " (cutoff:3.500A) Processing sheet with id=AC6, first strand: chain 'L' and resid 153 through 154 removed outlier: 3.654A pdb=" N LYS L 149 " --> pdb=" O ALA L 193 " (cutoff:3.500A) removed outlier: 3.670A pdb=" N ALA L 193 " --> pdb=" O LYS L 149 " (cutoff:3.500A) removed outlier: 3.899A pdb=" N LYS L 207 " --> pdb=" O CYS L 194 " (cutoff:3.500A) 196 hydrogen bonds defined for protein. 491 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.20 Time building geometry restraints manager: 0.78 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2653 1.34 - 1.47: 2219 1.47 - 1.60: 3535 1.60 - 1.73: 0 1.73 - 1.86: 42 Bond restraints: 8449 Sorted by residual: bond pdb=" C THR H 173 " pdb=" N PHE H 174 " ideal model delta sigma weight residual 1.332 1.384 -0.052 1.46e-02 4.69e+03 1.29e+01 bond pdb=" N ILE L 29 " pdb=" CA ILE L 29 " ideal model delta sigma weight residual 1.462 1.497 -0.034 1.06e-02 8.90e+03 1.04e+01 bond pdb=" N ASN L 34 " pdb=" CA ASN L 34 " ideal model delta sigma weight residual 1.454 1.492 -0.038 1.18e-02 7.18e+03 1.03e+01 bond pdb=" N GLY H 107 " pdb=" CA GLY H 107 " ideal model delta sigma weight residual 1.438 1.482 -0.044 1.41e-02 5.03e+03 9.54e+00 bond pdb=" N GLN L 89 " pdb=" CA GLN L 89 " ideal model delta sigma weight residual 1.454 1.487 -0.033 1.15e-02 7.56e+03 8.03e+00 ... (remaining 8444 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.65: 11265 2.65 - 5.29: 230 5.29 - 7.94: 14 7.94 - 10.58: 4 10.58 - 13.23: 1 Bond angle restraints: 11514 Sorted by residual: angle pdb=" N PRO A 621 " pdb=" CA PRO A 621 " pdb=" CB PRO A 621 " ideal model delta sigma weight residual 103.25 111.20 -7.95 1.05e+00 9.07e-01 5.74e+01 angle pdb=" N PRO A 631 " pdb=" CA PRO A 631 " pdb=" CB PRO A 631 " ideal model delta sigma weight residual 103.25 111.10 -7.85 1.05e+00 9.07e-01 5.58e+01 angle pdb=" C GLU H 156 " pdb=" N PRO H 157 " pdb=" CD PRO H 157 " ideal model delta sigma weight residual 120.60 107.37 13.23 2.20e+00 2.07e-01 3.61e+01 angle pdb=" N VAL H 64 " pdb=" CA VAL H 64 " pdb=" C VAL H 64 " ideal model delta sigma weight residual 113.10 108.57 4.53 9.70e-01 1.06e+00 2.18e+01 angle pdb=" N TRP H 111 " pdb=" CA TRP H 111 " pdb=" C TRP H 111 " ideal model delta sigma weight residual 110.91 116.38 -5.47 1.17e+00 7.31e-01 2.18e+01 ... (remaining 11509 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 4585 17.77 - 35.53: 330 35.53 - 53.30: 65 53.30 - 71.06: 18 71.06 - 88.83: 7 Dihedral angle restraints: 5005 sinusoidal: 1874 harmonic: 3131 Sorted by residual: dihedral pdb=" CA ASN H 163 " pdb=" C ASN H 163 " pdb=" N SER H 164 " pdb=" CA SER H 164 " ideal model delta harmonic sigma weight residual 180.00 139.04 40.96 0 5.00e+00 4.00e-02 6.71e+01 dihedral pdb=" CA TRP H 162 " pdb=" C TRP H 162 " pdb=" N ASN H 163 " pdb=" CA ASN H 163 " ideal model delta harmonic sigma weight residual 180.00 144.92 35.08 0 5.00e+00 4.00e-02 4.92e+01 dihedral pdb=" CA SER H 164 " pdb=" C SER H 164 " pdb=" N GLY H 165 " pdb=" CA GLY H 165 " ideal model delta harmonic sigma weight residual 180.00 145.88 34.12 0 5.00e+00 4.00e-02 4.66e+01 ... (remaining 5002 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.078: 1123 0.078 - 0.155: 153 0.155 - 0.233: 8 0.233 - 0.311: 4 0.311 - 0.389: 2 Chirality restraints: 1290 Sorted by residual: chirality pdb=" CA TYR H 33 " pdb=" N TYR H 33 " pdb=" C TYR H 33 " pdb=" CB TYR H 33 " both_signs ideal model delta sigma weight residual False 2.51 2.90 -0.39 2.00e-01 2.50e+01 3.78e+00 chirality pdb=" CA ILE H 51 " pdb=" N ILE H 51 " pdb=" C ILE H 51 " pdb=" CB ILE H 51 " both_signs ideal model delta sigma weight residual False 2.43 2.77 -0.34 2.00e-01 2.50e+01 2.83e+00 chirality pdb=" CA ILE L 29 " pdb=" N ILE L 29 " pdb=" C ILE L 29 " pdb=" CB ILE L 29 " both_signs ideal model delta sigma weight residual False 2.43 2.74 -0.31 2.00e-01 2.50e+01 2.39e+00 ... (remaining 1287 not shown) Planarity restraints: 1490 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU H 156 " -0.057 5.00e-02 4.00e+02 8.53e-02 1.16e+01 pdb=" N PRO H 157 " 0.147 5.00e-02 4.00e+02 pdb=" CA PRO H 157 " -0.053 5.00e-02 4.00e+02 pdb=" CD PRO H 157 " -0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LEU A 560 " -0.014 2.00e-02 2.50e+03 2.76e-02 7.60e+00 pdb=" C LEU A 560 " 0.048 2.00e-02 2.50e+03 pdb=" O LEU A 560 " -0.018 2.00e-02 2.50e+03 pdb=" N PRO A 561 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C GLN A 271 " -0.042 5.00e-02 4.00e+02 6.47e-02 6.69e+00 pdb=" N PRO A 272 " 0.112 5.00e-02 4.00e+02 pdb=" CA PRO A 272 " -0.034 5.00e-02 4.00e+02 pdb=" CD PRO A 272 " -0.036 5.00e-02 4.00e+02 ... (remaining 1487 not shown) Histogram of nonbonded interaction distances: 1.89 - 2.49: 78 2.49 - 3.09: 6018 3.09 - 3.69: 12982 3.69 - 4.30: 17789 4.30 - 4.90: 28277 Nonbonded interactions: 65144 Sorted by model distance: nonbonded pdb=" CG TYR H 33 " pdb=" OD2 ASP H 99 " model vdw 1.886 3.260 nonbonded pdb=" N GLY H 165 " pdb=" O TYR H 202 " model vdw 1.950 3.120 nonbonded pdb=" N ALA H 166 " pdb=" O THR H 201 " model vdw 2.090 3.120 nonbonded pdb=" OG1 THR H 28 " pdb=" OG SER H 31 " model vdw 2.133 3.040 nonbonded pdb=" OG SER A 469 " pdb=" OE1 GLU A 471 " model vdw 2.158 3.040 ... (remaining 65139 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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=0.04 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue 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: 7.260 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.020 Process input model: 9.560 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:1.130 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 18.230 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6857 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 : 0.004 0.052 8464 Z= 0.257 Angle : 0.871 13.225 11544 Z= 0.525 Chirality : 0.053 0.389 1290 Planarity : 0.006 0.085 1490 Dihedral : 13.436 88.828 2954 Min Nonbonded Distance : 1.886 Molprobity Statistics. All-atom Clashscore : 21.66 Ramachandran Plot: Outliers : 0.66 % Allowed : 8.06 % Favored : 91.27 % Rotamer: Outliers : 1.22 % Allowed : 0.78 % Favored : 98.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -1.76 (0.25), residues: 1059 helix: -2.63 (0.67), residues: 49 sheet: -0.61 (0.30), residues: 285 loop : -1.35 (0.22), residues: 725 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG L 142 TYR 0.016 0.002 TYR L 49 PHE 0.023 0.002 PHE A 329 TRP 0.034 0.003 TRP L 91 HIS 0.004 0.001 HIS H 208 Details of bonding type rmsd covalent geometry : bond 0.00422 ( 8449) covalent geometry : angle 0.86829 (11514) SS BOND : bond 0.00471 ( 15) SS BOND : angle 1.67068 ( 30) hydrogen bonds : bond 0.29437 ( 195) hydrogen bonds : angle 13.08654 ( 491) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 123 time to evaluate : 0.305 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 366 SER cc_start: 0.9061 (m) cc_final: 0.8841 (p) REVERT: A 374 PHE cc_start: 0.7806 (m-10) cc_final: 0.7441 (m-80) REVERT: A 392 PHE cc_start: 0.7798 (m-80) cc_final: 0.7174 (m-80) REVERT: A 418 ILE cc_start: 0.9282 (tt) cc_final: 0.8666 (tp) REVERT: A 455 LEU cc_start: 0.8401 (mm) cc_final: 0.7968 (mm) REVERT: H 5 VAL cc_start: 0.8765 (m) cc_final: 0.8560 (p) REVERT: H 20 LEU cc_start: 0.9397 (mt) cc_final: 0.7282 (mp) REVERT: H 49 SER cc_start: 0.8496 (OUTLIER) cc_final: 0.8097 (t) REVERT: H 54 SER cc_start: 0.6827 (OUTLIER) cc_final: 0.6423 (t) REVERT: H 58 THR cc_start: 0.8217 (t) cc_final: 0.7488 (m) REVERT: H 217 LYS cc_start: 0.8517 (mtpt) cc_final: 0.8217 (ptmt) REVERT: L 35 TRP cc_start: 0.8199 (m100) cc_final: 0.7975 (m100) REVERT: L 50 ASP cc_start: 0.8263 (m-30) cc_final: 0.8040 (m-30) REVERT: L 70 ASP cc_start: 0.8978 (p0) cc_final: 0.8586 (p0) REVERT: L 71 PHE cc_start: 0.7069 (m-80) cc_final: 0.6407 (t80) REVERT: L 98 PHE cc_start: 0.7618 (m-80) cc_final: 0.6922 (m-80) REVERT: L 136 LEU cc_start: 0.8689 (mp) cc_final: 0.8453 (mp) outliers start: 11 outliers final: 3 residues processed: 133 average time/residue: 0.0672 time to fit residues: 13.2331 Evaluate side-chains 85 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 80 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 5.9990 chunk 53 optimal weight: 2.9990 chunk 5 optimal weight: 8.9990 chunk 33 optimal weight: 2.9990 chunk 65 optimal weight: 6.9990 chunk 62 optimal weight: 9.9990 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 8.9990 chunk 38 optimal weight: 6.9990 chunk 61 optimal weight: 0.6980 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 165 ASN A 196 ASN ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 163 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 3 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** 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 = 0.3555 r_free = 0.3555 target = 0.069796 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.053430 restraints weight = 116884.475| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3211 r_free = 0.3211 target = 0.056501 restraints weight = 68235.965| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3258 r_free = 0.3258 target = 0.058289 restraints weight = 40204.359| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3282 r_free = 0.3282 target = 0.059163 restraints weight = 27890.528| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 30)----------------| | r_work = 0.3303 r_free = 0.3303 target = 0.059983 restraints weight = 23988.532| |-----------------------------------------------------------------------------| r_work (final): 0.3283 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3283 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3283 r_free = 0.3283 target_work(ls_wunit_k1) = 0.059 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3283 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7249 moved from start: 0.2955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.107 8464 Z= 0.299 Angle : 0.899 11.784 11544 Z= 0.478 Chirality : 0.051 0.300 1290 Planarity : 0.007 0.096 1490 Dihedral : 7.099 41.897 1159 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 28.28 Ramachandran Plot: Outliers : 0.38 % Allowed : 9.49 % Favored : 90.13 % Rotamer: Outliers : 0.33 % Allowed : 4.66 % Favored : 95.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.23 (0.24), residues: 1059 helix: -3.25 (0.52), residues: 54 sheet: -1.02 (0.29), residues: 288 loop : -1.60 (0.22), residues: 717 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG A 457 TYR 0.039 0.004 TYR H 33 PHE 0.033 0.003 PHE A 65 TRP 0.054 0.005 TRP A 353 HIS 0.012 0.003 HIS H 102 Details of bonding type rmsd covalent geometry : bond 0.00632 ( 8449) covalent geometry : angle 0.89474 (11514) SS BOND : bond 0.00911 ( 15) SS BOND : angle 1.95864 ( 30) hydrogen bonds : bond 0.05546 ( 195) hydrogen bonds : angle 9.81428 ( 491) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 98 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8688 (m-80) cc_final: 0.8326 (m-80) REVERT: A 392 PHE cc_start: 0.7653 (m-80) cc_final: 0.6490 (m-80) REVERT: H 153 TYR cc_start: 0.8152 (p90) cc_final: 0.7932 (p90) REVERT: L 70 ASP cc_start: 0.8885 (p0) cc_final: 0.8619 (p0) REVERT: L 71 PHE cc_start: 0.7756 (m-80) cc_final: 0.7145 (m-80) REVERT: L 175 LEU cc_start: 0.9089 (tp) cc_final: 0.8743 (tp) outliers start: 3 outliers final: 1 residues processed: 101 average time/residue: 0.0726 time to fit residues: 10.7794 Evaluate side-chains 68 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 67 time to evaluate : 0.211 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 52 optimal weight: 0.7980 chunk 93 optimal weight: 0.9980 chunk 27 optimal weight: 0.9990 chunk 78 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 32 optimal weight: 7.9990 chunk 72 optimal weight: 0.8980 chunk 66 optimal weight: 0.9980 chunk 95 optimal weight: 3.9990 chunk 84 optimal weight: 0.8980 chunk 61 optimal weight: 8.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 166 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3638 r_free = 0.3638 target = 0.073347 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3235 r_free = 0.3235 target = 0.057195 restraints weight = 87666.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 43)----------------| | r_work = 0.3295 r_free = 0.3295 target = 0.059458 restraints weight = 53798.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 32)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.061049 restraints weight = 37332.905| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 32)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.062201 restraints weight = 28143.096| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.063081 restraints weight = 22586.754| |-----------------------------------------------------------------------------| r_work (final): 0.3369 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3368 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3368 r_free = 0.3368 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| r_final: 0.3368 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7127 moved from start: 0.3122 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 8464 Z= 0.155 Angle : 0.727 14.431 11544 Z= 0.380 Chirality : 0.047 0.204 1290 Planarity : 0.005 0.053 1490 Dihedral : 6.123 36.107 1159 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 16.13 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.31 % Favored : 92.41 % Rotamer: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.16 (0.24), residues: 1059 helix: -3.31 (0.46), residues: 56 sheet: -1.07 (0.28), residues: 307 loop : -1.48 (0.23), residues: 696 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.020 0.002 TYR L 32 PHE 0.022 0.002 PHE A 275 TRP 0.028 0.003 TRP A 353 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00327 ( 8449) covalent geometry : angle 0.72402 (11514) SS BOND : bond 0.00471 ( 15) SS BOND : angle 1.40407 ( 30) hydrogen bonds : bond 0.04235 ( 195) hydrogen bonds : angle 8.72164 ( 491) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 107 time to evaluate : 0.263 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8554 (m-80) cc_final: 0.8309 (m-80) REVERT: A 392 PHE cc_start: 0.7710 (m-80) cc_final: 0.6802 (m-80) REVERT: A 398 ASP cc_start: 0.8476 (m-30) cc_final: 0.8216 (m-30) REVERT: H 46 GLU cc_start: 0.8818 (tt0) cc_final: 0.8612 (tt0) REVERT: H 111 TRP cc_start: 0.6928 (m100) cc_final: 0.6316 (m100) REVERT: H 158 VAL cc_start: 0.8178 (m) cc_final: 0.7946 (p) REVERT: H 217 LYS cc_start: 0.8542 (mtpt) cc_final: 0.8285 (mtpt) REVERT: L 35 TRP cc_start: 0.8726 (m100) cc_final: 0.8303 (m100) REVERT: L 70 ASP cc_start: 0.8800 (p0) cc_final: 0.8550 (p0) REVERT: L 71 PHE cc_start: 0.7069 (m-80) cc_final: 0.6294 (m-10) REVERT: L 94 TRP cc_start: 0.7149 (t-100) cc_final: 0.6525 (t60) REVERT: L 137 ASN cc_start: 0.7801 (t0) cc_final: 0.7464 (t0) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.0683 time to fit residues: 10.9839 Evaluate side-chains 76 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 76 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 95 optimal weight: 3.9990 chunk 58 optimal weight: 10.0000 chunk 43 optimal weight: 0.0370 chunk 80 optimal weight: 5.9990 chunk 23 optimal weight: 8.9990 chunk 76 optimal weight: 2.9990 chunk 6 optimal weight: 5.9990 chunk 98 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 57 optimal weight: 0.0170 chunk 33 optimal weight: 0.5980 overall best weight: 0.5096 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 52 GLN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 3 GLN ** L 90 GLN ** 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 = 0.3660 r_free = 0.3660 target = 0.074234 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.055760 restraints weight = 151745.592| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058684 restraints weight = 80831.059| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.060776 restraints weight = 51900.711| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 35)----------------| | r_work = 0.3366 r_free = 0.3366 target = 0.062269 restraints weight = 37129.837| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 35)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.063386 restraints weight = 28543.215| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3374 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 3 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3374 r_free = 0.3374 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3374 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7131 moved from start: 0.3473 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 8464 Z= 0.138 Angle : 0.697 14.734 11544 Z= 0.365 Chirality : 0.046 0.211 1290 Planarity : 0.005 0.056 1490 Dihedral : 5.720 29.908 1159 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 14.39 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.87 % Favored : 91.84 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.01 (0.24), residues: 1059 helix: -2.94 (0.52), residues: 53 sheet: -0.84 (0.28), residues: 315 loop : -1.49 (0.23), residues: 691 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG L 61 TYR 0.016 0.002 TYR H 33 PHE 0.023 0.002 PHE H 108 TRP 0.043 0.003 TRP A 353 HIS 0.006 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00289 ( 8449) covalent geometry : angle 0.69500 (11514) SS BOND : bond 0.00449 ( 15) SS BOND : angle 1.26994 ( 30) hydrogen bonds : bond 0.03692 ( 195) hydrogen bonds : angle 8.21365 ( 491) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 98 time to evaluate : 0.332 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8321 (m-80) cc_final: 0.8105 (m-80) REVERT: A 365 TYR cc_start: 0.8575 (m-80) cc_final: 0.8315 (m-80) REVERT: A 392 PHE cc_start: 0.7721 (m-80) cc_final: 0.6849 (m-80) REVERT: H 36 TRP cc_start: 0.8468 (m100) cc_final: 0.6852 (m100) REVERT: H 158 VAL cc_start: 0.8136 (m) cc_final: 0.7826 (p) REVERT: L 4 MET cc_start: 0.9007 (mpp) cc_final: 0.8565 (mpp) REVERT: L 94 TRP cc_start: 0.7249 (t-100) cc_final: 0.6694 (t60) REVERT: L 169 LYS cc_start: 0.9675 (mmmt) cc_final: 0.8860 (tmtt) REVERT: L 185 ASP cc_start: 0.8647 (t0) cc_final: 0.8272 (m-30) outliers start: 0 outliers final: 0 residues processed: 98 average time/residue: 0.0651 time to fit residues: 9.6505 Evaluate side-chains 72 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 46 optimal weight: 0.0980 chunk 98 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 chunk 45 optimal weight: 0.7980 chunk 78 optimal weight: 0.9980 chunk 49 optimal weight: 6.9990 chunk 39 optimal weight: 10.0000 chunk 103 optimal weight: 1.9990 chunk 32 optimal weight: 10.0000 chunk 3 optimal weight: 3.9990 chunk 30 optimal weight: 0.9980 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 52 GLN A 146 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** 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 = 0.3655 r_free = 0.3655 target = 0.073994 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.056668 restraints weight = 113180.132| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.059275 restraints weight = 64872.431| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.061139 restraints weight = 43473.041| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 33)----------------| | r_work = 0.3370 r_free = 0.3370 target = 0.062468 restraints weight = 31989.955| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3395 r_free = 0.3395 target = 0.063476 restraints weight = 25105.563| |-----------------------------------------------------------------------------| r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3373 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3373 r_free = 0.3373 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3373 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7124 moved from start: 0.3788 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.057 8464 Z= 0.134 Angle : 0.684 15.590 11544 Z= 0.358 Chirality : 0.045 0.197 1290 Planarity : 0.005 0.053 1490 Dihedral : 5.503 28.680 1159 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 14.75 Ramachandran Plot: Outliers : 0.28 % Allowed : 7.59 % Favored : 92.13 % Rotamer: Outliers : 0.00 % Allowed : 2.44 % Favored : 97.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.00 (0.24), residues: 1059 helix: -3.03 (0.52), residues: 57 sheet: -0.76 (0.28), residues: 307 loop : -1.50 (0.23), residues: 695 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.014 0.002 TYR A 421 PHE 0.035 0.002 PHE A 275 TRP 0.041 0.002 TRP A 353 HIS 0.004 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00286 ( 8449) covalent geometry : angle 0.68036 (11514) SS BOND : bond 0.00485 ( 15) SS BOND : angle 1.46064 ( 30) hydrogen bonds : bond 0.03576 ( 195) hydrogen bonds : angle 7.89070 ( 491) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 94 time to evaluate : 0.262 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 105 ILE cc_start: 0.8024 (mt) cc_final: 0.7723 (mt) REVERT: A 329 PHE cc_start: 0.8310 (m-80) cc_final: 0.8065 (m-80) REVERT: A 365 TYR cc_start: 0.8586 (m-80) cc_final: 0.8296 (m-80) REVERT: A 392 PHE cc_start: 0.7721 (m-80) cc_final: 0.6849 (m-80) REVERT: H 5 VAL cc_start: 0.8968 (m) cc_final: 0.8764 (p) REVERT: H 46 GLU cc_start: 0.8690 (tt0) cc_final: 0.8403 (tt0) REVERT: H 111 TRP cc_start: 0.6964 (m100) cc_final: 0.6240 (m100) REVERT: H 217 LYS cc_start: 0.8401 (mtpt) cc_final: 0.8134 (mtpt) REVERT: L 4 MET cc_start: 0.9010 (mpp) cc_final: 0.8612 (mpp) REVERT: L 137 ASN cc_start: 0.7969 (t0) cc_final: 0.7697 (t0) REVERT: L 169 LYS cc_start: 0.9715 (mmmt) cc_final: 0.8933 (tmtt) REVERT: L 185 ASP cc_start: 0.8717 (t0) cc_final: 0.8316 (m-30) outliers start: 0 outliers final: 0 residues processed: 94 average time/residue: 0.0679 time to fit residues: 9.6235 Evaluate side-chains 72 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 72 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 56 optimal weight: 8.9990 chunk 102 optimal weight: 4.9990 chunk 88 optimal weight: 8.9990 chunk 50 optimal weight: 7.9990 chunk 54 optimal weight: 0.7980 chunk 91 optimal weight: 0.0030 chunk 9 optimal weight: 5.9990 chunk 66 optimal weight: 0.9980 chunk 81 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 86 optimal weight: 7.9990 overall best weight: 2.1594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN L 38 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 GLN ** 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 = 0.3574 r_free = 0.3574 target = 0.070430 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3162 r_free = 0.3162 target = 0.054542 restraints weight = 94253.312| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3220 r_free = 0.3220 target = 0.056737 restraints weight = 57602.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.3261 r_free = 0.3261 target = 0.058286 restraints weight = 40015.901| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 30)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.059418 restraints weight = 30181.670| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 36)----------------| | r_work = 0.3312 r_free = 0.3312 target = 0.060261 restraints weight = 24164.810| |-----------------------------------------------------------------------------| r_work (final): 0.3294 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3293 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.04 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3293 r_free = 0.3293 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3293 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7262 moved from start: 0.4383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.085 8464 Z= 0.213 Angle : 0.760 14.546 11544 Z= 0.401 Chirality : 0.047 0.190 1290 Planarity : 0.005 0.073 1490 Dihedral : 6.106 32.429 1159 Min Nonbonded Distance : 2.378 Molprobity Statistics. All-atom Clashscore : 21.00 Ramachandran Plot: Outliers : 0.28 % Allowed : 9.20 % Favored : 90.51 % Rotamer: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.05 (0.25), residues: 1059 helix: -2.95 (0.56), residues: 51 sheet: -1.03 (0.28), residues: 319 loop : -1.43 (0.23), residues: 689 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG A 403 TYR 0.020 0.002 TYR A 28 PHE 0.031 0.002 PHE L 71 TRP 0.022 0.003 TRP A 353 HIS 0.006 0.001 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00458 ( 8449) covalent geometry : angle 0.75658 (11514) SS BOND : bond 0.00687 ( 15) SS BOND : angle 1.66882 ( 30) hydrogen bonds : bond 0.04160 ( 195) hydrogen bonds : angle 8.13404 ( 491) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.259 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8492 (m-80) cc_final: 0.8250 (m-80) REVERT: A 365 TYR cc_start: 0.8596 (m-80) cc_final: 0.8174 (m-80) REVERT: A 392 PHE cc_start: 0.7628 (m-80) cc_final: 0.6818 (m-80) REVERT: H 36 TRP cc_start: 0.8437 (m100) cc_final: 0.7179 (m100) REVERT: H 153 TYR cc_start: 0.8218 (p90) cc_final: 0.7884 (p90) REVERT: L 4 MET cc_start: 0.9121 (mpp) cc_final: 0.8756 (mpp) REVERT: L 185 ASP cc_start: 0.8627 (t0) cc_final: 0.8207 (m-30) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0679 time to fit residues: 9.1946 Evaluate side-chains 65 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 65 time to evaluate : 0.202 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 57 optimal weight: 0.9990 chunk 102 optimal weight: 1.9990 chunk 59 optimal weight: 9.9990 chunk 41 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 81 optimal weight: 1.9990 chunk 19 optimal weight: 0.7980 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 20.0000 chunk 87 optimal weight: 0.9990 chunk 23 optimal weight: 9.9990 overall best weight: 1.3588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 146 HIS ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 160 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3602 r_free = 0.3602 target = 0.071699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3153 r_free = 0.3153 target = 0.054130 restraints weight = 129819.363| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3221 r_free = 0.3221 target = 0.056772 restraints weight = 73079.918| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 44)----------------| | r_work = 0.3270 r_free = 0.3270 target = 0.058677 restraints weight = 48267.852| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 28)----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.060068 restraints weight = 35115.821| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 47)----------------| | r_work = 0.3332 r_free = 0.3332 target = 0.061110 restraints weight = 27261.104| |-----------------------------------------------------------------------------| r_work (final): 0.3313 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3313 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3313 r_free = 0.3313 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3313 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7224 moved from start: 0.4747 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.108 8464 Z= 0.162 Angle : 0.720 15.710 11544 Z= 0.378 Chirality : 0.046 0.177 1290 Planarity : 0.005 0.059 1490 Dihedral : 5.830 33.941 1159 Min Nonbonded Distance : 2.402 Molprobity Statistics. All-atom Clashscore : 17.14 Ramachandran Plot: Outliers : 0.28 % Allowed : 8.25 % Favored : 91.46 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.09 (0.25), residues: 1059 helix: -2.85 (0.54), residues: 57 sheet: -0.95 (0.28), residues: 331 loop : -1.52 (0.24), residues: 671 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.001 ARG H 98 TYR 0.024 0.002 TYR H 33 PHE 0.024 0.002 PHE L 71 TRP 0.016 0.002 TRP A 353 HIS 0.005 0.001 HIS H 35 Details of bonding type rmsd covalent geometry : bond 0.00362 ( 8449) covalent geometry : angle 0.71502 (11514) SS BOND : bond 0.00635 ( 15) SS BOND : angle 1.77912 ( 30) hydrogen bonds : bond 0.03646 ( 195) hydrogen bonds : angle 7.79718 ( 491) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 95 time to evaluate : 0.310 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 329 PHE cc_start: 0.8401 (m-80) cc_final: 0.8166 (m-80) REVERT: A 335 LEU cc_start: 0.9221 (pt) cc_final: 0.8893 (tp) REVERT: A 365 TYR cc_start: 0.8567 (m-80) cc_final: 0.8091 (m-80) REVERT: A 392 PHE cc_start: 0.7661 (m-80) cc_final: 0.6899 (m-80) REVERT: A 418 ILE cc_start: 0.9241 (pt) cc_final: 0.8967 (mm) REVERT: H 46 GLU cc_start: 0.8752 (tt0) cc_final: 0.8530 (tt0) REVERT: H 217 LYS cc_start: 0.7836 (mttt) cc_final: 0.7469 (ptmt) REVERT: H 218 LYS cc_start: 0.8582 (mttt) cc_final: 0.8361 (mmtt) REVERT: L 4 MET cc_start: 0.9138 (mpp) cc_final: 0.8851 (mpp) REVERT: L 94 TRP cc_start: 0.7602 (t-100) cc_final: 0.6979 (t60) REVERT: L 114 SER cc_start: 0.8234 (t) cc_final: 0.8028 (m) REVERT: L 169 LYS cc_start: 0.9688 (mmmt) cc_final: 0.8907 (tmtt) REVERT: L 185 ASP cc_start: 0.8743 (t0) cc_final: 0.8409 (m-30) outliers start: 0 outliers final: 0 residues processed: 95 average time/residue: 0.0769 time to fit residues: 10.5660 Evaluate side-chains 71 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 71 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 6 optimal weight: 8.9990 chunk 43 optimal weight: 6.9990 chunk 36 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 60 optimal weight: 5.9990 chunk 103 optimal weight: 5.9990 chunk 0 optimal weight: 20.0000 chunk 2 optimal weight: 0.1980 chunk 4 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 87 optimal weight: 6.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 69 HIS ** A 501 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 27 GLN ** L 90 GLN ** 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 = 0.3503 r_free = 0.3503 target = 0.067676 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.3054 r_free = 0.3054 target = 0.050823 restraints weight = 164927.707| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.053926 restraints weight = 87552.606| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3183 r_free = 0.3183 target = 0.055610 restraints weight = 48803.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 24)----------------| | r_work = 0.3198 r_free = 0.3198 target = 0.056125 restraints weight = 34931.260| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3212 r_free = 0.3212 target = 0.056654 restraints weight = 30843.723| |-----------------------------------------------------------------------------| r_work (final): 0.3190 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3190 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3190 r_free = 0.3190 target_work(ls_wunit_k1) = 0.056 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3190 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7395 moved from start: 0.5556 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.167 8464 Z= 0.264 Angle : 0.856 15.691 11544 Z= 0.453 Chirality : 0.049 0.196 1290 Planarity : 0.006 0.063 1490 Dihedral : 6.662 35.998 1159 Min Nonbonded Distance : 2.381 Molprobity Statistics. All-atom Clashscore : 26.18 Ramachandran Plot: Outliers : 0.19 % Allowed : 11.20 % Favored : 88.61 % Rotamer: Outliers : 0.00 % Allowed : 1.33 % Favored : 98.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.40 (0.24), residues: 1059 helix: -2.84 (0.58), residues: 51 sheet: -1.18 (0.30), residues: 305 loop : -1.76 (0.22), residues: 703 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG A 403 TYR 0.025 0.003 TYR A 28 PHE 0.050 0.003 PHE L 71 TRP 0.017 0.003 TRP A 353 HIS 0.010 0.002 HIS H 208 Details of bonding type rmsd covalent geometry : bond 0.00579 ( 8449) covalent geometry : angle 0.85101 (11514) SS BOND : bond 0.00759 ( 15) SS BOND : angle 1.93144 ( 30) hydrogen bonds : bond 0.04391 ( 195) hydrogen bonds : angle 8.41518 ( 491) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 90 time to evaluate : 0.196 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8548 (m-80) cc_final: 0.8002 (m-80) REVERT: A 392 PHE cc_start: 0.7609 (m-80) cc_final: 0.6400 (m-80) REVERT: A 418 ILE cc_start: 0.9253 (pt) cc_final: 0.8995 (mm) REVERT: H 153 TYR cc_start: 0.8162 (p90) cc_final: 0.7388 (p90) REVERT: H 214 LYS cc_start: 0.9132 (tptp) cc_final: 0.8728 (mttp) REVERT: L 32 TYR cc_start: 0.9093 (m-80) cc_final: 0.8717 (m-80) REVERT: L 48 ILE cc_start: 0.9381 (mt) cc_final: 0.9151 (mm) REVERT: L 137 ASN cc_start: 0.7747 (t0) cc_final: 0.7543 (t0) REVERT: L 175 LEU cc_start: 0.9299 (tp) cc_final: 0.9064 (tp) outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.0699 time to fit residues: 9.4335 Evaluate side-chains 59 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 59 time to evaluate : 0.291 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 92 optimal weight: 3.9990 chunk 12 optimal weight: 9.9990 chunk 29 optimal weight: 20.0000 chunk 79 optimal weight: 6.9990 chunk 51 optimal weight: 5.9990 chunk 86 optimal weight: 8.9990 chunk 16 optimal weight: 5.9990 chunk 52 optimal weight: 7.9990 chunk 2 optimal weight: 0.6980 chunk 38 optimal weight: 0.0970 chunk 39 optimal weight: 6.9990 overall best weight: 3.3584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 149 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 245 HIS ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN ** A 580 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 606 ASN L 27 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 166 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3458 r_free = 0.3458 target = 0.066018 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.2994 r_free = 0.2994 target = 0.048833 restraints weight = 189742.151| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 25)----------------| | r_work = 0.3102 r_free = 0.3102 target = 0.052717 restraints weight = 94555.102| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.054597 restraints weight = 49002.884| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 29)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.054673 restraints weight = 36930.487| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 27)----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.055394 restraints weight = 31950.672| |-----------------------------------------------------------------------------| r_work (final): 0.3163 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3163 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3163 r_free = 0.3163 target_work(ls_wunit_k1) = 0.055 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3163 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.6432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.175 8464 Z= 0.298 Angle : 0.913 16.574 11544 Z= 0.487 Chirality : 0.051 0.227 1290 Planarity : 0.006 0.057 1490 Dihedral : 7.320 41.157 1159 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 29.79 Ramachandran Plot: Outliers : 0.28 % Allowed : 12.24 % Favored : 87.48 % Rotamer: Outliers : 0.00 % Allowed : 1.11 % Favored : 98.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.30 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.72 (0.24), residues: 1059 helix: -2.95 (0.54), residues: 58 sheet: -1.42 (0.30), residues: 303 loop : -1.97 (0.21), residues: 698 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.001 ARG H 67 TYR 0.052 0.003 TYR H 33 PHE 0.056 0.003 PHE A 65 TRP 0.035 0.004 TRP H 36 HIS 0.007 0.002 HIS H 172 Details of bonding type rmsd covalent geometry : bond 0.00648 ( 8449) covalent geometry : angle 0.90911 (11514) SS BOND : bond 0.00767 ( 15) SS BOND : angle 1.85967 ( 30) hydrogen bonds : bond 0.04502 ( 195) hydrogen bonds : angle 8.84079 ( 491) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 84 time to evaluate : 0.313 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 365 TYR cc_start: 0.8557 (m-80) cc_final: 0.7984 (m-80) REVERT: A 392 PHE cc_start: 0.7642 (m-80) cc_final: 0.6560 (m-80) REVERT: A 398 ASP cc_start: 0.9052 (m-30) cc_final: 0.8827 (m-30) REVERT: H 36 TRP cc_start: 0.8570 (m100) cc_final: 0.7081 (m100) REVERT: H 153 TYR cc_start: 0.8112 (p90) cc_final: 0.7370 (p90) REVERT: L 32 TYR cc_start: 0.9160 (m-80) cc_final: 0.8862 (m-80) REVERT: L 98 PHE cc_start: 0.7820 (m-80) cc_final: 0.6840 (m-80) REVERT: L 175 LEU cc_start: 0.9382 (tp) cc_final: 0.9143 (tp) outliers start: 0 outliers final: 0 residues processed: 84 average time/residue: 0.0673 time to fit residues: 8.7533 Evaluate side-chains 62 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 62 time to evaluate : 0.316 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 19 optimal weight: 1.9990 chunk 102 optimal weight: 0.9990 chunk 20 optimal weight: 0.8980 chunk 69 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 92 optimal weight: 2.9990 chunk 11 optimal weight: 8.9990 chunk 18 optimal weight: 4.9990 chunk 101 optimal weight: 7.9990 chunk 86 optimal weight: 5.9990 chunk 49 optimal weight: 7.9990 overall best weight: 1.5586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 450 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 90 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 = 0.3522 r_free = 0.3522 target = 0.068599 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.051587 restraints weight = 129136.583| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3166 r_free = 0.3166 target = 0.054953 restraints weight = 72420.690| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 29)----------------| | r_work = 0.3232 r_free = 0.3232 target = 0.057399 restraints weight = 40507.963| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 34)----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.058600 restraints weight = 24685.584| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 24)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.058895 restraints weight = 19788.646| |-----------------------------------------------------------------------------| r_work (final): 0.3262 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3262 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3262 r_free = 0.3262 target_work(ls_wunit_k1) = 0.058 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3262 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7320 moved from start: 0.6386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.101 8464 Z= 0.184 Angle : 0.789 15.968 11544 Z= 0.416 Chirality : 0.048 0.200 1290 Planarity : 0.005 0.054 1490 Dihedral : 6.670 35.508 1159 Min Nonbonded Distance : 2.383 Molprobity Statistics. All-atom Clashscore : 21.19 Ramachandran Plot: Outliers : 0.19 % Allowed : 10.25 % Favored : 89.56 % Rotamer: Outliers : 0.00 % Allowed : 0.33 % Favored : 99.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.20 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.56 (0.24), residues: 1059 helix: -2.79 (0.56), residues: 56 sheet: -1.27 (0.29), residues: 320 loop : -1.89 (0.22), residues: 683 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 355 TYR 0.034 0.002 TYR H 33 PHE 0.047 0.002 PHE A 65 TRP 0.030 0.003 TRP L 94 HIS 0.009 0.002 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00404 ( 8449) covalent geometry : angle 0.78563 (11514) SS BOND : bond 0.00617 ( 15) SS BOND : angle 1.65668 ( 30) hydrogen bonds : bond 0.03780 ( 195) hydrogen bonds : angle 8.33690 ( 491) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2118 Ramachandran restraints generated. 1059 Oldfield, 0 Emsley, 1059 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 87 time to evaluate : 0.191 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 177 MET cc_start: 0.6817 (mtp) cc_final: 0.6525 (mtp) REVERT: A 335 LEU cc_start: 0.9152 (pt) cc_final: 0.8860 (tp) REVERT: A 365 TYR cc_start: 0.8320 (m-80) cc_final: 0.7658 (m-80) REVERT: A 392 PHE cc_start: 0.7588 (m-80) cc_final: 0.6908 (m-80) REVERT: A 398 ASP cc_start: 0.8875 (m-30) cc_final: 0.8593 (m-30) REVERT: A 418 ILE cc_start: 0.9179 (pt) cc_final: 0.8951 (mm) REVERT: H 83 MET cc_start: 0.8794 (mmp) cc_final: 0.8275 (mmp) REVERT: H 206 VAL cc_start: 0.9343 (t) cc_final: 0.9117 (m) REVERT: L 4 MET cc_start: 0.9037 (mpp) cc_final: 0.8735 (mpp) REVERT: L 32 TYR cc_start: 0.9159 (m-80) cc_final: 0.8877 (m-80) REVERT: L 98 PHE cc_start: 0.8286 (m-80) cc_final: 0.7332 (m-80) REVERT: L 106 ILE cc_start: 0.8231 (tp) cc_final: 0.7941 (tp) outliers start: 0 outliers final: 0 residues processed: 87 average time/residue: 0.0672 time to fit residues: 8.9228 Evaluate side-chains 64 residues out of total 935 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 64 time to evaluate : 0.310 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 106 random chunks: chunk 104 optimal weight: 0.0060 chunk 35 optimal weight: 0.1980 chunk 87 optimal weight: 4.9990 chunk 29 optimal weight: 10.0000 chunk 0 optimal weight: 20.0000 chunk 49 optimal weight: 0.1980 chunk 20 optimal weight: 3.9990 chunk 84 optimal weight: 0.4980 chunk 60 optimal weight: 5.9990 chunk 99 optimal weight: 2.9990 chunk 11 optimal weight: 4.9990 overall best weight: 0.7798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 146 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN A 563 GLN A 641 ASN H 3 GLN ** L 90 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.070450 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.055018 restraints weight = 82638.630| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3231 r_free = 0.3231 target = 0.057094 restraints weight = 51847.268| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 35)----------------| | r_work = 0.3274 r_free = 0.3274 target = 0.058638 restraints weight = 36437.435| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 4; iterations = 37)----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.059771 restraints weight = 27495.226| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 5; iterations = 37)----------------| | r_work = 0.3326 r_free = 0.3326 target = 0.060610 restraints weight = 21892.236| |-----------------------------------------------------------------------------| r_work (final): 0.3314 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.3315 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.3315 r_free = 0.3315 target_work(ls_wunit_k1) = 0.060 | | occupancies: max = 1.00 min = 0.00 number of occupancies < 0.1: 9 | |-----------------------------------------------------------------------------| r_final: 0.3315 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7239 moved from start: 0.6394 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 8464 Z= 0.143 Angle : 0.728 15.330 11544 Z= 0.381 Chirality : 0.047 0.196 1290 Planarity : 0.005 0.056 1490 Dihedral : 6.061 32.996 1159 Min Nonbonded Distance : 2.361 Molprobity Statistics. All-atom Clashscore : 16.08 Ramachandran Plot: Outliers : 0.19 % Allowed : 9.01 % Favored : 90.80 % Rotamer: Outliers : 0.00 % Allowed : 0.78 % Favored : 99.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 7.14 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.10 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they are not related in a simple way. whole: -2.25 (0.25), residues: 1059 helix: -2.74 (0.54), residues: 55 sheet: -0.91 (0.30), residues: 310 loop : -1.74 (0.23), residues: 694 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.001 ARG A 457 TYR 0.034 0.002 TYR H 33 PHE 0.039 0.002 PHE A 65 TRP 0.030 0.003 TRP L 94 HIS 0.007 0.002 HIS A 245 Details of bonding type rmsd covalent geometry : bond 0.00313 ( 8449) covalent geometry : angle 0.72474 (11514) SS BOND : bond 0.00577 ( 15) SS BOND : angle 1.54841 ( 30) hydrogen bonds : bond 0.03434 ( 195) hydrogen bonds : angle 7.81792 ( 491) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1645.09 seconds wall clock time: 29 minutes 8.63 seconds (1748.63 seconds total)