Starting phenix.real_space_refine on Sun Apr 5 09:44:41 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlg_14779/04_2026/7zlg_14779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlg_14779/04_2026/7zlg_14779.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.72 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { model { file = "/net/cci-nas-00/data/ceres_data/7zlg_14779/04_2026/7zlg_14779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlg_14779/04_2026/7zlg_14779.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/7zlg_14779/04_2026/7zlg_14779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlg_14779/04_2026/7zlg_14779.map" } resolution = 2.72 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= 0.001 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 44 5.16 5 C 6191 2.51 5 N 1593 2.21 5 O 1790 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 2 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.1rc1-6017/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 9618 Number of models: 1 Model: "" Number of chains: 7 Chain: "H" Number of atoms: 1679 Number of conformers: 1 Conformer: "" Number of residues, atoms: 226, 1679 Classifications: {'peptide': 226} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 214} Unresolved non-hydrogen bonds: 5 Unresolved non-hydrogen angles: 5 Unresolved non-hydrogen dihedrals: 5 Chain: "K" Number of atoms: 921 Number of conformers: 1 Conformer: "" Number of residues, atoms: 120, 921 Classifications: {'peptide': 120} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 116} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "L" Number of atoms: 1598 Number of conformers: 1 Conformer: "" Number of residues, atoms: 211, 1598 Classifications: {'peptide': 211} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PCIS': 1, 'PTRANS': 10, 'TRANS': 199} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "A" Number of atoms: 5352 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} Conformer: "B" Number of residues, atoms: 662, 5338 Classifications: {'peptide': 662} Link IDs: {'PTRANS': 24, 'TRANS': 637} bond proxies already assigned to first conformer: 5464 Chain: "P" Number of atoms: 58 Number of conformers: 1 Conformer: "" Number of residues, atoms: 7, 58 Classifications: {'peptide': 7} Link IDs: {'TRANS': 6} Chain: "A" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Chain: "P" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Classifications: {'water': 1} Residues with excluded nonbonded symmetry interactions: 1 residue: pdb=" N ATRP A 214 " occ=0.50 ... (26 atoms not shown) pdb=" CH2BTRP A 214 " occ=0.50 Time building chain proxies: 3.24, per 1000 atoms: 0.34 Number of scatterers: 9618 At special positions: 0 Unit cell: (101.64, 162.36, 97.68, 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 44 16.00 O 1790 8.00 N 1593 7.00 C 6191 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=8, symmetry=0 Simple disulfide: pdb=" SG CYS H 25 " - pdb=" SG CYS H 99 " distance=2.03 Simple disulfide: pdb=" SG CYS H 155 " - pdb=" SG CYS H 211 " distance=2.03 Simple disulfide: pdb=" SG CYS K 22 " - pdb=" SG CYS K 96 " distance=2.04 Simple disulfide: pdb=" SG CYS L 24 " - pdb=" SG CYS L 89 " distance=2.03 Simple disulfide: pdb=" SG CYS L 135 " - pdb=" SG CYS L 195 " distance=2.03 Simple disulfide: pdb=" SG CYS A 142 " - pdb=" SG CYS A 156 " distance=2.03 Simple disulfide: pdb=" SG CYS A 397 " - pdb=" SG CYS A 630 " distance=2.04 Simple disulfide: pdb=" SG CYS A 621 " - pdb=" SG CYS A 650 " 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: 0.73 Conformation dependent library (CDL) restraints added in 650.1 milliseconds 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2290 Finding SS restraints... Secondary structure from input PDB file: 43 helices and 14 sheets defined 42.0% alpha, 21.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.38 Creating SS restraints... Processing helix chain 'H' and resid 65 through 68 Processing helix chain 'H' and resid 104 through 108 Processing helix chain 'H' and resid 171 through 173 No H-bonds generated for 'chain 'H' and resid 171 through 173' Processing helix chain 'H' and resid 202 through 207 removed outlier: 3.988A pdb=" N GLN H 207 " --> pdb=" O LEU H 204 " (cutoff:3.500A) Processing helix chain 'K' and resid 62 through 65 removed outlier: 3.993A pdb=" N GLN K 65 " --> pdb=" O ASP K 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'K' and resid 62 through 65' Processing helix chain 'L' and resid 122 through 127 removed outlier: 4.199A pdb=" N LEU L 126 " --> pdb=" O ASP L 123 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N LYS L 127 " --> pdb=" O SER L 124 " (cutoff:3.500A) Processing helix chain 'L' and resid 183 through 188 removed outlier: 3.890A pdb=" N GLU L 188 " --> pdb=" O LYS L 184 " (cutoff:3.500A) Processing helix chain 'A' and resid 25 through 55 Processing helix chain 'A' and resid 56 through 59 removed outlier: 3.550A pdb=" N LEU A 59 " --> pdb=" O PHE A 56 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 56 through 59' Processing helix chain 'A' and resid 60 through 68 Processing helix chain 'A' and resid 71 through 85 removed outlier: 4.037A pdb=" N TYR A 78 " --> pdb=" O LEU A 74 " (cutoff:3.500A) removed outlier: 3.802A pdb=" N TYR A 79 " --> pdb=" O TYR A 75 " (cutoff:3.500A) Processing helix chain 'A' and resid 87 through 97 Processing helix chain 'A' and resid 108 through 113 Processing helix chain 'A' and resid 115 through 135 Proline residue: A 127 - end of helix Processing helix chain 'A' and resid 161 through 188 removed outlier: 4.080A pdb=" N THR A 176 " --> pdb=" O ILE A 172 " (cutoff:3.500A) removed outlier: 4.672A pdb=" N VAL A 177 " --> pdb=" O VAL A 173 " (cutoff:3.500A) removed outlier: 4.850A pdb=" N ALA A 178 " --> pdb=" O ALA A 174 " (cutoff:3.500A) removed outlier: 4.190A pdb=" N SER A 179 " --> pdb=" O GLY A 175 " (cutoff:3.500A) Processing helix chain 'A' and resid 191 through 205 removed outlier: 3.762A pdb=" N GLY A 195 " --> pdb=" O SER A 191 " (cutoff:3.500A) Processing helix chain 'A' and resid 205 through 210 Processing helix chain 'A' and resid 218 through 241 removed outlier: 3.933A pdb=" N PHE A 222 " --> pdb=" O LEU A 218 " (cutoff:3.500A) Proline residue: A 225 - end of helix Processing helix chain 'A' and resid 244 through 261 removed outlier: 3.616A pdb=" N MET A 254 " --> pdb=" O LEU A 250 " (cutoff:3.500A) Proline residue: A 257 - end of helix Processing helix chain 'A' and resid 264 through 281 Processing helix chain 'A' and resid 286 through 308 Processing helix chain 'A' and resid 311 through 315 Processing helix chain 'A' and resid 318 through 332 removed outlier: 3.576A pdb=" N SER A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 337 Processing helix chain 'A' and resid 341 through 366 Processing helix chain 'A' and resid 374 through 385 removed outlier: 3.579A pdb=" N PHE A 384 " --> pdb=" O LEU A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 389 through 396 Processing helix chain 'A' and resid 405 through 415 removed outlier: 3.604A pdb=" N ILE A 409 " --> pdb=" O GLN A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 417 through 436 Processing helix chain 'A' and resid 449 through 469 Processing helix chain 'A' and resid 472 through 485 removed outlier: 3.554A pdb=" N MET A 476 " --> pdb=" O LEU A 472 " (cutoff:3.500A) Proline residue: A 478 - end of helix removed outlier: 3.536A pdb=" N ALA A 485 " --> pdb=" O CYS A 481 " (cutoff:3.500A) Processing helix chain 'A' and resid 486 through 489 Processing helix chain 'A' and resid 500 through 517 Processing helix chain 'A' and resid 518 through 527 Processing helix chain 'A' and resid 534 through 548 removed outlier: 4.149A pdb=" N GLU A 538 " --> pdb=" O ASN A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 557 through 567 removed outlier: 3.652A pdb=" N ASN A 563 " --> pdb=" O PRO A 559 " (cutoff:3.500A) Processing helix chain 'A' and resid 583 through 591 Processing helix chain 'A' and resid 592 through 595 Processing helix chain 'A' and resid 598 through 610 Processing helix chain 'A' and resid 619 through 622 removed outlier: 3.862A pdb=" N SER A 622 " --> pdb=" O MET A 619 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 619 through 622' Processing helix chain 'A' and resid 631 through 640 removed outlier: 4.034A pdb=" N ASP A 637 " --> pdb=" O ARG A 633 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N GLU A 638 " --> pdb=" O GLY A 634 " (cutoff:3.500A) Processing helix chain 'A' and resid 641 through 644 Processing helix chain 'A' and resid 648 through 660 removed outlier: 3.652A pdb=" N LEU A 652 " --> pdb=" O ALA A 648 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'H' and resid 6 through 10 removed outlier: 3.777A pdb=" N THR H 81 " --> pdb=" O ASP H 76 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'H' and resid 14 through 15 removed outlier: 6.744A pdb=" N ILE H 37 " --> pdb=" O SER H 53 " (cutoff:3.500A) removed outlier: 4.577A pdb=" N SER H 53 " --> pdb=" O ILE H 37 " (cutoff:3.500A) removed outlier: 6.628A pdb=" N TRP H 39 " --> pdb=" O VAL H 51 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.244A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N VAL H 196 " --> pdb=" O HIS H 179 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N HIS H 179 " --> pdb=" O VAL H 196 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'H' and resid 135 through 139 removed outlier: 6.244A pdb=" N TYR H 191 " --> pdb=" O ASP H 159 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'H' and resid 166 through 169 Processing sheet with id=AA6, first strand: chain 'K' and resid 3 through 6 removed outlier: 4.073A pdb=" N GLN K 3 " --> pdb=" O SER K 25 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.431A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP K 99 " --> pdb=" O ALA K 33 " (cutoff:3.500A) removed outlier: 8.173A pdb=" N ILE K 98 " --> pdb=" O ASP K 109 " (cutoff:3.500A) removed outlier: 4.357A pdb=" N ASP K 109 " --> pdb=" O ILE K 98 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'K' and resid 58 through 60 removed outlier: 5.431A pdb=" N PHE K 47 " --> pdb=" O ARG K 38 " (cutoff:3.500A) removed outlier: 5.712A pdb=" N ARG K 38 " --> pdb=" O PHE K 47 " (cutoff:3.500A) removed outlier: 4.281A pdb=" N ALA K 33 " --> pdb=" O ASP K 99 " (cutoff:3.500A) removed outlier: 4.017A pdb=" N ASP K 99 " --> pdb=" O ALA K 33 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 5 through 6 Processing sheet with id=AB1, first strand: chain 'L' and resid 11 through 14 removed outlier: 3.618A pdb=" N ILE L 49 " --> pdb=" O TRP L 36 " (cutoff:3.500A) removed outlier: 6.193A pdb=" N GLN L 38 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.622A pdb=" N LEU L 47 " --> pdb=" O GLN L 38 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 115 through 119 removed outlier: 6.222A pdb=" N TYR L 174 " --> pdb=" O ASN L 139 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 145 through 150 Processing sheet with id=AB4, first strand: chain 'A' and resid 140 through 145 Processing sheet with id=AB5, first strand: chain 'A' and resid 554 through 556 removed outlier: 6.505A pdb=" N ALA A 555 " --> pdb=" O VAL A 615 " (cutoff:3.500A) removed outlier: 8.950A pdb=" N GLN A 617 " --> pdb=" O ALA A 555 " (cutoff:3.500A) removed outlier: 7.665A pdb=" N TYR A 678 " --> pdb=" O ASN A 673 " (cutoff:3.500A) removed outlier: 4.559A pdb=" N ASN A 673 " --> pdb=" O TYR A 678 " (cutoff:3.500A) removed outlier: 6.542A pdb=" N VAL A 680 " --> pdb=" O VAL A 671 " (cutoff:3.500A) 504 hydrogen bonds defined for protein. 1395 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: 1.50 Time building geometry restraints manager: 1.00 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.32: 1516 1.32 - 1.44: 2869 1.44 - 1.57: 5403 1.57 - 1.69: 0 1.69 - 1.82: 66 Bond restraints: 9854 Sorted by residual: bond pdb=" CG PRO H 44 " pdb=" CD PRO H 44 " ideal model delta sigma weight residual 1.503 1.239 0.264 3.40e-02 8.65e+02 6.02e+01 bond pdb=" C THR A 70 " pdb=" O THR A 70 " ideal model delta sigma weight residual 1.236 1.195 0.042 1.15e-02 7.56e+03 1.31e+01 bond pdb=" N VAL A 581 " pdb=" CA VAL A 581 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.15e-02 7.56e+03 1.23e+01 bond pdb=" N HIS A 580 " pdb=" CA HIS A 580 " ideal model delta sigma weight residual 1.456 1.497 -0.041 1.20e-02 6.94e+03 1.14e+01 bond pdb=" N ARG A 471 " pdb=" CA ARG A 471 " ideal model delta sigma weight residual 1.460 1.503 -0.043 1.28e-02 6.10e+03 1.14e+01 ... (remaining 9849 not shown) Histogram of bond angle deviations from ideal: 0.00 - 4.16: 13337 4.16 - 8.32: 49 8.32 - 12.47: 4 12.47 - 16.63: 0 16.63 - 20.79: 2 Bond angle restraints: 13392 Sorted by residual: angle pdb=" N PRO H 44 " pdb=" CD PRO H 44 " pdb=" CG PRO H 44 " ideal model delta sigma weight residual 103.20 84.45 18.75 1.50e+00 4.44e-01 1.56e+02 angle pdb=" CA PRO H 44 " pdb=" CB PRO H 44 " pdb=" CG PRO H 44 " ideal model delta sigma weight residual 104.50 83.71 20.79 1.90e+00 2.77e-01 1.20e+02 angle pdb=" N THR A 70 " pdb=" CA THR A 70 " pdb=" C THR A 70 " ideal model delta sigma weight residual 111.07 120.40 -9.33 1.07e+00 8.73e-01 7.60e+01 angle pdb=" N PRO H 44 " pdb=" CA PRO H 44 " pdb=" CB PRO H 44 " ideal model delta sigma weight residual 103.27 97.33 5.94 9.00e-01 1.23e+00 4.36e+01 angle pdb=" N LEU A 472 " pdb=" CA LEU A 472 " pdb=" C LEU A 472 " ideal model delta sigma weight residual 113.17 105.23 7.94 1.26e+00 6.30e-01 3.97e+01 ... (remaining 13387 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.70: 5319 17.70 - 35.39: 381 35.39 - 53.09: 65 53.09 - 70.78: 15 70.78 - 88.48: 12 Dihedral angle restraints: 5792 sinusoidal: 2221 harmonic: 3571 Sorted by residual: dihedral pdb=" CB CYS K 22 " pdb=" SG CYS K 22 " pdb=" SG CYS K 96 " pdb=" CB CYS K 96 " ideal model delta sinusoidal sigma weight residual 93.00 30.80 62.20 1 1.00e+01 1.00e-02 5.12e+01 dihedral pdb=" CA GLU A 629 " pdb=" C GLU A 629 " pdb=" N CYS A 630 " pdb=" CA CYS A 630 " ideal model delta harmonic sigma weight residual 180.00 158.12 21.88 0 5.00e+00 4.00e-02 1.91e+01 dihedral pdb=" CA SER H 108 " pdb=" C SER H 108 " pdb=" N TRP H 109 " pdb=" CA TRP H 109 " ideal model delta harmonic sigma weight residual 180.00 158.23 21.77 0 5.00e+00 4.00e-02 1.90e+01 ... (remaining 5789 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.045: 1095 0.045 - 0.090: 311 0.090 - 0.135: 84 0.135 - 0.180: 7 0.180 - 0.225: 4 Chirality restraints: 1501 Sorted by residual: chirality pdb=" CA ILE A 469 " pdb=" N ILE A 469 " pdb=" C ILE A 469 " pdb=" CB ILE A 469 " both_signs ideal model delta sigma weight residual False 2.43 2.66 -0.22 2.00e-01 2.50e+01 1.26e+00 chirality pdb=" CB VAL A 581 " pdb=" CA VAL A 581 " pdb=" CG1 VAL A 581 " pdb=" CG2 VAL A 581 " both_signs ideal model delta sigma weight residual False -2.63 -2.42 -0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CA MET A 470 " pdb=" N MET A 470 " pdb=" C MET A 470 " pdb=" CB MET A 470 " both_signs ideal model delta sigma weight residual False 2.51 2.71 -0.20 2.00e-01 2.50e+01 9.64e-01 ... (remaining 1498 not shown) Planarity restraints: 1687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LYS A 473 " 0.015 2.00e-02 2.50e+03 3.11e-02 9.65e+00 pdb=" C LYS A 473 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS A 473 " 0.020 2.00e-02 2.50e+03 pdb=" N LEU A 474 " 0.019 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 261 " -0.013 2.00e-02 2.50e+03 2.65e-02 7.04e+00 pdb=" C PHE A 261 " 0.046 2.00e-02 2.50e+03 pdb=" O PHE A 261 " -0.017 2.00e-02 2.50e+03 pdb=" N TRP A 262 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 68 " -0.012 2.00e-02 2.50e+03 2.41e-02 5.82e+00 pdb=" C TYR A 68 " 0.042 2.00e-02 2.50e+03 pdb=" O TYR A 68 " -0.016 2.00e-02 2.50e+03 pdb=" N ARG A 69 " -0.014 2.00e-02 2.50e+03 ... (remaining 1684 not shown) Histogram of nonbonded interaction distances: 2.19 - 2.73: 486 2.73 - 3.27: 9590 3.27 - 3.81: 15516 3.81 - 4.36: 18748 4.36 - 4.90: 32213 Nonbonded interactions: 76553 Sorted by model distance: nonbonded pdb=" O ALA A 388 " pdb=" OG1 THR A 392 " model vdw 2.187 3.040 nonbonded pdb=" OD2 ASP A 640 " pdb=" ND2 ASN A 643 " model vdw 2.212 3.120 nonbonded pdb=" OH TYR A 116 " pdb=" O LEU A 307 " model vdw 2.217 3.040 nonbonded pdb=" OG1 THR L 130 " pdb=" O LEU L 182 " model vdw 2.252 3.040 nonbonded pdb=" NH1 ARG A 342 " pdb=" O ASN A 437 " model vdw 2.261 3.120 ... (remaining 76548 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=0.50 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 4.230 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: 0.320 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 11.610 Find NCS groups from input model: 0.050 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:7.120 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.430 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7979 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 0.264 9862 Z= 0.216 Angle : 0.714 20.789 13408 Z= 0.421 Chirality : 0.045 0.225 1501 Planarity : 0.004 0.048 1687 Dihedral : 13.430 88.479 3478 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.36 % Favored : 95.23 % Rotamer: Outliers : 0.66 % Allowed : 0.47 % Favored : 98.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.03 (0.25), residues: 1219 helix: 1.06 (0.26), residues: 444 sheet: 0.91 (0.34), residues: 254 loop : -1.38 (0.26), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG A 393 TYR 0.016 0.001 TYR H 83 PHE 0.013 0.001 PHE A 348 TRP 0.015 0.001 TRP P 0 HIS 0.003 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00425 ( 9854) covalent geometry : angle 0.71327 (13392) SS BOND : bond 0.00323 ( 8) SS BOND : angle 0.99540 ( 16) hydrogen bonds : bond 0.15416 ( 479) hydrogen bonds : angle 6.00019 ( 1395) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 123 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 116 time to evaluate : 0.317 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 44 PRO cc_start: 0.4929 (OUTLIER) cc_final: 0.4540 (Cg_endo) REVERT: H 86 MET cc_start: 0.5848 (mpp) cc_final: 0.5559 (mpp) REVERT: L 5 MET cc_start: 0.4857 (mmm) cc_final: 0.4531 (mtp) REVERT: L 38 GLN cc_start: 0.5500 (tt0) cc_final: 0.5241 (tt0) REVERT: A 561 MET cc_start: 0.8716 (mmp) cc_final: 0.8476 (mmp) outliers start: 7 outliers final: 1 residues processed: 122 average time/residue: 0.6069 time to fit residues: 78.9212 Evaluate side-chains 94 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 92 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 44 PRO Chi-restraints excluded: chain A residue 70 THR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 108 optimal weight: 0.9980 chunk 49 optimal weight: 0.2980 chunk 97 optimal weight: 3.9990 chunk 113 optimal weight: 1.9990 chunk 53 optimal weight: 30.0000 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 10.0000 chunk 65 optimal weight: 0.6980 chunk 62 optimal weight: 0.3980 chunk 51 optimal weight: 6.9990 chunk 117 optimal weight: 2.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 431 ASN A 525 GLN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4372 r_free = 0.4372 target = 0.210997 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3341 r_free = 0.3341 target = 0.119392 restraints weight = 17272.441| |-----------------------------------------------------------------------------| r_work (start): 0.3241 rms_B_bonded: 2.95 r_work: 0.2956 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2956 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2974 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2974 r_free = 0.2974 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2973 r_free = 0.2973 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2973 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.0992 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 9862 Z= 0.146 Angle : 0.610 9.079 13408 Z= 0.321 Chirality : 0.045 0.149 1501 Planarity : 0.005 0.056 1687 Dihedral : 4.413 31.152 1333 Min Nonbonded Distance : 2.489 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.35 % Favored : 94.41 % Rotamer: Outliers : 1.14 % Allowed : 7.79 % Favored : 91.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % 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: 0.24 (0.25), residues: 1219 helix: 1.32 (0.25), residues: 456 sheet: 0.93 (0.34), residues: 250 loop : -1.34 (0.27), residues: 513 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.001 ARG A 69 TYR 0.021 0.001 TYR H 83 PHE 0.014 0.001 PHE A 320 TRP 0.027 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00326 ( 9854) covalent geometry : angle 0.60916 (13392) SS BOND : bond 0.00409 ( 8) SS BOND : angle 1.00990 ( 16) hydrogen bonds : bond 0.04773 ( 479) hydrogen bonds : angle 4.72581 ( 1395) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 96 time to evaluate : 0.442 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3498 (p90) cc_final: 0.2946 (p90) REVERT: H 171 SER cc_start: 0.6287 (t) cc_final: 0.6026 (t) REVERT: L 38 GLN cc_start: 0.5461 (tt0) cc_final: 0.5137 (tt0) REVERT: A 51 GLU cc_start: 0.8191 (mm-30) cc_final: 0.7828 (tp30) outliers start: 12 outliers final: 6 residues processed: 106 average time/residue: 0.5276 time to fit residues: 60.2331 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 91 time to evaluate : 0.301 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 2 optimal weight: 7.9990 chunk 65 optimal weight: 0.8980 chunk 21 optimal weight: 0.8980 chunk 40 optimal weight: 8.9990 chunk 90 optimal weight: 0.8980 chunk 66 optimal weight: 4.9990 chunk 95 optimal weight: 2.9990 chunk 26 optimal weight: 20.0000 chunk 79 optimal weight: 0.2980 chunk 33 optimal weight: 50.0000 chunk 44 optimal weight: 9.9990 overall best weight: 1.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN A 375 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN ** A 662 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4356 r_free = 0.4356 target = 0.209378 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114961 restraints weight = 16006.343| |-----------------------------------------------------------------------------| r_work (start): 0.3211 rms_B_bonded: 2.61 r_work: 0.3001 rms_B_bonded: 2.84 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.42 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2838 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2838 r_free = 0.2838 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2838 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8212 moved from start: 0.1268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 9862 Z= 0.165 Angle : 0.619 9.777 13408 Z= 0.327 Chirality : 0.046 0.166 1501 Planarity : 0.005 0.058 1687 Dihedral : 4.511 32.675 1330 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.59 % Favored : 94.24 % Rotamer: Outliers : 1.52 % Allowed : 9.97 % Favored : 88.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.21 (0.25), residues: 1219 helix: 1.37 (0.25), residues: 454 sheet: 0.85 (0.35), residues: 246 loop : -1.36 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 664 TYR 0.017 0.002 TYR A 319 PHE 0.016 0.002 PHE A 387 TRP 0.014 0.002 TRP H 110 HIS 0.006 0.001 HIS A 375 Details of bonding type rmsd covalent geometry : bond 0.00384 ( 9854) covalent geometry : angle 0.61864 (13392) SS BOND : bond 0.00416 ( 8) SS BOND : angle 1.10357 ( 16) hydrogen bonds : bond 0.05121 ( 479) hydrogen bonds : angle 4.54920 ( 1395) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6435 (OUTLIER) cc_final: 0.6069 (mpp) REVERT: H 160 TYR cc_start: 0.3298 (p90) cc_final: 0.2780 (p90) REVERT: A 51 GLU cc_start: 0.8424 (mm-30) cc_final: 0.7941 (tp30) REVERT: A 493 LEU cc_start: 0.8424 (OUTLIER) cc_final: 0.8187 (mp) REVERT: A 542 ASP cc_start: 0.8499 (OUTLIER) cc_final: 0.8217 (m-30) outliers start: 16 outliers final: 8 residues processed: 107 average time/residue: 0.5657 time to fit residues: 65.0469 Evaluate side-chains 103 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 92 time to evaluate : 0.367 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 57 SER Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 47 optimal weight: 6.9990 chunk 81 optimal weight: 2.9990 chunk 18 optimal weight: 9.9990 chunk 22 optimal weight: 70.0000 chunk 44 optimal weight: 6.9990 chunk 75 optimal weight: 1.9990 chunk 66 optimal weight: 6.9990 chunk 45 optimal weight: 5.9990 chunk 53 optimal weight: 6.9990 chunk 0 optimal weight: 20.0000 chunk 90 optimal weight: 1.9990 overall best weight: 3.9990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 179 HIS ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 55 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 662 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4308 r_free = 0.4308 target = 0.204389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3234 r_free = 0.3234 target = 0.111780 restraints weight = 19797.025| |-----------------------------------------------------------------------------| r_work (start): 0.3115 rms_B_bonded: 3.49 r_work: 0.2833 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2833 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2833 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2833 r_free = 0.2833 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2833 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8239 moved from start: 0.1822 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.103 9862 Z= 0.420 Angle : 0.882 18.211 13408 Z= 0.469 Chirality : 0.059 0.340 1501 Planarity : 0.007 0.080 1687 Dihedral : 5.350 37.009 1330 Min Nonbonded Distance : 2.401 Molprobity Statistics. All-atom Clashscore : 7.97 Ramachandran Plot: Outliers : 0.41 % Allowed : 5.92 % Favored : 93.67 % Rotamer: Outliers : 1.90 % Allowed : 11.87 % Favored : 86.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.43 (0.24), residues: 1219 helix: 0.56 (0.24), residues: 451 sheet: 0.57 (0.33), residues: 263 loop : -1.52 (0.27), residues: 505 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 393 TYR 0.022 0.003 TYR A 345 PHE 0.026 0.003 PHE A 387 TRP 0.051 0.004 TRP H 109 HIS 0.008 0.003 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.01048 ( 9854) covalent geometry : angle 0.87636 (13392) SS BOND : bond 0.01267 ( 8) SS BOND : angle 2.95976 ( 16) hydrogen bonds : bond 0.07747 ( 479) hydrogen bonds : angle 4.96845 ( 1395) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 76 time to evaluate : 0.358 Fit side-chains REVERT: H 160 TYR cc_start: 0.3291 (p90) cc_final: 0.2774 (p90) REVERT: A 51 GLU cc_start: 0.8328 (mm-30) cc_final: 0.7835 (tp30) REVERT: A 493 LEU cc_start: 0.8450 (OUTLIER) cc_final: 0.8176 (mp) REVERT: A 542 ASP cc_start: 0.8521 (OUTLIER) cc_final: 0.8077 (m-30) outliers start: 20 outliers final: 9 residues processed: 91 average time/residue: 0.5526 time to fit residues: 54.1131 Evaluate side-chains 87 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 76 time to evaluate : 0.350 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 33 optimal weight: 50.0000 chunk 11 optimal weight: 4.9990 chunk 37 optimal weight: 3.9990 chunk 92 optimal weight: 0.9980 chunk 40 optimal weight: 8.9990 chunk 96 optimal weight: 0.5980 chunk 31 optimal weight: 20.0000 chunk 58 optimal weight: 0.6980 chunk 109 optimal weight: 0.6980 chunk 13 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 overall best weight: 1.3982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 156 GLN A 431 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4338 r_free = 0.4338 target = 0.207813 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.111175 restraints weight = 13721.125| |-----------------------------------------------------------------------------| r_work (start): 0.3145 rms_B_bonded: 2.25 r_work: 0.3012 rms_B_bonded: 2.37 restraints_weight: 0.5000 r_work: 0.2880 rms_B_bonded: 3.74 restraints_weight: 0.2500 r_work (final): 0.2880 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2859 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.28 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2859 r_free = 0.2859 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2859 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8169 moved from start: 0.1710 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.087 9862 Z= 0.187 Angle : 0.673 16.754 13408 Z= 0.355 Chirality : 0.047 0.257 1501 Planarity : 0.005 0.049 1687 Dihedral : 4.946 33.472 1330 Min Nonbonded Distance : 2.436 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.59 % Favored : 94.16 % Rotamer: Outliers : 1.90 % Allowed : 13.11 % Favored : 85.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.13 (0.24), residues: 1219 helix: 1.01 (0.25), residues: 455 sheet: 0.61 (0.35), residues: 240 loop : -1.43 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 69 TYR 0.020 0.002 TYR A 319 PHE 0.016 0.002 PHE A 387 TRP 0.014 0.002 TRP L 149 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00450 ( 9854) covalent geometry : angle 0.66846 (13392) SS BOND : bond 0.00927 ( 8) SS BOND : angle 2.38478 ( 16) hydrogen bonds : bond 0.05446 ( 479) hydrogen bonds : angle 4.59264 ( 1395) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 88 time to evaluate : 0.386 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 115 PHE cc_start: 0.5881 (m-80) cc_final: 0.5613 (m-80) REVERT: H 160 TYR cc_start: 0.3126 (p90) cc_final: 0.2563 (p90) REVERT: L 182 LEU cc_start: 0.4630 (mp) cc_final: 0.4205 (tt) REVERT: A 51 GLU cc_start: 0.8344 (mm-30) cc_final: 0.7783 (tp30) REVERT: A 493 LEU cc_start: 0.8364 (OUTLIER) cc_final: 0.8145 (mp) REVERT: A 542 ASP cc_start: 0.8501 (OUTLIER) cc_final: 0.8173 (m-30) outliers start: 20 outliers final: 9 residues processed: 105 average time/residue: 0.6001 time to fit residues: 67.4732 Evaluate side-chains 98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.315 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 306 LEU Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 35 optimal weight: 2.9990 chunk 101 optimal weight: 0.0770 chunk 66 optimal weight: 0.4980 chunk 33 optimal weight: 0.3980 chunk 21 optimal weight: 2.9990 chunk 40 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 117 optimal weight: 2.9990 chunk 75 optimal weight: 0.6980 chunk 46 optimal weight: 0.0870 chunk 13 optimal weight: 3.9990 overall best weight: 0.3516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 575 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.211727 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3357 r_free = 0.3357 target = 0.119471 restraints weight = 14383.093| |-----------------------------------------------------------------------------| r_work (start): 0.3261 rms_B_bonded: 2.53 r_work: 0.3052 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2923 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2923 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2921 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2921 r_free = 0.2921 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2921 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8112 moved from start: 0.1678 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.075 9862 Z= 0.119 Angle : 0.580 15.246 13408 Z= 0.302 Chirality : 0.044 0.211 1501 Planarity : 0.004 0.048 1687 Dihedral : 4.416 31.077 1330 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.35 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 1.33 % Allowed : 14.15 % Favored : 84.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.40 (0.25), residues: 1219 helix: 1.62 (0.25), residues: 455 sheet: 0.73 (0.35), residues: 242 loop : -1.23 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 664 TYR 0.020 0.001 TYR H 63 PHE 0.013 0.001 PHE A 348 TRP 0.014 0.001 TRP H 110 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00257 ( 9854) covalent geometry : angle 0.57545 (13392) SS BOND : bond 0.00802 ( 8) SS BOND : angle 2.07971 ( 16) hydrogen bonds : bond 0.03671 ( 479) hydrogen bonds : angle 4.27758 ( 1395) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 94 time to evaluate : 0.363 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6079 (mpp) REVERT: H 160 TYR cc_start: 0.3183 (p90) cc_final: 0.2612 (p90) REVERT: L 38 GLN cc_start: 0.5593 (tt0) cc_final: 0.5234 (tt0) REVERT: L 182 LEU cc_start: 0.4576 (mp) cc_final: 0.4174 (tt) REVERT: A 51 GLU cc_start: 0.8233 (mm-30) cc_final: 0.7795 (tp30) REVERT: A 70 THR cc_start: 0.8373 (OUTLIER) cc_final: 0.7835 (t) REVERT: A 298 ILE cc_start: 0.8248 (mt) cc_final: 0.7930 (tp) REVERT: A 434 LYS cc_start: 0.7428 (mmtm) cc_final: 0.6838 (tttp) REVERT: A 542 ASP cc_start: 0.8435 (OUTLIER) cc_final: 0.8182 (m-30) REVERT: P 2 LYS cc_start: 0.7905 (pptt) cc_final: 0.7697 (pptt) outliers start: 14 outliers final: 4 residues processed: 103 average time/residue: 0.5694 time to fit residues: 62.7984 Evaluate side-chains 98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 91 time to evaluate : 0.219 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 625 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 58 optimal weight: 3.9990 chunk 26 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 chunk 33 optimal weight: 30.0000 chunk 50 optimal weight: 4.9990 chunk 46 optimal weight: 10.0000 chunk 31 optimal weight: 40.0000 chunk 47 optimal weight: 20.0000 chunk 21 optimal weight: 30.0000 chunk 49 optimal weight: 4.9990 chunk 102 optimal weight: 0.6980 overall best weight: 3.7388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 214 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4302 r_free = 0.4302 target = 0.204071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3289 r_free = 0.3289 target = 0.116213 restraints weight = 13227.581| |-----------------------------------------------------------------------------| r_work (start): 0.3181 rms_B_bonded: 4.09 r_work: 0.2878 rms_B_bonded: 2.90 restraints_weight: 0.5000 r_work: 0.2739 rms_B_bonded: 4.67 restraints_weight: 0.2500 r_work (final): 0.2739 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2731 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.16 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2731 r_free = 0.2731 target_work(ls_wunit_k1) = 0.074 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2731 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8320 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.010 0.085 9862 Z= 0.393 Angle : 0.838 17.160 13408 Z= 0.446 Chirality : 0.058 0.267 1501 Planarity : 0.007 0.070 1687 Dihedral : 5.250 35.842 1330 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.25 % Favored : 93.42 % Rotamer: Outliers : 2.47 % Allowed : 14.06 % Favored : 83.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: -0.37 (0.24), residues: 1219 helix: 0.75 (0.24), residues: 445 sheet: 0.48 (0.34), residues: 240 loop : -1.45 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG A 393 TYR 0.021 0.003 TYR A 79 PHE 0.023 0.003 PHE A 224 TRP 0.052 0.004 TRP H 109 HIS 0.009 0.002 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00982 ( 9854) covalent geometry : angle 0.83365 (13392) SS BOND : bond 0.01042 ( 8) SS BOND : angle 2.50833 ( 16) hydrogen bonds : bond 0.07451 ( 479) hydrogen bonds : angle 4.82129 ( 1395) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 82 time to evaluate : 0.384 Fit side-chains REVERT: H 86 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6028 (mpp) REVERT: H 160 TYR cc_start: 0.2837 (p90) cc_final: 0.2426 (p90) REVERT: L 182 LEU cc_start: 0.4791 (mp) cc_final: 0.4271 (tt) REVERT: A 51 GLU cc_start: 0.8522 (mm-30) cc_final: 0.7933 (tp30) REVERT: A 542 ASP cc_start: 0.8591 (OUTLIER) cc_final: 0.8196 (m-30) REVERT: A 638 GLU cc_start: 0.7811 (tt0) cc_final: 0.7541 (tt0) outliers start: 26 outliers final: 13 residues processed: 102 average time/residue: 0.5587 time to fit residues: 61.3562 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 82 time to evaluate : 0.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 81 THR Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain L residue 27 SER Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 69 optimal weight: 0.5980 chunk 76 optimal weight: 0.9980 chunk 101 optimal weight: 0.7980 chunk 20 optimal weight: 4.9990 chunk 115 optimal weight: 1.9990 chunk 7 optimal weight: 0.6980 chunk 77 optimal weight: 0.6980 chunk 30 optimal weight: 40.0000 chunk 25 optimal weight: 50.0000 chunk 35 optimal weight: 7.9990 chunk 47 optimal weight: 20.0000 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 431 ASN ** 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 = 0.4352 r_free = 0.4352 target = 0.209407 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.115791 restraints weight = 14174.789| |-----------------------------------------------------------------------------| r_work (start): 0.3209 rms_B_bonded: 2.59 r_work: 0.3002 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2867 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2867 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2860 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.24 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2860 r_free = 0.2860 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2860 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8181 moved from start: 0.1902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.074 9862 Z= 0.140 Angle : 0.616 15.635 13408 Z= 0.322 Chirality : 0.045 0.216 1501 Planarity : 0.004 0.051 1687 Dihedral : 4.706 33.545 1330 Min Nonbonded Distance : 2.442 Molprobity Statistics. All-atom Clashscore : 7.13 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.26 % Favored : 94.49 % Rotamer: Outliers : 1.42 % Allowed : 15.38 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.11 (0.24), residues: 1219 helix: 1.30 (0.25), residues: 455 sheet: 0.61 (0.35), residues: 240 loop : -1.31 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.018 0.001 TYR H 63 PHE 0.011 0.001 PHE H 115 TRP 0.041 0.002 TRP H 110 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00316 ( 9854) covalent geometry : angle 0.61192 (13392) SS BOND : bond 0.00842 ( 8) SS BOND : angle 2.06864 ( 16) hydrogen bonds : bond 0.04582 ( 479) hydrogen bonds : angle 4.39955 ( 1395) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 91 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6455 (OUTLIER) cc_final: 0.6079 (mpp) REVERT: H 160 TYR cc_start: 0.2920 (p90) cc_final: 0.2447 (p90) REVERT: L 182 LEU cc_start: 0.4528 (mp) cc_final: 0.4094 (tt) REVERT: A 51 GLU cc_start: 0.8365 (mm-30) cc_final: 0.7813 (tp30) REVERT: A 70 THR cc_start: 0.8455 (OUTLIER) cc_final: 0.7965 (t) REVERT: A 542 ASP cc_start: 0.8492 (OUTLIER) cc_final: 0.8203 (m-30) outliers start: 15 outliers final: 7 residues processed: 101 average time/residue: 0.5935 time to fit residues: 64.1709 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 79 LEU Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 118 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 50 optimal weight: 9.9990 chunk 71 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 51 optimal weight: 8.9990 chunk 96 optimal weight: 3.9990 chunk 116 optimal weight: 3.9990 chunk 98 optimal weight: 0.8980 chunk 22 optimal weight: 100.0000 chunk 103 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4337 r_free = 0.4337 target = 0.207577 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3310 r_free = 0.3310 target = 0.116733 restraints weight = 14748.723| |-----------------------------------------------------------------------------| r_work (start): 0.3235 rms_B_bonded: 2.55 r_work: 0.2968 rms_B_bonded: 2.87 restraints_weight: 0.5000 r_work: 0.2840 rms_B_bonded: 4.43 restraints_weight: 0.2500 r_work (final): 0.2840 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2822 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2822 r_free = 0.2822 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2822 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8248 moved from start: 0.1991 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.075 9862 Z= 0.196 Angle : 0.668 15.985 13408 Z= 0.350 Chirality : 0.048 0.225 1501 Planarity : 0.005 0.048 1687 Dihedral : 4.774 33.366 1330 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.25 % Allowed : 5.92 % Favored : 93.83 % Rotamer: Outliers : 1.52 % Allowed : 15.29 % Favored : 83.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.07 (0.24), residues: 1219 helix: 1.26 (0.25), residues: 449 sheet: 0.58 (0.34), residues: 240 loop : -1.30 (0.26), residues: 530 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 441 TYR 0.020 0.002 TYR A 319 PHE 0.015 0.002 PHE A 320 TRP 0.028 0.002 TRP H 110 HIS 0.005 0.001 HIS A 391 Details of bonding type rmsd covalent geometry : bond 0.00476 ( 9854) covalent geometry : angle 0.66406 (13392) SS BOND : bond 0.00871 ( 8) SS BOND : angle 2.16860 ( 16) hydrogen bonds : bond 0.05419 ( 479) hydrogen bonds : angle 4.47217 ( 1395) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 87 time to evaluate : 0.381 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6458 (OUTLIER) cc_final: 0.6083 (mpp) REVERT: H 160 TYR cc_start: 0.2862 (p90) cc_final: 0.2484 (p90) REVERT: L 182 LEU cc_start: 0.4470 (mp) cc_final: 0.4018 (tt) REVERT: A 51 GLU cc_start: 0.8472 (mm-30) cc_final: 0.7918 (tp30) REVERT: A 542 ASP cc_start: 0.8553 (OUTLIER) cc_final: 0.8244 (m-30) outliers start: 16 outliers final: 9 residues processed: 98 average time/residue: 0.5927 time to fit residues: 62.3515 Evaluate side-chains 98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 87 time to evaluate : 0.335 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 611 VAL Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 64 optimal weight: 0.7980 chunk 44 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 30 optimal weight: 30.0000 chunk 77 optimal weight: 0.4980 chunk 21 optimal weight: 10.0000 chunk 99 optimal weight: 0.5980 chunk 1 optimal weight: 10.0000 chunk 82 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 13 optimal weight: 40.0000 overall best weight: 0.9582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 431 ASN ** 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 = 0.4352 r_free = 0.4352 target = 0.209432 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3314 r_free = 0.3314 target = 0.117476 restraints weight = 14077.915| |-----------------------------------------------------------------------------| r_work (start): 0.3239 rms_B_bonded: 3.05 r_work: 0.2949 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2949 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2947 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2947 r_free = 0.2947 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2947 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8151 moved from start: 0.1975 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.071 9862 Z= 0.149 Angle : 0.622 15.514 13408 Z= 0.324 Chirality : 0.046 0.209 1501 Planarity : 0.004 0.048 1687 Dihedral : 4.610 32.748 1330 Min Nonbonded Distance : 2.443 Molprobity Statistics. All-atom Clashscore : 6.97 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 1.33 % Allowed : 15.67 % Favored : 83.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.20 (0.25), residues: 1219 helix: 1.43 (0.25), residues: 455 sheet: 0.58 (0.34), residues: 242 loop : -1.28 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 69 TYR 0.018 0.001 TYR A 319 PHE 0.015 0.001 PHE H 115 TRP 0.031 0.002 TRP H 110 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00346 ( 9854) covalent geometry : angle 0.61843 (13392) SS BOND : bond 0.00826 ( 8) SS BOND : angle 2.06277 ( 16) hydrogen bonds : bond 0.04630 ( 479) hydrogen bonds : angle 4.33843 ( 1395) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6567 (OUTLIER) cc_final: 0.6187 (mpp) REVERT: H 160 TYR cc_start: 0.2913 (p90) cc_final: 0.2446 (p90) REVERT: L 182 LEU cc_start: 0.4512 (mp) cc_final: 0.4086 (tt) REVERT: A 51 GLU cc_start: 0.8228 (mm-30) cc_final: 0.7779 (tp30) REVERT: A 70 THR cc_start: 0.8397 (OUTLIER) cc_final: 0.7903 (t) REVERT: A 542 ASP cc_start: 0.8398 (OUTLIER) cc_final: 0.8079 (m-30) outliers start: 14 outliers final: 7 residues processed: 97 average time/residue: 0.5840 time to fit residues: 60.7272 Evaluate side-chains 95 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 85 time to evaluate : 0.385 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 328 MET Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 573 VAL Chi-restraints excluded: chain A residue 611 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 113 optimal weight: 0.0270 chunk 115 optimal weight: 0.7980 chunk 97 optimal weight: 0.9980 chunk 110 optimal weight: 0.0770 chunk 46 optimal weight: 0.7980 chunk 76 optimal weight: 0.9990 chunk 77 optimal weight: 0.8980 chunk 49 optimal weight: 7.9990 chunk 100 optimal weight: 2.9990 chunk 62 optimal weight: 0.6980 chunk 33 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 58 HIS ** A 431 ASN ** 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 = 0.4367 r_free = 0.4367 target = 0.211111 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3389 r_free = 0.3389 target = 0.123200 restraints weight = 12707.935| |-----------------------------------------------------------------------------| r_work (start): 0.3296 rms_B_bonded: 3.58 r_work: 0.3006 rms_B_bonded: 2.93 restraints_weight: 0.5000 r_work: 0.2868 rms_B_bonded: 4.68 restraints_weight: 0.2500 r_work (final): 0.2868 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2871 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2871 r_free = 0.2871 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2871 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.069 9862 Z= 0.122 Angle : 0.589 14.812 13408 Z= 0.305 Chirality : 0.044 0.196 1501 Planarity : 0.004 0.047 1687 Dihedral : 4.407 31.568 1330 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 0.85 % Allowed : 16.24 % Favored : 82.91 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % 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: 0.36 (0.25), residues: 1219 helix: 1.68 (0.25), residues: 455 sheet: 0.76 (0.36), residues: 224 loop : -1.30 (0.26), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 664 TYR 0.016 0.001 TYR A 319 PHE 0.015 0.001 PHE H 115 TRP 0.064 0.002 TRP H 110 HIS 0.004 0.001 HIS A 479 Details of bonding type rmsd covalent geometry : bond 0.00269 ( 9854) covalent geometry : angle 0.58572 (13392) SS BOND : bond 0.00757 ( 8) SS BOND : angle 1.98866 ( 16) hydrogen bonds : bond 0.03877 ( 479) hydrogen bonds : angle 4.20390 ( 1395) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5514.02 seconds wall clock time: 94 minutes 3.81 seconds (5643.81 seconds total)