Starting phenix.real_space_refine on Fri Mar 14 05:20:34 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlg_14779/03_2025/7zlg_14779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlg_14779/03_2025/7zlg_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 { real_map_files = "/net/cci-nas-00/data/ceres_data/7zlg_14779/03_2025/7zlg_14779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlg_14779/03_2025/7zlg_14779.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlg_14779/03_2025/7zlg_14779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlg_14779/03_2025/7zlg_14779.cif" } resolution = 2.72 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.001 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): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/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: 8.42, per 1000 atoms: 0.88 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: 2.25 Conformation dependent library (CDL) restraints added in 1.6 seconds 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: 1.20 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: 2.97 Time building geometry restraints manager: 2.70 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: 28.890 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.440 Check model and map are aligned: 0.070 Set scattering table: 0.080 Process input model: 27.460 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.050 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.870 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 68.980 ------------------------------------------------------------------------------- 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 9854 Z= 0.292 Angle : 0.713 20.789 13392 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (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 TRP 0.015 0.001 TRP P 0 HIS 0.003 0.001 HIS A 375 PHE 0.013 0.001 PHE A 348 TYR 0.016 0.001 TYR H 83 ARG 0.005 0.000 ARG A 393 *********************** 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 : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 44 PRO cc_start: 0.4930 (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: 1.3839 time to fit residues: 180.9811 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 : 1.096 ------------------------------------------------------------------------------- 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 102 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 50 optimal weight: 0.0010 chunk 31 optimal weight: 50.0000 chunk 61 optimal weight: 0.9990 chunk 48 optimal weight: 0.0770 chunk 94 optimal weight: 0.0070 chunk 36 optimal weight: 4.9990 chunk 57 optimal weight: 2.9990 chunk 70 optimal weight: 0.5980 chunk 109 optimal weight: 2.9990 overall best weight: 0.3364 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 458 GLN 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 = 0.4395 r_free = 0.4395 target = 0.213422 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3374 r_free = 0.3374 target = 0.121222 restraints weight = 13987.074| |-----------------------------------------------------------------------------| r_work (start): 0.3285 rms_B_bonded: 2.49 r_work: 0.3082 rms_B_bonded: 2.68 restraints_weight: 0.5000 r_work: 0.2955 rms_B_bonded: 4.13 restraints_weight: 0.2500 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2953 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2953 r_free = 0.2953 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2953 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8097 moved from start: 0.1027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9854 Z= 0.157 Angle : 0.573 9.048 13392 Z= 0.300 Chirality : 0.044 0.149 1501 Planarity : 0.004 0.044 1687 Dihedral : 4.252 31.613 1333 Min Nonbonded Distance : 2.520 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 0.95 % Allowed : 7.22 % Favored : 91.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.37 (0.25), residues: 1219 helix: 1.52 (0.25), residues: 455 sheet: 0.95 (0.34), residues: 250 loop : -1.34 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.031 0.001 TRP H 110 HIS 0.004 0.001 HIS H 38 PHE 0.011 0.001 PHE A 348 TYR 0.021 0.001 TYR H 83 ARG 0.007 0.000 ARG A 69 *********************** 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 111 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 101 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 TYR cc_start: 0.5845 (m-80) cc_final: 0.5556 (m-80) REVERT: H 160 TYR cc_start: 0.3410 (p90) cc_final: 0.2865 (p90) REVERT: H 171 SER cc_start: 0.6296 (t) cc_final: 0.6033 (t) REVERT: L 38 GLN cc_start: 0.5534 (tt0) cc_final: 0.5213 (tt0) REVERT: A 51 GLU cc_start: 0.8190 (mm-30) cc_final: 0.7801 (tp30) REVERT: A 298 ILE cc_start: 0.8241 (mt) cc_final: 0.7914 (tp) outliers start: 10 outliers final: 5 residues processed: 108 average time/residue: 1.1836 time to fit residues: 138.3858 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 92 time to evaluate : 1.086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 42 optimal weight: 0.0980 chunk 26 optimal weight: 30.0000 chunk 45 optimal weight: 6.9990 chunk 12 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 9.9990 chunk 115 optimal weight: 0.0770 chunk 118 optimal weight: 0.9980 chunk 5 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 overall best weight: 0.7540 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.211313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3391 r_free = 0.3391 target = 0.123222 restraints weight = 14762.678| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 3.28 r_work: 0.3001 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2850 rms_B_bonded: 4.97 restraints_weight: 0.2500 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2841 r_free = 0.2841 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2841 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8197 moved from start: 0.1204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 9854 Z= 0.192 Angle : 0.579 9.862 13392 Z= 0.305 Chirality : 0.044 0.144 1501 Planarity : 0.004 0.050 1687 Dihedral : 4.242 29.420 1330 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 1.42 % Allowed : 9.59 % Favored : 88.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.42 (0.25), residues: 1219 helix: 1.63 (0.25), residues: 454 sheet: 0.95 (0.35), residues: 244 loop : -1.33 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.029 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 PHE 0.012 0.001 PHE A 320 TYR 0.017 0.001 TYR H 83 ARG 0.005 0.000 ARG A 664 *********************** 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 111 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.966 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3255 (p90) cc_final: 0.2743 (p90) REVERT: L 38 GLN cc_start: 0.5410 (tt0) cc_final: 0.5062 (tt0) REVERT: A 51 GLU cc_start: 0.8379 (mm-30) cc_final: 0.7927 (tp30) REVERT: A 70 THR cc_start: 0.8409 (OUTLIER) cc_final: 0.8193 (p) REVERT: A 493 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8195 (mp) REVERT: A 542 ASP cc_start: 0.8495 (OUTLIER) cc_final: 0.8241 (m-30) outliers start: 15 outliers final: 6 residues processed: 107 average time/residue: 1.1325 time to fit residues: 131.0313 Evaluate side-chains 100 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 1.051 ------------------------------------------------------------------------------- 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 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 Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 94 optimal weight: 2.9990 chunk 56 optimal weight: 0.9990 chunk 71 optimal weight: 0.1980 chunk 75 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 101 optimal weight: 0.5980 chunk 20 optimal weight: 20.0000 chunk 52 optimal weight: 0.6980 chunk 85 optimal weight: 1.9990 chunk 120 optimal weight: 0.0270 chunk 76 optimal weight: 0.9980 overall best weight: 0.5038 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 179 HIS ** L 156 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 42 ASN A 297 HIS ** A 431 ASN ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4382 r_free = 0.4382 target = 0.212431 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.118917 restraints weight = 16764.277| |-----------------------------------------------------------------------------| r_work (start): 0.3251 rms_B_bonded: 2.80 r_work: 0.3026 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work: 0.2890 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2873 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2873 r_free = 0.2873 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 = 0.2873 r_free = 0.2873 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2873 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8148 moved from start: 0.1356 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.080 9854 Z= 0.180 Angle : 0.582 15.864 13392 Z= 0.302 Chirality : 0.044 0.238 1501 Planarity : 0.004 0.046 1687 Dihedral : 4.164 30.509 1330 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 1.61 % Allowed : 10.16 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.55 (0.25), residues: 1219 helix: 1.76 (0.25), residues: 455 sheet: 0.98 (0.35), residues: 245 loop : -1.27 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP H 110 HIS 0.003 0.001 HIS A 479 PHE 0.010 0.001 PHE A 348 TYR 0.015 0.001 TYR H 63 ARG 0.003 0.000 ARG A 69 *********************** 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 110 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 93 time to evaluate : 0.991 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3243 (p90) cc_final: 0.2723 (p90) REVERT: L 38 GLN cc_start: 0.5459 (tt0) cc_final: 0.5082 (tt0) REVERT: A 51 GLU cc_start: 0.8314 (mm-30) cc_final: 0.7862 (tp30) REVERT: A 71 GLU cc_start: 0.7704 (OUTLIER) cc_final: 0.7311 (mp0) REVERT: A 542 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8242 (m-30) REVERT: P 2 LYS cc_start: 0.7863 (pptt) cc_final: 0.7618 (pptt) outliers start: 17 outliers final: 8 residues processed: 105 average time/residue: 1.1579 time to fit residues: 131.1613 Evaluate side-chains 102 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 92 time to evaluate : 1.035 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 LEU 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 71 GLU 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 542 ASP 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 109 optimal weight: 0.9980 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 90 optimal weight: 0.8980 chunk 15 optimal weight: 6.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 10.0000 chunk 7 optimal weight: 4.9990 chunk 114 optimal weight: 3.9990 chunk 45 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- 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** L 156 GLN 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 = 0.4337 r_free = 0.4337 target = 0.207699 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3290 r_free = 0.3290 target = 0.115405 restraints weight = 16578.519| |-----------------------------------------------------------------------------| r_work (start): 0.3192 rms_B_bonded: 2.71 r_work: 0.2912 rms_B_bonded: 3.16 restraints_weight: 0.5000 r_work: 0.2783 rms_B_bonded: 4.83 restraints_weight: 0.2500 r_work (final): 0.2783 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2778 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2778 r_free = 0.2778 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2778 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8255 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.086 9854 Z= 0.371 Angle : 0.702 16.520 13392 Z= 0.370 Chirality : 0.049 0.234 1501 Planarity : 0.005 0.086 1687 Dihedral : 4.691 36.207 1329 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 6.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.09 % Favored : 93.75 % Rotamer: Outliers : 1.61 % Allowed : 11.97 % Favored : 86.42 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.13 (0.24), residues: 1219 helix: 1.24 (0.24), residues: 454 sheet: 0.72 (0.34), residues: 255 loop : -1.33 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.002 TRP H 109 HIS 0.005 0.002 HIS A 391 PHE 0.021 0.002 PHE A 387 TYR 0.018 0.002 TYR A 116 ARG 0.006 0.001 ARG A 393 *********************** 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 106 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 89 time to evaluate : 0.955 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3282 (p90) cc_final: 0.2718 (p90) REVERT: A 51 GLU cc_start: 0.8496 (mm-30) cc_final: 0.7937 (tp30) REVERT: A 71 GLU cc_start: 0.7840 (OUTLIER) cc_final: 0.7358 (mp0) REVERT: A 493 LEU cc_start: 0.8421 (OUTLIER) cc_final: 0.8137 (mp) REVERT: A 542 ASP cc_start: 0.8597 (OUTLIER) cc_final: 0.8268 (m-30) outliers start: 17 outliers final: 9 residues processed: 101 average time/residue: 1.2397 time to fit residues: 134.8748 Evaluate side-chains 99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 0.948 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 179 THR Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 3.9990 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 42 optimal weight: 0.7980 chunk 92 optimal weight: 0.9980 chunk 40 optimal weight: 7.9990 chunk 77 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 0.9990 chunk 22 optimal weight: 100.0000 chunk 4 optimal weight: 9.9990 overall best weight: 1.9586 ------------------------------------------------------------------------------- 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 662 ASN ** 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 = 0.4336 r_free = 0.4336 target = 0.207678 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3272 r_free = 0.3272 target = 0.113779 restraints weight = 19177.607| |-----------------------------------------------------------------------------| r_work (start): 0.3178 rms_B_bonded: 3.19 r_work: 0.2877 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2877 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2879 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2879 r_free = 0.2879 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2879 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8154 moved from start: 0.1749 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 9854 Z= 0.361 Angle : 0.688 15.849 13392 Z= 0.363 Chirality : 0.049 0.222 1501 Planarity : 0.005 0.089 1687 Dihedral : 4.749 35.099 1329 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 6.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.76 % Favored : 94.08 % Rotamer: Outliers : 1.99 % Allowed : 13.11 % Favored : 84.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.02 (0.24), residues: 1219 helix: 1.10 (0.25), residues: 455 sheet: 0.69 (0.34), residues: 242 loop : -1.30 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP H 109 HIS 0.006 0.001 HIS A 391 PHE 0.019 0.002 PHE A 387 TYR 0.018 0.002 TYR A 319 ARG 0.006 0.001 ARG A 393 *********************** 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 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 88 time to evaluate : 0.967 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3251 (p90) cc_final: 0.2651 (p90) REVERT: L 182 LEU cc_start: 0.4733 (mp) cc_final: 0.4242 (tt) REVERT: A 51 GLU cc_start: 0.8300 (mm-30) cc_final: 0.7754 (tp30) REVERT: A 71 GLU cc_start: 0.7640 (OUTLIER) cc_final: 0.7122 (mp0) REVERT: A 278 LEU cc_start: 0.8691 (OUTLIER) cc_final: 0.8464 (tm) REVERT: A 493 LEU cc_start: 0.8404 (OUTLIER) cc_final: 0.8148 (mp) REVERT: A 542 ASP cc_start: 0.8474 (OUTLIER) cc_final: 0.8107 (m-30) REVERT: P 2 LYS cc_start: 0.7940 (pptt) cc_final: 0.7731 (pptt) outliers start: 21 outliers final: 10 residues processed: 102 average time/residue: 1.2144 time to fit residues: 133.8755 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 : 1.140 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 104 LYS 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 71 GLU Chi-restraints excluded: chain A residue 153 VAL Chi-restraints excluded: chain A residue 278 LEU 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 644 SER Chi-restraints excluded: chain A residue 647 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 0.9990 chunk 14 optimal weight: 4.9990 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 1.9990 chunk 26 optimal weight: 30.0000 chunk 36 optimal weight: 2.9990 chunk 46 optimal weight: 7.9990 chunk 32 optimal weight: 30.0000 chunk 110 optimal weight: 0.0570 chunk 115 optimal weight: 2.9990 chunk 61 optimal weight: 0.4980 overall best weight: 1.3104 ------------------------------------------------------------------------------- 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 662 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4344 r_free = 0.4344 target = 0.208332 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3276 r_free = 0.3276 target = 0.112546 restraints weight = 22815.931| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.36 r_work: 0.2898 rms_B_bonded: 3.67 restraints_weight: 0.5000 r_work (final): 0.2898 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2904 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2904 r_free = 0.2904 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2904 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.1768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.066 9854 Z= 0.272 Angle : 0.636 15.129 13392 Z= 0.335 Chirality : 0.047 0.283 1501 Planarity : 0.005 0.070 1687 Dihedral : 4.599 34.959 1329 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.09 % Favored : 93.75 % Rotamer: Outliers : 1.80 % Allowed : 14.25 % Favored : 83.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.24), residues: 1219 helix: 1.27 (0.25), residues: 455 sheet: 0.70 (0.34), residues: 242 loop : -1.27 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 109 HIS 0.005 0.001 HIS A 391 PHE 0.014 0.002 PHE A 387 TYR 0.018 0.002 TYR A 319 ARG 0.004 0.000 ARG A 393 *********************** 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 107 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 88 time to evaluate : 1.140 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3136 (p90) cc_final: 0.2532 (p90) REVERT: L 182 LEU cc_start: 0.4562 (mp) cc_final: 0.4123 (tt) REVERT: A 51 GLU cc_start: 0.8326 (mm-30) cc_final: 0.7756 (tp30) REVERT: A 71 GLU cc_start: 0.7597 (OUTLIER) cc_final: 0.7089 (mp0) REVERT: A 493 LEU cc_start: 0.8383 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 542 ASP cc_start: 0.8463 (OUTLIER) cc_final: 0.8134 (m-30) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 1.1693 time to fit residues: 130.1034 Evaluate side-chains 99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 86 time to evaluate : 1.077 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU 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 644 SER 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 26 optimal weight: 20.0000 chunk 113 optimal weight: 0.9980 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 0.7980 chunk 48 optimal weight: 20.0000 chunk 31 optimal weight: 9.9990 overall best weight: 3.2784 ------------------------------------------------------------------------------- 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 55 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 = 0.4313 r_free = 0.4313 target = 0.205278 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3219 r_free = 0.3219 target = 0.111665 restraints weight = 20917.869| |-----------------------------------------------------------------------------| r_work (start): 0.3116 rms_B_bonded: 3.95 r_work: 0.2850 rms_B_bonded: 3.37 restraints_weight: 0.5000 r_work (final): 0.2850 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.2071 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.009 0.075 9854 Z= 0.552 Angle : 0.795 15.641 13392 Z= 0.423 Chirality : 0.055 0.307 1501 Planarity : 0.006 0.095 1687 Dihedral : 5.109 36.099 1329 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 7.60 Ramachandran Plot: Outliers : 0.25 % Allowed : 6.41 % Favored : 93.34 % Rotamer: Outliers : 1.80 % Allowed : 14.62 % Favored : 83.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.24), residues: 1219 helix: 0.75 (0.24), residues: 450 sheet: 0.53 (0.35), residues: 240 loop : -1.40 (0.26), residues: 529 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.047 0.003 TRP H 109 HIS 0.008 0.002 HIS A 391 PHE 0.021 0.003 PHE A 224 TYR 0.020 0.003 TYR A 319 ARG 0.008 0.001 ARG A 393 *********************** 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 100 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 81 time to evaluate : 1.058 Fit side-chains REVERT: H 160 TYR cc_start: 0.3006 (p90) cc_final: 0.2590 (p90) REVERT: L 46 LYS cc_start: 0.7573 (ptmt) cc_final: 0.7359 (ptmm) REVERT: L 182 LEU cc_start: 0.4484 (mp) cc_final: 0.4055 (tt) REVERT: A 51 GLU cc_start: 0.8308 (mm-30) cc_final: 0.7788 (tp30) REVERT: A 71 GLU cc_start: 0.7718 (OUTLIER) cc_final: 0.7186 (mp0) REVERT: A 493 LEU cc_start: 0.8463 (OUTLIER) cc_final: 0.8153 (mp) REVERT: A 542 ASP cc_start: 0.8503 (OUTLIER) cc_final: 0.8079 (m-30) outliers start: 19 outliers final: 11 residues processed: 95 average time/residue: 1.2341 time to fit residues: 126.3878 Evaluate side-chains 94 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 80 time to evaluate : 1.006 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain L residue 104 LYS Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 0.9990 chunk 120 optimal weight: 0.9990 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 0.7980 chunk 52 optimal weight: 0.8980 chunk 111 optimal weight: 0.8980 chunk 101 optimal weight: 0.9980 chunk 69 optimal weight: 0.5980 chunk 99 optimal weight: 0.8980 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 10.0000 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4348 r_free = 0.4348 target = 0.208839 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.117250 restraints weight = 15471.856| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 2.64 r_work: 0.3005 rms_B_bonded: 2.82 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.50 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2842 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.25 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2842 r_free = 0.2842 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8215 moved from start: 0.1909 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 9854 Z= 0.212 Angle : 0.616 15.062 13392 Z= 0.324 Chirality : 0.045 0.268 1501 Planarity : 0.004 0.060 1687 Dihedral : 4.641 34.914 1329 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 1.80 % Allowed : 15.00 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.11 (0.24), residues: 1219 helix: 1.27 (0.25), residues: 455 sheet: 0.64 (0.35), residues: 239 loop : -1.29 (0.27), residues: 525 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP H 110 HIS 0.004 0.001 HIS A 391 PHE 0.014 0.001 PHE A 348 TYR 0.018 0.001 TYR A 319 ARG 0.006 0.000 ARG A 664 *********************** 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 110 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 91 time to evaluate : 0.942 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.2920 (p90) cc_final: 0.2442 (p90) REVERT: L 182 LEU cc_start: 0.4475 (mp) cc_final: 0.4018 (tt) REVERT: A 51 GLU cc_start: 0.8416 (mm-30) cc_final: 0.7902 (tp30) REVERT: A 71 GLU cc_start: 0.7646 (OUTLIER) cc_final: 0.7238 (mp0) REVERT: A 542 ASP cc_start: 0.8532 (OUTLIER) cc_final: 0.8234 (m-30) outliers start: 19 outliers final: 10 residues processed: 103 average time/residue: 1.1889 time to fit residues: 132.1017 Evaluate side-chains 99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 87 time to evaluate : 1.043 ------------------------------------------------------------------------------- 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 59 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU 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 611 VAL Chi-restraints excluded: chain A residue 644 SER 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 13 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 4 optimal weight: 10.0000 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 6.9990 chunk 70 optimal weight: 0.8980 chunk 3 optimal weight: 9.9990 chunk 26 optimal weight: 20.0000 chunk 107 optimal weight: 1.9990 overall best weight: 1.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 161 GLN ** 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 = 0.4336 r_free = 0.4336 target = 0.207548 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.112627 restraints weight = 19611.398| |-----------------------------------------------------------------------------| r_work (start): 0.3158 rms_B_bonded: 3.29 r_work: 0.2890 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2890 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2900 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2900 r_free = 0.2900 target_work(ls_wunit_k1) = 0.084 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2900 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8153 moved from start: 0.1973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.069 9854 Z= 0.305 Angle : 0.666 14.904 13392 Z= 0.349 Chirality : 0.048 0.280 1501 Planarity : 0.005 0.074 1687 Dihedral : 4.690 35.029 1329 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.00 % Favored : 93.83 % Rotamer: Outliers : 1.33 % Allowed : 15.57 % Favored : 83.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.08 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.09 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.03 (0.24), residues: 1219 helix: 1.21 (0.25), residues: 455 sheet: 0.47 (0.34), residues: 244 loop : -1.28 (0.27), residues: 520 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.024 0.002 TRP H 109 HIS 0.005 0.001 HIS A 391 PHE 0.016 0.002 PHE A 320 TYR 0.020 0.002 TYR A 319 ARG 0.006 0.001 ARG A 664 ********************** 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 99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 85 time to evaluate : 1.025 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6407 (mpp) cc_final: 0.6150 (mpp) REVERT: H 160 TYR cc_start: 0.2877 (p90) cc_final: 0.2497 (p90) REVERT: L 182 LEU cc_start: 0.4517 (mp) cc_final: 0.4053 (tt) REVERT: A 51 GLU cc_start: 0.8284 (mm-30) cc_final: 0.7734 (tp30) REVERT: A 71 GLU cc_start: 0.7620 (OUTLIER) cc_final: 0.7105 (mp0) REVERT: A 542 ASP cc_start: 0.8450 (OUTLIER) cc_final: 0.8101 (m-30) outliers start: 14 outliers final: 9 residues processed: 95 average time/residue: 1.2191 time to fit residues: 124.9825 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 86 time to evaluate : 0.995 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain L residue 34 VAL Chi-restraints excluded: chain L residue 59 VAL Chi-restraints excluded: chain L residue 107 ILE Chi-restraints excluded: chain A residue 70 THR Chi-restraints excluded: chain A residue 71 GLU 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 611 VAL Chi-restraints excluded: chain A residue 644 SER 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 12 optimal weight: 10.0000 chunk 74 optimal weight: 0.6980 chunk 83 optimal weight: 1.9990 chunk 86 optimal weight: 0.4980 chunk 32 optimal weight: 30.0000 chunk 106 optimal weight: 0.8980 chunk 19 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.7980 chunk 35 optimal weight: 8.9990 chunk 78 optimal weight: 0.7980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 161 GLN ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4356 r_free = 0.4356 target = 0.209685 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3321 r_free = 0.3321 target = 0.116742 restraints weight = 17007.885| |-----------------------------------------------------------------------------| r_work (start): 0.3233 rms_B_bonded: 2.74 r_work: 0.3010 rms_B_bonded: 2.85 restraints_weight: 0.5000 r_work: 0.2870 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2870 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2852 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2852 r_free = 0.2852 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2852 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8177 moved from start: 0.1934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.068 9854 Z= 0.201 Angle : 0.602 14.414 13392 Z= 0.313 Chirality : 0.045 0.264 1501 Planarity : 0.004 0.053 1687 Dihedral : 4.455 33.787 1329 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.74 % 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 (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.25), residues: 1219 helix: 1.47 (0.25), residues: 461 sheet: 0.60 (0.35), residues: 242 loop : -1.24 (0.27), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP H 110 HIS 0.004 0.001 HIS A 479 PHE 0.014 0.001 PHE H 115 TYR 0.017 0.001 TYR A 319 ARG 0.006 0.000 ARG A 664 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11344.43 seconds wall clock time: 196 minutes 8.67 seconds (11768.67 seconds total)