Starting phenix.real_space_refine on Sun Jul 27 18:34:18 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlg_14779/07_2025/7zlg_14779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlg_14779/07_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_14779/07_2025/7zlg_14779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlg_14779/07_2025/7zlg_14779.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlg_14779/07_2025/7zlg_14779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlg_14779/07_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): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5711/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: 8.39, per 1000 atoms: 0.87 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: 2.24 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: 1.18 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: 2.69 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: 22.700 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: 0.000 Extract box with map and model: 0.420 Check model and map are aligned: 0.060 Set scattering table: 0.080 Process input model: 27.430 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:11.340 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 62.190 ------------------------------------------------------------------------------- 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 (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 Details of bonding type rmsd hydrogen bonds : bond 0.15416 ( 479) hydrogen bonds : angle 6.00019 ( 1395) SS BOND : bond 0.00323 ( 8) SS BOND : angle 0.99540 ( 16) covalent geometry : bond 0.00425 ( 9854) covalent geometry : angle 0.71327 (13392) *********************** 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 : 0.945 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: 1.4877 time to fit residues: 193.8972 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 : 1.107 ------------------------------------------------------------------------------- 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: 0.9990 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: 0.5208 ------------------------------------------------------------------------------- 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 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: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4385 r_free = 0.4385 target = 0.212392 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3353 r_free = 0.3353 target = 0.119786 restraints weight = 13899.422| |-----------------------------------------------------------------------------| r_work (start): 0.3264 rms_B_bonded: 2.52 r_work: 0.3066 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.2932 rms_B_bonded: 4.16 restraints_weight: 0.2500 r_work (final): 0.2932 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2936 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2936 r_free = 0.2936 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2936 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8126 moved from start: 0.0961 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 9862 Z= 0.128 Angle : 0.584 9.074 13408 Z= 0.307 Chirality : 0.044 0.148 1501 Planarity : 0.004 0.045 1687 Dihedral : 4.298 31.465 1333 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.26 % Favored : 94.57 % Rotamer: Outliers : 1.04 % Allowed : 7.31 % Favored : 91.64 % 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: 0.32 (0.25), residues: 1219 helix: 1.45 (0.25), residues: 455 sheet: 0.94 (0.34), residues: 250 loop : -1.35 (0.27), residues: 514 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.001 TRP H 110 HIS 0.004 0.001 HIS A 391 PHE 0.011 0.001 PHE A 320 TYR 0.019 0.001 TYR H 83 ARG 0.006 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04327 ( 479) hydrogen bonds : angle 4.67973 ( 1395) SS BOND : bond 0.00432 ( 8) SS BOND : angle 0.99465 ( 16) covalent geometry : bond 0.00265 ( 9854) covalent geometry : angle 0.58367 (13392) *********************** 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 107 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 96 time to evaluate : 1.155 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 TYR cc_start: 0.5858 (m-80) cc_final: 0.5584 (m-80) REVERT: H 160 TYR cc_start: 0.3421 (p90) cc_final: 0.2864 (p90) REVERT: H 171 SER cc_start: 0.6302 (t) cc_final: 0.6042 (t) REVERT: L 38 GLN cc_start: 0.5525 (tt0) cc_final: 0.5214 (tt0) REVERT: A 51 GLU cc_start: 0.8242 (mm-30) cc_final: 0.7811 (tp30) REVERT: A 493 LEU cc_start: 0.8447 (OUTLIER) cc_final: 0.8211 (mp) outliers start: 11 outliers final: 6 residues processed: 104 average time/residue: 1.7667 time to fit residues: 198.2193 Evaluate side-chains 97 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 90 time to evaluate : 1.447 ------------------------------------------------------------------------------- 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 Chi-restraints excluded: chain A residue 493 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 42 optimal weight: 7.9990 chunk 26 optimal weight: 20.0000 chunk 45 optimal weight: 20.0000 chunk 12 optimal weight: 8.9990 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 0.3980 chunk 115 optimal weight: 3.9990 chunk 118 optimal weight: 0.7980 chunk 5 optimal weight: 9.9990 chunk 95 optimal weight: 3.9990 chunk 109 optimal weight: 0.0980 overall best weight: 1.4584 ------------------------------------------------------------------------------- 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 = 0.4353 r_free = 0.4353 target = 0.209094 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115329 restraints weight = 14692.246| |-----------------------------------------------------------------------------| r_work (start): 0.3186 rms_B_bonded: 2.61 r_work: 0.2976 rms_B_bonded: 2.77 restraints_weight: 0.5000 r_work: 0.2845 rms_B_bonded: 4.22 restraints_weight: 0.2500 r_work (final): 0.2845 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2839 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2839 r_free = 0.2839 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 = 0.2839 r_free = 0.2839 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2839 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8195 moved from start: 0.1256 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.049 9862 Z= 0.188 Angle : 0.638 9.749 13408 Z= 0.338 Chirality : 0.047 0.172 1501 Planarity : 0.005 0.060 1687 Dihedral : 4.529 31.337 1330 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.51 % Favored : 94.33 % Rotamer: Outliers : 1.52 % Allowed : 9.31 % Favored : 89.17 % 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: 0.22 (0.25), residues: 1219 helix: 1.30 (0.25), residues: 456 sheet: 0.90 (0.34), residues: 251 loop : -1.35 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 110 HIS 0.006 0.001 HIS A 375 PHE 0.017 0.002 PHE A 387 TYR 0.017 0.002 TYR A 319 ARG 0.004 0.001 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.05411 ( 479) hydrogen bonds : angle 4.60884 ( 1395) SS BOND : bond 0.00327 ( 8) SS BOND : angle 1.07058 ( 16) covalent geometry : bond 0.00449 ( 9854) covalent geometry : angle 0.63688 (13392) *********************** 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 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 92 time to evaluate : 1.258 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3392 (p90) cc_final: 0.2836 (p90) REVERT: A 51 GLU cc_start: 0.8397 (mm-30) cc_final: 0.7900 (tp30) REVERT: A 493 LEU cc_start: 0.8427 (OUTLIER) cc_final: 0.8160 (mp) REVERT: A 542 ASP cc_start: 0.8489 (OUTLIER) cc_final: 0.8191 (m-30) outliers start: 16 outliers final: 8 residues processed: 105 average time/residue: 1.3982 time to fit residues: 159.5677 Evaluate side-chains 99 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 89 time to evaluate : 1.013 ------------------------------------------------------------------------------- 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 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 94 optimal weight: 1.9990 chunk 56 optimal weight: 0.6980 chunk 71 optimal weight: 0.0370 chunk 75 optimal weight: 0.5980 chunk 18 optimal weight: 9.9990 chunk 101 optimal weight: 0.9990 chunk 20 optimal weight: 30.0000 chunk 52 optimal weight: 8.9990 chunk 85 optimal weight: 0.9990 chunk 120 optimal weight: 0.7980 chunk 76 optimal weight: 0.9980 overall best weight: 0.6258 ------------------------------------------------------------------------------- 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 297 HIS A 431 ASN ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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 = 0.4370 r_free = 0.4370 target = 0.210985 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.117628 restraints weight = 16194.554| |-----------------------------------------------------------------------------| r_work (start): 0.3220 rms_B_bonded: 2.70 r_work: 0.3002 rms_B_bonded: 2.91 restraints_weight: 0.5000 r_work: 0.2873 rms_B_bonded: 4.46 restraints_weight: 0.2500 r_work (final): 0.2873 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2868 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2868 r_free = 0.2868 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2868 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8139 moved from start: 0.1337 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 9862 Z= 0.131 Angle : 0.603 16.344 13408 Z= 0.313 Chirality : 0.045 0.259 1501 Planarity : 0.004 0.047 1687 Dihedral : 4.347 31.387 1330 Min Nonbonded Distance : 2.480 Molprobity Statistics. All-atom Clashscore : 6.19 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.35 % Favored : 94.49 % Rotamer: Outliers : 1.52 % Allowed : 11.11 % Favored : 87.37 % 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: 0.41 (0.25), residues: 1219 helix: 1.57 (0.25), residues: 455 sheet: 0.84 (0.34), residues: 255 loop : -1.27 (0.27), residues: 509 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 387 TYR 0.015 0.001 TYR A 319 ARG 0.003 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04217 ( 479) hydrogen bonds : angle 4.40009 ( 1395) SS BOND : bond 0.00847 ( 8) SS BOND : angle 2.23551 ( 16) covalent geometry : bond 0.00294 ( 9854) covalent geometry : angle 0.59834 (13392) *********************** 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 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 1.037 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3260 (p90) cc_final: 0.2730 (p90) REVERT: L 38 GLN cc_start: 0.5500 (tt0) cc_final: 0.5125 (tt0) REVERT: A 51 GLU cc_start: 0.8335 (mm-30) cc_final: 0.7833 (tp30) REVERT: A 71 GLU cc_start: 0.7687 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: A 298 ILE cc_start: 0.8262 (mt) cc_final: 0.7920 (tp) REVERT: A 493 LEU cc_start: 0.8380 (OUTLIER) cc_final: 0.8168 (mp) REVERT: A 542 ASP cc_start: 0.8456 (OUTLIER) cc_final: 0.8191 (m-30) outliers start: 16 outliers final: 8 residues processed: 103 average time/residue: 1.2523 time to fit residues: 139.0534 Evaluate side-chains 100 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 89 time to evaluate : 1.066 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 171 SER 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 328 MET Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 625 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 109 optimal weight: 0.9990 chunk 88 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 90 optimal weight: 3.9990 chunk 15 optimal weight: 10.0000 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 2.9990 chunk 48 optimal weight: 7.9990 chunk 7 optimal weight: 6.9990 chunk 114 optimal weight: 1.9990 chunk 45 optimal weight: 5.9990 overall best weight: 1.9990 ------------------------------------------------------------------------------- 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 ** 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 = 0.4338 r_free = 0.4338 target = 0.207628 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3284 r_free = 0.3284 target = 0.114440 restraints weight = 16389.178| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.66 r_work: 0.2926 rms_B_bonded: 3.03 restraints_weight: 0.5000 r_work: 0.2796 rms_B_bonded: 4.58 restraints_weight: 0.2500 r_work (final): 0.2796 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2792 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2792 r_free = 0.2792 target_work(ls_wunit_k1) = 0.077 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2792 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.1598 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.085 9862 Z= 0.235 Angle : 0.700 16.551 13408 Z= 0.369 Chirality : 0.049 0.239 1501 Planarity : 0.005 0.092 1687 Dihedral : 4.742 36.080 1329 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 7.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 1.71 % Allowed : 12.25 % Favored : 86.04 % 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: 0.08 (0.24), residues: 1219 helix: 1.14 (0.24), residues: 456 sheet: 0.70 (0.34), residues: 255 loop : -1.32 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP H 109 HIS 0.006 0.002 HIS A 391 PHE 0.018 0.002 PHE A 224 TYR 0.017 0.002 TYR A 116 ARG 0.005 0.001 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.05956 ( 479) hydrogen bonds : angle 4.58267 ( 1395) SS BOND : bond 0.00927 ( 8) SS BOND : angle 2.41204 ( 16) covalent geometry : bond 0.00576 ( 9854) covalent geometry : angle 0.69542 (13392) *********************** 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 105 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 87 time to evaluate : 0.943 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3248 (p90) cc_final: 0.2685 (p90) REVERT: A 51 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7876 (tp30) REVERT: A 71 GLU cc_start: 0.7758 (OUTLIER) cc_final: 0.7252 (mp0) REVERT: A 493 LEU cc_start: 0.8417 (OUTLIER) cc_final: 0.8146 (mp) REVERT: A 542 ASP cc_start: 0.8568 (OUTLIER) cc_final: 0.8239 (m-30) REVERT: A 638 GLU cc_start: 0.7642 (OUTLIER) cc_final: 0.7411 (tt0) outliers start: 18 outliers final: 7 residues processed: 100 average time/residue: 1.2021 time to fit residues: 129.4382 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 : 0.952 ------------------------------------------------------------------------------- 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 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 493 LEU Chi-restraints excluded: chain A residue 542 ASP Chi-restraints excluded: chain A residue 638 GLU 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: 30.0000 chunk 36 optimal weight: 3.9990 chunk 66 optimal weight: 4.9990 chunk 42 optimal weight: 0.9980 chunk 92 optimal weight: 0.9990 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 3.9990 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 90.0000 chunk 4 optimal weight: 9.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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 = 0.4336 r_free = 0.4336 target = 0.207532 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3278 r_free = 0.3278 target = 0.114307 restraints weight = 19004.506| |-----------------------------------------------------------------------------| r_work (start): 0.3202 rms_B_bonded: 2.95 r_work: 0.2926 rms_B_bonded: 3.34 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2914 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2914 r_free = 0.2914 target_work(ls_wunit_k1) = 0.085 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2914 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8192 moved from start: 0.1712 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.080 9862 Z= 0.225 Angle : 0.690 16.062 13408 Z= 0.363 Chirality : 0.049 0.227 1501 Planarity : 0.005 0.086 1687 Dihedral : 4.778 35.156 1329 Min Nonbonded Distance : 2.475 Molprobity Statistics. All-atom Clashscore : 7.71 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 2.28 % Allowed : 12.54 % Favored : 85.19 % 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: -0.00 (0.24), residues: 1219 helix: 1.06 (0.25), residues: 455 sheet: 0.66 (0.34), residues: 242 loop : -1.29 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.002 TRP H 109 HIS 0.006 0.001 HIS A 391 PHE 0.017 0.002 PHE A 387 TYR 0.018 0.002 TYR A 319 ARG 0.005 0.001 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.05732 ( 479) hydrogen bonds : angle 4.54394 ( 1395) SS BOND : bond 0.00877 ( 8) SS BOND : angle 2.27033 ( 16) covalent geometry : bond 0.00551 ( 9854) covalent geometry : angle 0.68558 (13392) *********************** 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 110 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 86 time to evaluate : 0.981 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3229 (p90) cc_final: 0.2637 (p90) REVERT: L 182 LEU cc_start: 0.4742 (mp) cc_final: 0.4252 (tt) REVERT: A 51 GLU cc_start: 0.8269 (mm-30) cc_final: 0.7790 (tp30) REVERT: A 71 GLU cc_start: 0.7604 (OUTLIER) cc_final: 0.7060 (mp0) REVERT: A 493 LEU cc_start: 0.8438 (OUTLIER) cc_final: 0.8213 (mp) REVERT: A 542 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8121 (m-30) outliers start: 24 outliers final: 9 residues processed: 105 average time/residue: 1.2099 time to fit residues: 136.6215 Evaluate side-chains 98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.817 ------------------------------------------------------------------------------- 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 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 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 86 optimal weight: 0.6980 chunk 14 optimal weight: 0.4980 chunk 47 optimal weight: 9.9990 chunk 42 optimal weight: 0.9990 chunk 26 optimal weight: 20.0000 chunk 36 optimal weight: 3.9990 chunk 46 optimal weight: 2.9990 chunk 32 optimal weight: 40.0000 chunk 110 optimal weight: 1.9990 chunk 115 optimal weight: 0.8980 chunk 61 optimal weight: 0.9980 overall best weight: 0.8182 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.209717 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3293 r_free = 0.3293 target = 0.114004 restraints weight = 22779.617| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 3.17 r_work: 0.2943 rms_B_bonded: 3.35 restraints_weight: 0.5000 r_work (final): 0.2943 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2958 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2958 r_free = 0.2958 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2958 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.1662 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= 0.141 Angle : 0.605 15.202 13408 Z= 0.316 Chirality : 0.045 0.197 1501 Planarity : 0.004 0.054 1687 Dihedral : 4.488 33.901 1329 Min Nonbonded Distance : 2.476 Molprobity Statistics. All-atom Clashscore : 6.76 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.84 % Favored : 94.00 % Rotamer: Outliers : 1.42 % Allowed : 14.06 % 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 (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: 0.29 (0.25), residues: 1219 helix: 1.45 (0.25), residues: 455 sheet: 0.69 (0.35), residues: 242 loop : -1.22 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP H 110 HIS 0.004 0.001 HIS A 479 PHE 0.011 0.001 PHE A 320 TYR 0.017 0.001 TYR H 63 ARG 0.006 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04470 ( 479) hydrogen bonds : angle 4.36451 ( 1395) SS BOND : bond 0.00812 ( 8) SS BOND : angle 2.09812 ( 16) covalent geometry : bond 0.00321 ( 9854) covalent geometry : angle 0.60058 (13392) *********************** 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 109 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.975 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6518 (OUTLIER) cc_final: 0.6146 (mpp) REVERT: H 160 TYR cc_start: 0.3215 (p90) cc_final: 0.2618 (p90) REVERT: L 182 LEU cc_start: 0.4501 (mp) cc_final: 0.4075 (tt) REVERT: A 51 GLU cc_start: 0.8183 (mm-30) cc_final: 0.7703 (tp30) REVERT: A 71 GLU cc_start: 0.7482 (OUTLIER) cc_final: 0.7017 (mp0) REVERT: A 542 ASP cc_start: 0.8387 (OUTLIER) cc_final: 0.8068 (m-30) outliers start: 15 outliers final: 5 residues processed: 103 average time/residue: 1.1495 time to fit residues: 128.1611 Evaluate side-chains 96 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 88 time to evaluate : 0.957 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET 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 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: 0.6980 chunk 73 optimal weight: 4.9990 chunk 37 optimal weight: 10.0000 chunk 30 optimal weight: 9.9990 chunk 12 optimal weight: 8.9990 chunk 14 optimal weight: 8.9990 chunk 48 optimal weight: 20.0000 chunk 31 optimal weight: 8.9990 overall best weight: 4.9386 ------------------------------------------------------------------------------- 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** A 643 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4297 r_free = 0.4297 target = 0.203379 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3224 r_free = 0.3224 target = 0.111054 restraints weight = 21033.386| |-----------------------------------------------------------------------------| r_work (start): 0.3135 rms_B_bonded: 3.84 r_work: 0.2848 rms_B_bonded: 3.36 restraints_weight: 0.5000 r_work (final): 0.2848 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2827 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2827 r_free = 0.2827 target_work(ls_wunit_k1) = 0.079 | | occupancies: max = 1.00 min = 0.26 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2827 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8273 moved from start: 0.2214 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.013 0.106 9862 Z= 0.502 Angle : 0.945 16.127 13408 Z= 0.506 Chirality : 0.064 0.331 1501 Planarity : 0.008 0.099 1687 Dihedral : 5.475 34.993 1329 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.33 % Allowed : 6.99 % Favored : 92.68 % Rotamer: Outliers : 1.90 % Allowed : 14.43 % Favored : 83.67 % 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: -0.67 (0.24), residues: 1219 helix: 0.34 (0.24), residues: 445 sheet: 0.41 (0.34), residues: 240 loop : -1.52 (0.26), residues: 534 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.060 0.005 TRP H 109 HIS 0.010 0.003 HIS A 206 PHE 0.026 0.004 PHE A 224 TYR 0.024 0.004 TYR A 345 ARG 0.014 0.001 ARG A 393 Details of bonding type rmsd hydrogen bonds : bond 0.08351 ( 479) hydrogen bonds : angle 5.00271 ( 1395) SS BOND : bond 0.01162 ( 8) SS BOND : angle 2.53046 ( 16) covalent geometry : bond 0.01256 ( 9854) covalent geometry : angle 0.94163 (13392) *********************** 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 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 81 time to evaluate : 0.990 Fit side-chains REVERT: H 160 TYR cc_start: 0.2929 (p90) cc_final: 0.2506 (p90) REVERT: L 38 GLN cc_start: 0.5723 (tt0) cc_final: 0.5338 (tt0) REVERT: L 169 SER cc_start: 0.5628 (m) cc_final: 0.5414 (t) REVERT: L 182 LEU cc_start: 0.4537 (mp) cc_final: 0.4095 (tt) REVERT: A 51 GLU cc_start: 0.8342 (mm-30) cc_final: 0.7843 (tp30) REVERT: A 71 GLU cc_start: 0.7786 (OUTLIER) cc_final: 0.7220 (mp0) outliers start: 20 outliers final: 8 residues processed: 95 average time/residue: 1.1918 time to fit residues: 122.5705 Evaluate side-chains 88 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 79 time to evaluate : 1.056 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 180 THR 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 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 105 optimal weight: 0.8980 chunk 120 optimal weight: 0.9980 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 52 optimal weight: 9.9990 chunk 111 optimal weight: 0.9990 chunk 101 optimal weight: 0.0570 chunk 69 optimal weight: 0.6980 chunk 99 optimal weight: 1.9990 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 50.0000 overall best weight: 0.7098 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 199 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 580 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4350 r_free = 0.4350 target = 0.209344 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3271 r_free = 0.3271 target = 0.112306 restraints weight = 15513.558| |-----------------------------------------------------------------------------| r_work (start): 0.3156 rms_B_bonded: 2.63 r_work: 0.2986 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2834 rms_B_bonded: 4.56 restraints_weight: 0.2500 r_work (final): 0.2834 ------------------------------------------------------------------------------- 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 = 0.26 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 = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2842 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 9862 Z= 0.142 Angle : 0.620 15.550 13408 Z= 0.325 Chirality : 0.045 0.268 1501 Planarity : 0.004 0.054 1687 Dihedral : 4.696 34.572 1329 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.02 % Favored : 94.82 % Rotamer: Outliers : 1.14 % Allowed : 15.57 % Favored : 83.29 % 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: 0.00 (0.24), residues: 1219 helix: 1.20 (0.25), residues: 455 sheet: 0.52 (0.34), residues: 241 loop : -1.34 (0.26), residues: 523 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.049 0.002 TRP H 110 HIS 0.004 0.001 HIS A 479 PHE 0.013 0.001 PHE A 348 TYR 0.018 0.001 TYR A 319 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04558 ( 479) hydrogen bonds : angle 4.39293 ( 1395) SS BOND : bond 0.00741 ( 8) SS BOND : angle 2.03855 ( 16) covalent geometry : bond 0.00315 ( 9854) covalent geometry : angle 0.61607 (13392) *********************** 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 98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6437 (mpp) cc_final: 0.6178 (mpp) REVERT: H 160 TYR cc_start: 0.2697 (p90) cc_final: 0.2232 (p90) REVERT: L 38 GLN cc_start: 0.5679 (tt0) cc_final: 0.5276 (tt0) REVERT: L 182 LEU cc_start: 0.4456 (mp) cc_final: 0.4004 (tt) REVERT: A 51 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7742 (tp30) REVERT: A 71 GLU cc_start: 0.7560 (OUTLIER) cc_final: 0.7113 (mp0) outliers start: 12 outliers final: 6 residues processed: 94 average time/residue: 1.2164 time to fit residues: 123.1015 Evaluate side-chains 92 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 85 time to evaluate : 0.959 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 13 optimal weight: 20.0000 chunk 69 optimal weight: 1.9990 chunk 71 optimal weight: 0.0040 chunk 4 optimal weight: 2.9990 chunk 106 optimal weight: 1.9990 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 4.9990 chunk 70 optimal weight: 0.8980 chunk 3 optimal weight: 5.9990 chunk 26 optimal weight: 20.0000 chunk 107 optimal weight: 0.4980 overall best weight: 0.8394 ------------------------------------------------------------------------------- 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 643 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4351 r_free = 0.4351 target = 0.209470 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3288 r_free = 0.3288 target = 0.115672 restraints weight = 19657.075| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 3.04 r_work: 0.2955 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2955 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2948 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2948 r_free = 0.2948 target_work(ls_wunit_k1) = 0.087 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2948 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8134 moved from start: 0.1937 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9862 Z= 0.144 Angle : 0.617 14.929 13408 Z= 0.322 Chirality : 0.045 0.259 1501 Planarity : 0.005 0.059 1687 Dihedral : 4.500 33.681 1329 Min Nonbonded Distance : 2.452 Molprobity Statistics. All-atom Clashscore : 7.08 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.33 % Favored : 93.50 % Rotamer: Outliers : 0.85 % Allowed : 15.67 % 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 (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: 0.23 (0.25), residues: 1219 helix: 1.41 (0.25), residues: 461 sheet: 0.71 (0.35), residues: 237 loop : -1.29 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.002 TRP H 110 HIS 0.004 0.001 HIS A 391 PHE 0.015 0.001 PHE H 115 TYR 0.017 0.001 TYR A 319 ARG 0.005 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.04603 ( 479) hydrogen bonds : angle 4.30401 ( 1395) SS BOND : bond 0.00734 ( 8) SS BOND : angle 2.04254 ( 16) covalent geometry : bond 0.00332 ( 9854) covalent geometry : angle 0.61366 (13392) ********************** 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 94 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.989 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6548 (mpp) cc_final: 0.6277 (mpp) REVERT: H 160 TYR cc_start: 0.2904 (p90) cc_final: 0.2453 (p90) REVERT: L 38 GLN cc_start: 0.5759 (tt0) cc_final: 0.5341 (tt0) REVERT: L 182 LEU cc_start: 0.4520 (mp) cc_final: 0.4059 (tt) REVERT: A 51 GLU cc_start: 0.8182 (mm-30) cc_final: 0.7740 (tp30) REVERT: A 71 GLU cc_start: 0.7465 (OUTLIER) cc_final: 0.7029 (mp0) outliers start: 9 outliers final: 5 residues processed: 91 average time/residue: 1.3457 time to fit residues: 131.3544 Evaluate side-chains 90 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.954 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 611 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 12 optimal weight: 2.9990 chunk 74 optimal weight: 0.0970 chunk 83 optimal weight: 0.6980 chunk 86 optimal weight: 0.6980 chunk 32 optimal weight: 20.0000 chunk 106 optimal weight: 0.0020 chunk 19 optimal weight: 2.9990 chunk 80 optimal weight: 0.2980 chunk 85 optimal weight: 0.9980 chunk 35 optimal weight: 3.9990 chunk 78 optimal weight: 0.5980 overall best weight: 0.3386 ------------------------------------------------------------------------------- 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 = 0.4375 r_free = 0.4375 target = 0.212067 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.116036 restraints weight = 17142.308| |-----------------------------------------------------------------------------| r_work (start): 0.3223 rms_B_bonded: 2.85 r_work: 0.3049 rms_B_bonded: 2.89 restraints_weight: 0.5000 r_work: 0.2908 rms_B_bonded: 4.61 restraints_weight: 0.2500 r_work (final): 0.2908 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2895 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.19 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2895 r_free = 0.2895 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.18 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2895 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8110 moved from start: 0.1971 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 9862 Z= 0.116 Angle : 0.575 14.389 13408 Z= 0.298 Chirality : 0.044 0.245 1501 Planarity : 0.004 0.047 1687 Dihedral : 4.258 31.424 1329 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 6.14 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 0.47 % Allowed : 16.14 % Favored : 83.38 % 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: 0.49 (0.25), residues: 1219 helix: 1.70 (0.25), residues: 461 sheet: 0.82 (0.35), residues: 237 loop : -1.22 (0.27), residues: 521 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.064 0.002 TRP H 110 HIS 0.004 0.001 HIS A 479 PHE 0.015 0.001 PHE H 115 TYR 0.014 0.001 TYR A 319 ARG 0.008 0.000 ARG A 69 Details of bonding type rmsd hydrogen bonds : bond 0.03618 ( 479) hydrogen bonds : angle 4.15207 ( 1395) SS BOND : bond 0.00684 ( 8) SS BOND : angle 1.93924 ( 16) covalent geometry : bond 0.00246 ( 9854) covalent geometry : angle 0.57177 (13392) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 11505.92 seconds wall clock time: 199 minutes 59.22 seconds (11999.22 seconds total)