Starting phenix.real_space_refine on Fri Feb 14 01:18:51 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7zlg_14779/02_2025/7zlg_14779.cif Found real_map, /net/cci-nas-00/data/ceres_data/7zlg_14779/02_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_14779/02_2025/7zlg_14779.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7zlg_14779/02_2025/7zlg_14779.map" model { file = "/net/cci-nas-00/data/ceres_data/7zlg_14779/02_2025/7zlg_14779.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7zlg_14779/02_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-5592/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: 8.52, per 1000 atoms: 0.89 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: 2.38 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: 1.10 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: 3.27 Time building geometry restraints manager: 2.79 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: 5.390 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: 0.550 Check model and map are aligned: 0.070 Set scattering table: 0.090 Process input model: 27.980 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: 0.010 Load rotamer database and sin/cos tables:11.640 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 45.880 ------------------------------------------------------------------------------- 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 : 1.022 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: 1.3504 time to fit residues: 176.3177 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 : 1.023 ------------------------------------------------------------------------------- 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 = 0.3375 r_free = 0.3375 target = 0.121227 restraints weight = 13987.071| |-----------------------------------------------------------------------------| r_work (start): 0.3290 rms_B_bonded: 2.49 r_work: 0.3089 rms_B_bonded: 2.69 restraints_weight: 0.5000 r_work: 0.2958 rms_B_bonded: 4.17 restraints_weight: 0.2500 r_work (final): 0.2958 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2946 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2946 r_free = 0.2946 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 = 0.2946 r_free = 0.2946 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2946 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 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 : 1.003 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 97 TYR cc_start: 0.5839 (m-80) cc_final: 0.5550 (m-80) REVERT: H 160 TYR cc_start: 0.3399 (p90) cc_final: 0.2854 (p90) REVERT: H 171 SER cc_start: 0.6297 (t) cc_final: 0.6035 (t) REVERT: L 38 GLN cc_start: 0.5529 (tt0) cc_final: 0.5207 (tt0) REVERT: A 51 GLU cc_start: 0.8196 (mm-30) cc_final: 0.7811 (tp30) REVERT: A 298 ILE cc_start: 0.8249 (mt) cc_final: 0.7920 (tp) outliers start: 10 outliers final: 5 residues processed: 108 average time/residue: 1.1838 time to fit residues: 138.3508 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 : 1.018 ------------------------------------------------------------------------------- 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: 0.4980 chunk 26 optimal weight: 20.0000 chunk 45 optimal weight: 9.9990 chunk 12 optimal weight: 6.9990 chunk 85 optimal weight: 1.9990 chunk 44 optimal weight: 10.0000 chunk 115 optimal weight: 0.0370 chunk 118 optimal weight: 1.9990 chunk 5 optimal weight: 10.0000 chunk 95 optimal weight: 2.9990 chunk 109 optimal weight: 0.5980 overall best weight: 1.0262 ------------------------------------------------------------------------------- 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 = 0.4367 r_free = 0.4367 target = 0.210507 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3315 r_free = 0.3315 target = 0.116950 restraints weight = 14701.781| |-----------------------------------------------------------------------------| r_work (start): 0.3231 rms_B_bonded: 2.57 r_work: 0.3030 rms_B_bonded: 2.74 restraints_weight: 0.5000 r_work: 0.2902 rms_B_bonded: 4.19 restraints_weight: 0.2500 r_work (final): 0.2902 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2875 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2875 r_free = 0.2875 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 = 0.2875 r_free = 0.2875 target_work(ls_wunit_k1) = 0.082 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2875 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.1202 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9854 Z= 0.226 Angle : 0.599 9.747 13392 Z= 0.316 Chirality : 0.045 0.153 1501 Planarity : 0.004 0.056 1687 Dihedral : 4.341 30.246 1330 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.51 % Favored : 94.33 % Rotamer: Outliers : 1.52 % Allowed : 9.40 % Favored : 89.08 % 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: 0.34 (0.25), residues: 1219 helix: 1.49 (0.25), residues: 456 sheet: 0.95 (0.35), residues: 244 loop : -1.33 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP H 110 HIS 0.005 0.001 HIS A 375 PHE 0.014 0.001 PHE A 387 TYR 0.017 0.001 TYR A 319 ARG 0.004 0.000 ARG A 69 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2438 Ramachandran restraints generated. 1219 Oldfield, 0 Emsley, 1219 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 112 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.982 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3316 (p90) cc_final: 0.2780 (p90) REVERT: L 38 GLN cc_start: 0.5508 (tt0) cc_final: 0.5154 (tt0) REVERT: A 51 GLU cc_start: 0.8348 (mm-30) cc_final: 0.7923 (tp30) REVERT: A 493 LEU cc_start: 0.8439 (OUTLIER) cc_final: 0.8207 (mp) REVERT: A 542 ASP cc_start: 0.8473 (OUTLIER) cc_final: 0.8194 (m-30) outliers start: 16 outliers final: 7 residues processed: 107 average time/residue: 1.2077 time to fit residues: 139.2158 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 : 1.007 ------------------------------------------------------------------------------- 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 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: 0.0870 chunk 56 optimal weight: 0.8980 chunk 71 optimal weight: 0.0970 chunk 75 optimal weight: 0.6980 chunk 18 optimal weight: 8.9990 chunk 101 optimal weight: 1.9990 chunk 20 optimal weight: 9.9990 chunk 52 optimal weight: 5.9990 chunk 85 optimal weight: 0.9980 chunk 120 optimal weight: 0.9980 chunk 76 optimal weight: 0.8980 overall best weight: 0.5356 ------------------------------------------------------------------------------- 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 375 HIS ** A 431 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** 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: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4377 r_free = 0.4377 target = 0.211832 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3337 r_free = 0.3337 target = 0.118718 restraints weight = 16148.175| |-----------------------------------------------------------------------------| r_work (start): 0.3252 rms_B_bonded: 2.67 r_work: 0.3034 rms_B_bonded: 2.95 restraints_weight: 0.5000 r_work: 0.2905 rms_B_bonded: 4.57 restraints_weight: 0.2500 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2882 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2882 r_free = 0.2882 target_work(ls_wunit_k1) = 0.083 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2882 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8157 moved from start: 0.1328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.087 9854 Z= 0.183 Angle : 0.591 16.876 13392 Z= 0.307 Chirality : 0.044 0.265 1501 Planarity : 0.004 0.047 1687 Dihedral : 4.240 30.350 1330 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.43 % Favored : 94.41 % Rotamer: Outliers : 1.61 % Allowed : 10.26 % Favored : 88.13 % 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: 1.69 (0.25), residues: 455 sheet: 0.95 (0.35), residues: 245 loop : -1.28 (0.27), residues: 519 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP H 110 HIS 0.003 0.001 HIS A 479 PHE 0.010 0.001 PHE A 320 TYR 0.015 0.001 TYR H 63 ARG 0.004 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 114 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 97 time to evaluate : 0.937 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3313 (p90) cc_final: 0.2787 (p90) REVERT: L 38 GLN cc_start: 0.5487 (tt0) cc_final: 0.5115 (tt0) REVERT: A 51 GLU cc_start: 0.8323 (mm-30) cc_final: 0.7889 (tp30) REVERT: A 71 GLU cc_start: 0.7689 (OUTLIER) cc_final: 0.7275 (mp0) REVERT: A 298 ILE cc_start: 0.8276 (mt) cc_final: 0.7952 (tp) REVERT: A 493 LEU cc_start: 0.8414 (OUTLIER) cc_final: 0.8208 (mp) REVERT: A 542 ASP cc_start: 0.8472 (OUTLIER) cc_final: 0.8216 (m-30) outliers start: 17 outliers final: 6 residues processed: 108 average time/residue: 1.2098 time to fit residues: 140.6534 Evaluate side-chains 102 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 93 time to evaluate : 1.135 ------------------------------------------------------------------------------- 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 328 MET Chi-restraints excluded: chain A residue 493 LEU Chi-restraints excluded: chain A residue 542 ASP 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: 1.9990 chunk 90 optimal weight: 2.9990 chunk 15 optimal weight: 8.9990 chunk 59 optimal weight: 1.9990 chunk 43 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 chunk 7 optimal weight: 0.0980 chunk 114 optimal weight: 1.9990 chunk 45 optimal weight: 1.9990 overall best weight: 1.4186 ------------------------------------------------------------------------------- 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 = 0.4350 r_free = 0.4350 target = 0.209071 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.117224 restraints weight = 16502.937| |-----------------------------------------------------------------------------| r_work (start): 0.3205 rms_B_bonded: 2.78 r_work: 0.2948 rms_B_bonded: 3.04 restraints_weight: 0.5000 r_work (final): 0.2948 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2965 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2965 r_free = 0.2965 target_work(ls_wunit_k1) = 0.088 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2965 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8149 moved from start: 0.1510 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 9854 Z= 0.289 Angle : 0.648 16.143 13392 Z= 0.340 Chirality : 0.047 0.223 1501 Planarity : 0.005 0.073 1687 Dihedral : 4.517 34.837 1329 Min Nonbonded Distance : 2.485 Molprobity Statistics. All-atom Clashscore : 6.24 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.09 % Favored : 93.75 % Rotamer: Outliers : 1.42 % Allowed : 12.16 % 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: 0.30 (0.25), residues: 1219 helix: 1.45 (0.25), residues: 454 sheet: 0.78 (0.34), residues: 255 loop : -1.29 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP H 109 HIS 0.005 0.001 HIS A 391 PHE 0.017 0.002 PHE A 387 TYR 0.017 0.002 TYR A 319 ARG 0.004 0.000 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 107 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 1.047 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 160 TYR cc_start: 0.3422 (p90) cc_final: 0.2849 (p90) REVERT: L 38 GLN cc_start: 0.5512 (tt0) cc_final: 0.5195 (tt0) REVERT: A 51 GLU cc_start: 0.8203 (mm-30) cc_final: 0.7836 (tp30) REVERT: A 71 GLU cc_start: 0.7579 (OUTLIER) cc_final: 0.7076 (mp0) REVERT: A 493 LEU cc_start: 0.8468 (OUTLIER) cc_final: 0.8244 (mp) REVERT: A 542 ASP cc_start: 0.8411 (OUTLIER) cc_final: 0.8085 (m-30) outliers start: 15 outliers final: 7 residues processed: 103 average time/residue: 1.2455 time to fit residues: 138.1734 Evaluate side-chains 100 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 1.030 ------------------------------------------------------------------------------- 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 647 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 49 optimal weight: 0.6980 chunk 36 optimal weight: 4.9990 chunk 66 optimal weight: 2.9990 chunk 42 optimal weight: 0.8980 chunk 92 optimal weight: 0.5980 chunk 40 optimal weight: 6.9990 chunk 77 optimal weight: 0.8980 chunk 112 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 22 optimal weight: 70.0000 chunk 4 optimal weight: 9.9990 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** ** 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 = 0.4363 r_free = 0.4363 target = 0.210435 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3327 r_free = 0.3327 target = 0.118514 restraints weight = 18919.640| |-----------------------------------------------------------------------------| r_work (start): 0.3246 rms_B_bonded: 3.14 r_work: 0.2957 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2957 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2932 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2932 r_free = 0.2932 target_work(ls_wunit_k1) = 0.086 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2932 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8145 moved from start: 0.1553 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.076 9854 Z= 0.210 Angle : 0.592 14.961 13392 Z= 0.309 Chirality : 0.045 0.191 1501 Planarity : 0.004 0.054 1687 Dihedral : 4.340 33.173 1329 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 5.87 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.10 % Favored : 94.74 % Rotamer: Outliers : 1.80 % Allowed : 12.73 % Favored : 85.47 % 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: 0.43 (0.25), residues: 1219 helix: 1.60 (0.25), residues: 455 sheet: 0.78 (0.34), residues: 255 loop : -1.22 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 440 HIS 0.003 0.001 HIS A 479 PHE 0.012 0.001 PHE A 387 TYR 0.017 0.001 TYR H 63 ARG 0.004 0.000 ARG A 69 *********************** 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 112 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 93 time to evaluate : 1.017 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6443 (OUTLIER) cc_final: 0.6095 (mpp) REVERT: H 160 TYR cc_start: 0.3344 (p90) cc_final: 0.2774 (p90) REVERT: L 38 GLN cc_start: 0.5440 (tt0) cc_final: 0.5172 (tt0) REVERT: L 182 LEU cc_start: 0.4557 (mp) cc_final: 0.4174 (tp) REVERT: A 51 GLU cc_start: 0.8244 (mm-30) cc_final: 0.7794 (tp30) REVERT: A 71 GLU cc_start: 0.7538 (OUTLIER) cc_final: 0.7136 (mp0) REVERT: A 298 ILE cc_start: 0.8277 (mt) cc_final: 0.7951 (tp) REVERT: A 542 ASP cc_start: 0.8425 (OUTLIER) cc_final: 0.8126 (m-30) REVERT: A 558 MET cc_start: 0.8526 (OUTLIER) cc_final: 0.8326 (ptp) outliers start: 19 outliers final: 9 residues processed: 105 average time/residue: 1.2625 time to fit residues: 142.9868 Evaluate side-chains 104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.998 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 89 LEU Chi-restraints excluded: chain H residue 180 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 542 ASP Chi-restraints excluded: chain A residue 558 MET Chi-restraints excluded: chain A residue 625 GLU 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: 0.4980 chunk 14 optimal weight: 10.0000 chunk 47 optimal weight: 10.0000 chunk 42 optimal weight: 8.9990 chunk 26 optimal weight: 30.0000 chunk 36 optimal weight: 4.9990 chunk 46 optimal weight: 8.9990 chunk 32 optimal weight: 40.0000 chunk 110 optimal weight: 2.9990 chunk 115 optimal weight: 0.0470 chunk 61 optimal weight: 0.6980 overall best weight: 1.8482 ------------------------------------------------------------------------------- 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 ** A 662 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 = 0.4339 r_free = 0.4339 target = 0.207864 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.111174 restraints weight = 21948.407| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 3.15 r_work: 0.2918 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work: 0.2784 rms_B_bonded: 4.98 restraints_weight: 0.2500 r_work (final): 0.2784 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2782 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2782 r_free = 0.2782 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 = 0.2782 r_free = 0.2782 target_work(ls_wunit_k1) = 0.076 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2782 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8221 moved from start: 0.1700 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= 0.343 Angle : 0.673 15.038 13392 Z= 0.355 Chirality : 0.049 0.286 1501 Planarity : 0.005 0.078 1687 Dihedral : 4.604 34.658 1329 Min Nonbonded Distance : 2.472 Molprobity Statistics. All-atom Clashscore : 6.92 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 1.52 % Allowed : 13.68 % Favored : 84.81 % 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: 0.19 (0.24), residues: 1219 helix: 1.27 (0.25), residues: 454 sheet: 0.73 (0.34), residues: 255 loop : -1.27 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.027 0.002 TRP H 109 HIS 0.005 0.001 HIS A 391 PHE 0.018 0.002 PHE A 387 TYR 0.017 0.002 TYR A 319 ARG 0.004 0.000 ARG A 441 *********************** 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 104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 88 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6389 (OUTLIER) cc_final: 0.6060 (mpp) REVERT: H 160 TYR cc_start: 0.3161 (p90) cc_final: 0.2652 (p90) REVERT: L 182 LEU cc_start: 0.4745 (mp) cc_final: 0.4289 (tp) REVERT: A 51 GLU cc_start: 0.8519 (mm-30) cc_final: 0.7892 (tp30) REVERT: A 71 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7332 (mp0) REVERT: A 542 ASP cc_start: 0.8579 (OUTLIER) cc_final: 0.8255 (m-30) outliers start: 16 outliers final: 7 residues processed: 98 average time/residue: 1.2393 time to fit residues: 131.0096 Evaluate side-chains 98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 1.049 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 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 328 MET Chi-restraints excluded: chain A residue 542 ASP 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: 0.0870 chunk 0 optimal weight: 20.0000 chunk 56 optimal weight: 0.5980 chunk 73 optimal weight: 3.9990 chunk 37 optimal weight: 9.9990 chunk 30 optimal weight: 30.0000 chunk 12 optimal weight: 6.9990 chunk 14 optimal weight: 0.0370 chunk 48 optimal weight: 0.8980 chunk 31 optimal weight: 9.9990 overall best weight: 1.1238 ------------------------------------------------------------------------------- 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 = 0.4352 r_free = 0.4352 target = 0.209153 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114400 restraints weight = 20198.952| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.90 r_work: 0.2971 rms_B_bonded: 3.08 restraints_weight: 0.5000 r_work: 0.2837 rms_B_bonded: 4.77 restraints_weight: 0.2500 r_work (final): 0.2837 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2813 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.23 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2813 r_free = 0.2813 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.22 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2813 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8188 moved from start: 0.1701 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9854 Z= 0.245 Angle : 0.618 15.052 13392 Z= 0.325 Chirality : 0.046 0.269 1501 Planarity : 0.004 0.062 1687 Dihedral : 4.476 34.521 1329 Min Nonbonded Distance : 2.445 Molprobity Statistics. All-atom Clashscore : 6.50 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.35 % Favored : 94.49 % Rotamer: Outliers : 1.71 % Allowed : 14.06 % Favored : 84.24 % 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 (0.25), residues: 1219 helix: 1.40 (0.25), residues: 455 sheet: 0.74 (0.34), residues: 255 loop : -1.21 (0.27), residues: 509 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP A 440 HIS 0.004 0.001 HIS A 391 PHE 0.014 0.002 PHE A 387 TYR 0.017 0.001 TYR A 319 ARG 0.004 0.000 ARG A 471 *********************** 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 108 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 90 time to evaluate : 1.097 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6447 (OUTLIER) cc_final: 0.6094 (mpp) REVERT: H 160 TYR cc_start: 0.3182 (p90) cc_final: 0.2671 (p90) REVERT: L 38 GLN cc_start: 0.5456 (tt0) cc_final: 0.5141 (tt0) REVERT: L 182 LEU cc_start: 0.4592 (mp) cc_final: 0.4134 (tt) REVERT: A 51 GLU cc_start: 0.8476 (mm-30) cc_final: 0.7885 (tp30) REVERT: A 71 GLU cc_start: 0.7660 (OUTLIER) cc_final: 0.7229 (mp0) REVERT: A 542 ASP cc_start: 0.8533 (OUTLIER) cc_final: 0.8248 (m-30) outliers start: 18 outliers final: 10 residues processed: 101 average time/residue: 1.2774 time to fit residues: 138.9937 Evaluate side-chains 102 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 89 time to evaluate : 1.099 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 180 THR 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 328 MET 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 121 random chunks: chunk 105 optimal weight: 1.9990 chunk 120 optimal weight: 0.3980 chunk 76 optimal weight: 0.9980 chunk 75 optimal weight: 0.6980 chunk 52 optimal weight: 2.9990 chunk 111 optimal weight: 2.9990 chunk 101 optimal weight: 2.9990 chunk 69 optimal weight: 1.9990 chunk 99 optimal weight: 0.7980 chunk 90 optimal weight: 1.9990 chunk 30 optimal weight: 40.0000 overall best weight: 0.9782 ------------------------------------------------------------------------------- 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 = 0.4357 r_free = 0.4357 target = 0.209907 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.112364 restraints weight = 15495.779| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.47 r_work: 0.3014 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.2881 rms_B_bonded: 4.15 restraints_weight: 0.2500 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2863 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2863 r_free = 0.2863 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 = 0.2863 r_free = 0.2863 target_work(ls_wunit_k1) = 0.081 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2863 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1751 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= 0.229 Angle : 0.607 14.740 13392 Z= 0.318 Chirality : 0.045 0.266 1501 Planarity : 0.004 0.057 1687 Dihedral : 4.403 33.522 1329 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.16 % Allowed : 6.17 % Favored : 93.67 % Rotamer: Outliers : 1.42 % Allowed : 14.25 % Favored : 84.33 % 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: 0.37 (0.25), residues: 1219 helix: 1.50 (0.25), residues: 455 sheet: 0.74 (0.34), residues: 242 loop : -1.16 (0.27), residues: 522 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 387 TYR 0.016 0.001 TYR A 319 ARG 0.004 0.000 ARG A 471 *********************** 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 104 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 89 time to evaluate : 1.184 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6476 (OUTLIER) cc_final: 0.6133 (mpp) REVERT: H 160 TYR cc_start: 0.3036 (p90) cc_final: 0.2508 (p90) REVERT: L 38 GLN cc_start: 0.5426 (tt0) cc_final: 0.5111 (tt0) REVERT: L 182 LEU cc_start: 0.4560 (mp) cc_final: 0.4102 (tt) REVERT: A 51 GLU cc_start: 0.8378 (mm-30) cc_final: 0.7800 (tp30) REVERT: A 71 GLU cc_start: 0.7562 (OUTLIER) cc_final: 0.7188 (mp0) REVERT: A 542 ASP cc_start: 0.8483 (OUTLIER) cc_final: 0.8182 (m-30) outliers start: 15 outliers final: 9 residues processed: 99 average time/residue: 1.3504 time to fit residues: 144.9317 Evaluate side-chains 101 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 89 time to evaluate : 1.104 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 171 SER Chi-restraints excluded: chain H residue 180 THR 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 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: 9.9990 chunk 106 optimal weight: 3.9990 chunk 90 optimal weight: 0.7980 chunk 8 optimal weight: 2.9990 chunk 70 optimal weight: 0.9980 chunk 3 optimal weight: 10.0000 chunk 26 optimal weight: 20.0000 chunk 107 optimal weight: 0.4980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.208835 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3291 r_free = 0.3291 target = 0.114679 restraints weight = 19568.009| |-----------------------------------------------------------------------------| r_work (start): 0.3179 rms_B_bonded: 2.91 r_work: 0.2936 rms_B_bonded: 3.11 restraints_weight: 0.5000 r_work: 0.2804 rms_B_bonded: 4.79 restraints_weight: 0.2500 r_work (final): 0.2804 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2818 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2818 r_free = 0.2818 target_work(ls_wunit_k1) = 0.078 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2818 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8193 moved from start: 0.1833 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 9854 Z= 0.264 Angle : 0.631 14.800 13392 Z= 0.331 Chirality : 0.046 0.269 1501 Planarity : 0.005 0.064 1687 Dihedral : 4.488 34.135 1329 Min Nonbonded Distance : 2.460 Molprobity Statistics. All-atom Clashscore : 6.55 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 1.14 % Allowed : 14.62 % Favored : 84.24 % 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: 0.30 (0.25), residues: 1219 helix: 1.39 (0.25), residues: 455 sheet: 0.76 (0.33), residues: 253 loop : -1.21 (0.28), residues: 511 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.002 TRP H 110 HIS 0.004 0.001 HIS A 391 PHE 0.014 0.002 PHE A 387 TYR 0.016 0.002 TYR A 319 ARG 0.004 0.000 ARG A 393 ********************** 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 98 residues out of total 1056 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 86 time to evaluate : 0.968 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: H 86 MET cc_start: 0.6506 (OUTLIER) cc_final: 0.6166 (mpp) REVERT: H 160 TYR cc_start: 0.3027 (p90) cc_final: 0.2581 (p90) REVERT: L 182 LEU cc_start: 0.4617 (mp) cc_final: 0.4134 (tt) REVERT: A 51 GLU cc_start: 0.8497 (mm-30) cc_final: 0.7878 (tp30) REVERT: A 71 GLU cc_start: 0.7693 (OUTLIER) cc_final: 0.7260 (mp0) REVERT: A 542 ASP cc_start: 0.8531 (OUTLIER) cc_final: 0.8231 (m-30) outliers start: 12 outliers final: 9 residues processed: 94 average time/residue: 1.3153 time to fit residues: 133.1949 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 : 1.032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 86 MET Chi-restraints excluded: chain H residue 180 THR Chi-restraints excluded: chain L residue 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: 0.7980 chunk 74 optimal weight: 0.9990 chunk 83 optimal weight: 2.9990 chunk 86 optimal weight: 0.9990 chunk 32 optimal weight: 40.0000 chunk 106 optimal weight: 2.9990 chunk 19 optimal weight: 30.0000 chunk 80 optimal weight: 0.3980 chunk 85 optimal weight: 0.8980 chunk 35 optimal weight: 10.0000 chunk 78 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 = 0.4361 r_free = 0.4361 target = 0.210238 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3318 r_free = 0.3318 target = 0.117726 restraints weight = 16657.176| |-----------------------------------------------------------------------------| r_work (start): 0.3201 rms_B_bonded: 3.00 r_work: 0.2983 rms_B_bonded: 2.94 restraints_weight: 0.5000 r_work: 0.2843 rms_B_bonded: 4.71 restraints_weight: 0.2500 r_work (final): 0.2843 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2837 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.21 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2837 r_free = 0.2837 target_work(ls_wunit_k1) = 0.080 | | occupancies: max = 1.00 min = 0.20 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2837 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8186 moved from start: 0.1820 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 9854 Z= 0.205 Angle : 0.592 14.495 13392 Z= 0.310 Chirality : 0.045 0.259 1501 Planarity : 0.004 0.051 1687 Dihedral : 4.336 33.275 1329 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 6.03 Ramachandran Plot: Outliers : 0.16 % Allowed : 5.92 % Favored : 93.91 % Rotamer: Outliers : 1.23 % Allowed : 14.62 % Favored : 84.14 % 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: 0.40 (0.25), residues: 1219 helix: 1.54 (0.25), residues: 461 sheet: 0.65 (0.33), residues: 259 loop : -1.17 (0.28), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.042 0.002 TRP H 110 HIS 0.004 0.001 HIS A 479 PHE 0.013 0.001 PHE H 115 TYR 0.015 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: 11305.29 seconds wall clock time: 199 minutes 18.09 seconds (11958.09 seconds total)