Starting phenix.real_space_refine on Sat Jun 14 09:23:21 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnz_61632/06_2025/9jnz_61632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnz_61632/06_2025/9jnz_61632.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9jnz_61632/06_2025/9jnz_61632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnz_61632/06_2025/9jnz_61632.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnz_61632/06_2025/9jnz_61632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnz_61632/06_2025/9jnz_61632.cif" } resolution = 3.0 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= 0.001 sd= 0.010 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: 6 Type Number sf(0) Gaussians P 292 5.49 5 S 25 5.16 5 Cl 1 4.86 5 C 9394 2.51 5 N 2993 2.21 5 O 3618 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5710/modules/chem_data/mon_lib" Total number of atoms: 16323 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 801 Number of conformers: 1 Conformer: "" Number of residues, atoms: 98, 801 Classifications: {'peptide': 98} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 4, 'TRANS': 93} Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "B" Number of atoms: 703 Number of conformers: 1 Conformer: "" Number of residues, atoms: 87, 703 Classifications: {'peptide': 87} Link IDs: {'PTRANS': 1, 'TRANS': 85} Chain: "C" Number of atoms: 811 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 811 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Chain: "D" Number of atoms: 718 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 718 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 2, 'TRANS': 90} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "E" Number of atoms: 779 Number of conformers: 1 Conformer: "" Number of residues, atoms: 95, 779 Classifications: {'peptide': 95} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 3, 'TRANS': 91} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 7 Unresolved non-hydrogen dihedrals: 5 Planarities with less than four sites: {'ARG:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "F" Number of atoms: 672 Number of conformers: 1 Conformer: "" Number of residues, atoms: 86, 672 Classifications: {'peptide': 86} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 1, 'TRANS': 84} Unresolved non-hydrogen bonds: 22 Unresolved non-hydrogen angles: 25 Unresolved non-hydrogen dihedrals: 19 Planarities with less than four sites: {'ARG:plan': 3} Unresolved non-hydrogen planarities: 15 Chain: "G" Number of atoms: 815 Number of conformers: 1 Conformer: "" Number of residues, atoms: 107, 815 Classifications: {'peptide': 107} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Chain: "H" Number of atoms: 726 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 726 Classifications: {'peptide': 93} Link IDs: {'PTRANS': 2, 'TRANS': 90} Chain: "I" Number of atoms: 2975 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 2975 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "J" Number of atoms: 3011 Number of conformers: 1 Conformer: "" Number of residues, atoms: 146, 3011 Classifications: {'DNA': 146} Link IDs: {'rna3p': 145} Chain: "K" Number of atoms: 4311 Number of conformers: 1 Conformer: "" Number of residues, atoms: 525, 4311 Classifications: {'peptide': 525} Link IDs: {'PCIS': 2, 'PTRANS': 17, 'TRANS': 505} Chain breaks: 2 Chain: "K" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' CL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 9.35, per 1000 atoms: 0.57 Number of scatterers: 16323 At special positions: 0 Unit cell: (96.3425, 116.91, 156.962, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 25 16.00 P 292 15.00 O 3618 8.00 N 2993 7.00 C 9394 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 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: 4.54 Conformation dependent library (CDL) restraints added in 1.7 seconds 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2444 Finding SS restraints... Secondary structure from input PDB file: 63 helices and 10 sheets defined 64.4% alpha, 4.0% beta 144 base pairs and 254 stacking pairs defined. Time for finding SS restraints: 7.01 Creating SS restraints... Processing helix chain 'A' and resid 46 through 55 Processing helix chain 'A' and resid 63 through 74 Processing helix chain 'A' and resid 85 through 114 Processing helix chain 'A' and resid 120 through 131 Processing helix chain 'B' and resid 24 through 29 Processing helix chain 'B' and resid 30 through 42 Processing helix chain 'B' and resid 49 through 76 removed outlier: 4.333A pdb=" N ARG B 55 " --> pdb=" O TYR B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 82 through 94 Processing helix chain 'C' and resid 16 through 21 Processing helix chain 'C' and resid 26 through 36 removed outlier: 3.588A pdb=" N VAL C 30 " --> pdb=" O PRO C 26 " (cutoff:3.500A) Processing helix chain 'C' and resid 45 through 73 removed outlier: 4.442A pdb=" N VAL C 49 " --> pdb=" O ALA C 45 " (cutoff:3.500A) Processing helix chain 'C' and resid 79 through 90 Processing helix chain 'C' and resid 112 through 116 Processing helix chain 'D' and resid 34 through 46 removed outlier: 3.563A pdb=" N LYS D 40 " --> pdb=" O ILE D 36 " (cutoff:3.500A) Processing helix chain 'D' and resid 52 through 81 Processing helix chain 'D' and resid 87 through 99 Processing helix chain 'D' and resid 101 through 121 Processing helix chain 'E' and resid 44 through 55 Processing helix chain 'E' and resid 63 through 76 removed outlier: 3.920A pdb=" N GLN E 76 " --> pdb=" O ARG E 72 " (cutoff:3.500A) Processing helix chain 'E' and resid 85 through 114 removed outlier: 3.509A pdb=" N ASP E 106 " --> pdb=" O ALA E 102 " (cutoff:3.500A) removed outlier: 3.908A pdb=" N LEU E 109 " --> pdb=" O GLU E 105 " (cutoff:3.500A) Processing helix chain 'E' and resid 120 through 131 Processing helix chain 'F' and resid 24 through 29 Processing helix chain 'F' and resid 30 through 42 Processing helix chain 'F' and resid 49 through 76 removed outlier: 4.051A pdb=" N GLU F 53 " --> pdb=" O LEU F 49 " (cutoff:3.500A) Processing helix chain 'F' and resid 82 through 94 Processing helix chain 'G' and resid 16 through 22 Processing helix chain 'G' and resid 26 through 37 Processing helix chain 'G' and resid 46 through 73 Processing helix chain 'G' and resid 79 through 89 Processing helix chain 'G' and resid 90 through 97 Processing helix chain 'G' and resid 112 through 116 Processing helix chain 'H' and resid 34 through 46 removed outlier: 3.975A pdb=" N LYS H 40 " --> pdb=" O ILE H 36 " (cutoff:3.500A) removed outlier: 5.228A pdb=" N LYS H 43 " --> pdb=" O TYR H 39 " (cutoff:3.500A) removed outlier: 3.625A pdb=" N GLN H 44 " --> pdb=" O LYS H 40 " (cutoff:3.500A) Processing helix chain 'H' and resid 52 through 81 removed outlier: 3.532A pdb=" N ASN H 81 " --> pdb=" O LEU H 77 " (cutoff:3.500A) Processing helix chain 'H' and resid 87 through 99 Processing helix chain 'H' and resid 101 through 121 Processing helix chain 'K' and resid 82 through 91 removed outlier: 3.518A pdb=" N ARG K 89 " --> pdb=" O SER K 85 " (cutoff:3.500A) removed outlier: 3.951A pdb=" N LEU K 91 " --> pdb=" O LYS K 87 " (cutoff:3.500A) Processing helix chain 'K' and resid 101 through 116 removed outlier: 3.989A pdb=" N THR K 105 " --> pdb=" O ASP K 101 " (cutoff:3.500A) Processing helix chain 'K' and resid 119 through 127 Processing helix chain 'K' and resid 131 through 143 removed outlier: 3.829A pdb=" N ASN K 143 " --> pdb=" O VAL K 139 " (cutoff:3.500A) Processing helix chain 'K' and resid 197 through 213 Processing helix chain 'K' and resid 228 through 241 Processing helix chain 'K' and resid 253 through 255 No H-bonds generated for 'chain 'K' and resid 253 through 255' Processing helix chain 'K' and resid 256 through 268 Processing helix chain 'K' and resid 279 through 290 Processing helix chain 'K' and resid 303 through 309 Processing helix chain 'K' and resid 309 through 315 removed outlier: 3.775A pdb=" N LEU K 313 " --> pdb=" O GLU K 309 " (cutoff:3.500A) removed outlier: 3.623A pdb=" N LYS K 315 " --> pdb=" O SER K 311 " (cutoff:3.500A) Processing helix chain 'K' and resid 325 through 329 Processing helix chain 'K' and resid 334 through 343 Processing helix chain 'K' and resid 360 through 371 removed outlier: 3.578A pdb=" N TRP K 364 " --> pdb=" O LEU K 360 " (cutoff:3.500A) removed outlier: 3.503A pdb=" N PHE K 369 " --> pdb=" O ALA K 365 " (cutoff:3.500A) Processing helix chain 'K' and resid 377 through 385 removed outlier: 3.810A pdb=" N PHE K 381 " --> pdb=" O ASP K 377 " (cutoff:3.500A) removed outlier: 4.054A pdb=" N PHE K 385 " --> pdb=" O PHE K 381 " (cutoff:3.500A) Processing helix chain 'K' and resid 391 through 394 Processing helix chain 'K' and resid 395 through 401 Processing helix chain 'K' and resid 402 through 406 Processing helix chain 'K' and resid 434 through 446 Processing helix chain 'K' and resid 469 through 478 removed outlier: 3.715A pdb=" N ARG K 473 " --> pdb=" O MET K 469 " (cutoff:3.500A) Processing helix chain 'K' and resid 479 through 482 Processing helix chain 'K' and resid 495 through 500 removed outlier: 3.892A pdb=" N TYR K 499 " --> pdb=" O GLU K 495 " (cutoff:3.500A) Processing helix chain 'K' and resid 502 through 518 removed outlier: 3.821A pdb=" N VAL K 506 " --> pdb=" O ALA K 502 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU K 516 " --> pdb=" O LYS K 512 " (cutoff:3.500A) removed outlier: 4.450A pdb=" N GLU K 517 " --> pdb=" O LYS K 513 " (cutoff:3.500A) Processing helix chain 'K' and resid 527 through 541 removed outlier: 3.752A pdb=" N ILE K 533 " --> pdb=" O ARG K 529 " (cutoff:3.500A) Processing helix chain 'K' and resid 553 through 565 Processing helix chain 'K' and resid 601 through 614 removed outlier: 3.740A pdb=" N ASP K 605 " --> pdb=" O ASN K 601 " (cutoff:3.500A) removed outlier: 4.090A pdb=" N ALA K 612 " --> pdb=" O ALA K 608 " (cutoff:3.500A) Processing helix chain 'K' and resid 631 through 651 removed outlier: 4.140A pdb=" N LYS K 635 " --> pdb=" O SER K 631 " (cutoff:3.500A) Processing helix chain 'K' and resid 652 through 656 removed outlier: 3.943A pdb=" N THR K 656 " --> pdb=" O GLN K 653 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 118 through 119 removed outlier: 3.548A pdb=" N ILE A 119 " --> pdb=" O ARG B 45 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 97 through 98 Processing sheet with id=AA3, first strand: chain 'C' and resid 42 through 43 removed outlier: 6.899A pdb=" N ARG C 42 " --> pdb=" O ILE D 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'C' and resid 101 through 102 removed outlier: 6.796A pdb=" N THR C 101 " --> pdb=" O TYR F 98 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'E' and resid 83 through 84 removed outlier: 7.074A pdb=" N ARG E 83 " --> pdb=" O VAL F 81 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'E' and resid 118 through 119 Processing sheet with id=AA7, first strand: chain 'G' and resid 42 through 43 removed outlier: 6.856A pdb=" N ARG G 42 " --> pdb=" O ILE H 86 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA7 Processing sheet with id=AA8, first strand: chain 'G' and resid 77 through 78 Processing sheet with id=AA9, first strand: chain 'K' and resid 273 through 275 removed outlier: 6.104A pdb=" N PHE K 274 " --> pdb=" O ILE K 300 " (cutoff:3.500A) removed outlier: 8.278A pdb=" N SER K 302 " --> pdb=" O PHE K 274 " (cutoff:3.500A) removed outlier: 6.647A pdb=" N PHE K 248 " --> pdb=" O VAL K 299 " (cutoff:3.500A) removed outlier: 7.355A pdb=" N ALA K 301 " --> pdb=" O PHE K 248 " (cutoff:3.500A) removed outlier: 5.879A pdb=" N VAL K 250 " --> pdb=" O ALA K 301 " (cutoff:3.500A) removed outlier: 5.780A pdb=" N ILE K 321 " --> pdb=" O LEU K 349 " (cutoff:3.500A) removed outlier: 7.333A pdb=" N ILE K 351 " --> pdb=" O ILE K 321 " (cutoff:3.500A) removed outlier: 6.250A pdb=" N ILE K 323 " --> pdb=" O ILE K 351 " (cutoff:3.500A) removed outlier: 7.038A pdb=" N ILE K 218 " --> pdb=" O LEU K 410 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'K' and resid 427 through 431 removed outlier: 6.254A pdb=" N LEU K 427 " --> pdb=" O ARG K 625 " (cutoff:3.500A) removed outlier: 7.292A pdb=" N VAL K 627 " --> pdb=" O LEU K 427 " (cutoff:3.500A) removed outlier: 5.672A pdb=" N LEU K 429 " --> pdb=" O VAL K 627 " (cutoff:3.500A) removed outlier: 3.518A pdb=" N LEU K 626 " --> pdb=" O LEU K 595 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N VAL K 521 " --> pdb=" O PHE K 574 " (cutoff:3.500A) 570 hydrogen bonds defined for protein. 1659 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 370 hydrogen bonds 740 hydrogen bond angles 0 basepair planarities 144 basepair parallelities 254 stacking parallelities Total time for adding SS restraints: 8.30 Time building geometry restraints manager: 5.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3027 1.33 - 1.45: 5220 1.45 - 1.57: 8342 1.57 - 1.69: 582 1.69 - 1.81: 43 Bond restraints: 17214 Sorted by residual: bond pdb=" CA ASP K 416 " pdb=" C ASP K 416 " ideal model delta sigma weight residual 1.523 1.454 0.069 1.34e-02 5.57e+03 2.63e+01 bond pdb=" CA SER K 415 " pdb=" C SER K 415 " ideal model delta sigma weight residual 1.523 1.455 0.069 1.34e-02 5.57e+03 2.62e+01 bond pdb=" N ASP K 416 " pdb=" CA ASP K 416 " ideal model delta sigma weight residual 1.457 1.402 0.055 1.29e-02 6.01e+03 1.84e+01 bond pdb=" N SER K 415 " pdb=" CA SER K 415 " ideal model delta sigma weight residual 1.457 1.405 0.053 1.29e-02 6.01e+03 1.66e+01 bond pdb=" CA ASP K 416 " pdb=" CB ASP K 416 " ideal model delta sigma weight residual 1.530 1.470 0.060 1.69e-02 3.50e+03 1.28e+01 ... (remaining 17209 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.32: 24169 2.32 - 4.65: 298 4.65 - 6.97: 33 6.97 - 9.30: 5 9.30 - 11.62: 2 Bond angle restraints: 24507 Sorted by residual: angle pdb=" N SER K 415 " pdb=" CA SER K 415 " pdb=" C SER K 415 " ideal model delta sigma weight residual 110.80 99.18 11.62 2.13e+00 2.20e-01 2.98e+01 angle pdb=" N ASP K 416 " pdb=" CA ASP K 416 " pdb=" C ASP K 416 " ideal model delta sigma weight residual 110.80 100.98 9.82 2.13e+00 2.20e-01 2.13e+01 angle pdb=" C PRO K 423 " pdb=" N LYS K 424 " pdb=" CA LYS K 424 " ideal model delta sigma weight residual 122.81 115.55 7.26 1.68e+00 3.54e-01 1.87e+01 angle pdb=" N GLU K 418 " pdb=" CA GLU K 418 " pdb=" C GLU K 418 " ideal model delta sigma weight residual 113.20 118.36 -5.16 1.21e+00 6.83e-01 1.82e+01 angle pdb=" C GLU C 91 " pdb=" N GLU C 92 " pdb=" CA GLU C 92 " ideal model delta sigma weight residual 121.54 128.19 -6.65 1.91e+00 2.74e-01 1.21e+01 ... (remaining 24502 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 35.11: 8162 35.11 - 70.23: 1427 70.23 - 105.34: 33 105.34 - 140.45: 9 140.45 - 175.56: 8 Dihedral angle restraints: 9639 sinusoidal: 5867 harmonic: 3772 Sorted by residual: dihedral pdb=" CA PRO K 489 " pdb=" C PRO K 489 " pdb=" N PRO K 490 " pdb=" CA PRO K 490 " ideal model delta harmonic sigma weight residual 180.00 138.66 41.34 0 5.00e+00 4.00e-02 6.83e+01 dihedral pdb=" CA VAL A 71 " pdb=" C VAL A 71 " pdb=" N ARG A 72 " pdb=" CA ARG A 72 " ideal model delta harmonic sigma weight residual 180.00 139.88 40.12 0 5.00e+00 4.00e-02 6.44e+01 dihedral pdb=" CA GLU C 92 " pdb=" C GLU C 92 " pdb=" N LEU C 93 " pdb=" CA LEU C 93 " ideal model delta harmonic sigma weight residual 180.00 155.76 24.24 0 5.00e+00 4.00e-02 2.35e+01 ... (remaining 9636 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.042: 2080 0.042 - 0.083: 550 0.083 - 0.125: 132 0.125 - 0.167: 16 0.167 - 0.209: 3 Chirality restraints: 2781 Sorted by residual: chirality pdb=" CB ILE K 323 " pdb=" CA ILE K 323 " pdb=" CG1 ILE K 323 " pdb=" CG2 ILE K 323 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.09e+00 chirality pdb=" CB ILE H 86 " pdb=" CA ILE H 86 " pdb=" CG1 ILE H 86 " pdb=" CG2 ILE H 86 " both_signs ideal model delta sigma weight residual False 2.64 2.47 0.17 2.00e-01 2.50e+01 7.61e-01 chirality pdb=" CB VAL K 417 " pdb=" CA VAL K 417 " pdb=" CG1 VAL K 417 " pdb=" CG2 VAL K 417 " both_signs ideal model delta sigma weight residual False -2.63 -2.46 -0.17 2.00e-01 2.50e+01 7.51e-01 ... (remaining 2778 not shown) Planarity restraints: 2100 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO K 489 " 0.073 5.00e-02 4.00e+02 1.12e-01 2.01e+01 pdb=" N PRO K 490 " -0.194 5.00e-02 4.00e+02 pdb=" CA PRO K 490 " 0.060 5.00e-02 4.00e+02 pdb=" CD PRO K 490 " 0.060 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY K 488 " 0.056 5.00e-02 4.00e+02 8.59e-02 1.18e+01 pdb=" N PRO K 489 " -0.149 5.00e-02 4.00e+02 pdb=" CA PRO K 489 " 0.046 5.00e-02 4.00e+02 pdb=" CD PRO K 489 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA LYS K 414 " 0.015 2.00e-02 2.50e+03 3.12e-02 9.71e+00 pdb=" C LYS K 414 " -0.054 2.00e-02 2.50e+03 pdb=" O LYS K 414 " 0.021 2.00e-02 2.50e+03 pdb=" N SER K 415 " 0.019 2.00e-02 2.50e+03 ... (remaining 2097 not shown) Histogram of nonbonded interaction distances: 2.17 - 2.72: 1017 2.72 - 3.26: 15625 3.26 - 3.81: 30691 3.81 - 4.35: 37233 4.35 - 4.90: 55144 Nonbonded interactions: 139710 Sorted by model distance: nonbonded pdb=" OD2 ASP A 106 " pdb=" NH2 ARG A 131 " model vdw 2.171 3.120 nonbonded pdb=" OH TYR E 99 " pdb=" OE1 GLU E 133 " model vdw 2.177 3.040 nonbonded pdb=" OD2 ASP D 65 " pdb=" OH TYR F 98 " model vdw 2.197 3.040 nonbonded pdb=" OD1 ASP K 494 " pdb=" ND1 HIS K 496 " model vdw 2.203 3.120 nonbonded pdb=" OE2 GLU K 638 " pdb=" NE2 GLN K 642 " model vdw 2.204 3.120 ... (remaining 139705 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 Found NCS groups: ncs_group { reference = (chain 'A' and resid 40 through 134) selection = chain 'E' } ncs_group { reference = (chain 'B' and ((resid 17 and (name N or name CA or name C or name O or name CB \ )) or resid 18 or (resid 19 through 20 and (name N or name CA or name C or name \ O or name CB )) or resid 21 through 22 or (resid 23 and (name N or name CA or na \ me C or name O or name CB )) or resid 24 through 101)) selection = (chain 'F' and resid 17 through 101) } ncs_group { reference = (chain 'C' and (resid 12 through 73 or (resid 74 and (name N or name CA or name \ C or name O or name CB )) or resid 75 through 118)) selection = (chain 'G' and ((resid 12 through 14 and (name N or name CA or name C or name O \ or name CB )) or resid 15 through 35 or (resid 36 and (name N or name CA or name \ C or name O or name CB )) or resid 37 through 118)) } ncs_group { reference = chain 'D' selection = (chain 'H' and (resid 29 through 30 or (resid 31 and (name N or name CA or name \ C or name O or name CB )) or resid 32 through 53 or (resid 54 through 55 and (na \ me N or name CA or name C or name O or name CB )) or resid 56 through 121)) } 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=1.00 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: 1.160 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.020 Extract box with map and model: 0.670 Check model and map are aligned: 0.120 Set scattering table: 0.170 Process input model: 44.620 Find NCS groups from input model: 0.520 Set up NCS constraints: 0.070 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:15.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 63.280 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8500 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 : 0.005 0.077 17214 Z= 0.256 Angle : 0.694 11.622 24507 Z= 0.405 Chirality : 0.040 0.209 2781 Planarity : 0.005 0.112 2100 Dihedral : 26.602 175.564 7195 Min Nonbonded Distance : 2.171 Molprobity Statistics. All-atom Clashscore : 12.23 Ramachandran Plot: Outliers : 0.08 % Allowed : 5.20 % Favored : 94.72 % Rotamer: Outliers : 0.54 % Allowed : 0.36 % Favored : 99.09 % Cbeta Deviations : 0.08 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: -0.14 (0.24), residues: 1269 helix: 1.17 (0.19), residues: 764 sheet: -2.65 (0.62), residues: 73 loop : -1.93 (0.27), residues: 432 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.037 0.002 TRP K 267 HIS 0.005 0.001 HIS K 402 PHE 0.019 0.002 PHE C 25 TYR 0.016 0.002 TYR K 441 ARG 0.006 0.001 ARG H 83 Details of bonding type rmsd hydrogen bonds : bond 0.09697 ( 940) hydrogen bonds : angle 4.21842 ( 2399) covalent geometry : bond 0.00540 (17214) covalent geometry : angle 0.69354 (24507) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 217 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 211 time to evaluate : 1.475 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 72 ASP cc_start: 0.8436 (t70) cc_final: 0.8206 (t0) REVERT: C 90 ASP cc_start: 0.8650 (t0) cc_final: 0.8393 (t0) REVERT: D 68 GLU cc_start: 0.7861 (tp30) cc_final: 0.7610 (tp30) REVERT: G 15 LYS cc_start: 0.8690 (tptm) cc_final: 0.8436 (tptm) REVERT: H 65 ASP cc_start: 0.8512 (t0) cc_final: 0.8295 (t0) REVERT: K 133 PHE cc_start: 0.9042 (m-80) cc_final: 0.8506 (m-80) outliers start: 6 outliers final: 3 residues processed: 217 average time/residue: 1.5647 time to fit residues: 369.5375 Evaluate side-chains 169 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 166 time to evaluate : 1.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain K residue 415 SER Chi-restraints excluded: chain K residue 416 ASP Chi-restraints excluded: chain K residue 417 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 128 optimal weight: 3.9990 chunk 115 optimal weight: 8.9990 chunk 63 optimal weight: 3.9990 chunk 39 optimal weight: 0.9990 chunk 77 optimal weight: 6.9990 chunk 61 optimal weight: 5.9990 chunk 119 optimal weight: 3.9990 chunk 46 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 88 optimal weight: 6.9990 chunk 138 optimal weight: 9.9990 overall best weight: 2.7988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 110 ASN D 60 ASN D 106 HIS E 76 GLN G 73 ASN G 104 GLN K 357 GLN Total number of N/Q/H flips: 8 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3674 r_free = 0.3674 target = 0.085766 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3159 r_free = 0.3159 target = 0.059994 restraints weight = 46366.611| |-----------------------------------------------------------------------------| r_work (start): 0.3067 rms_B_bonded: 2.21 r_work: 0.2894 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.2894 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8719 moved from start: 0.1035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 17214 Z= 0.248 Angle : 0.654 9.573 24507 Z= 0.369 Chirality : 0.040 0.156 2781 Planarity : 0.005 0.100 2100 Dihedral : 30.483 177.008 4615 Min Nonbonded Distance : 2.434 Molprobity Statistics. All-atom Clashscore : 8.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.36 % Favored : 94.64 % Rotamer: Outliers : 1.72 % Allowed : 12.34 % Favored : 85.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.16 (0.24), residues: 1269 helix: 1.35 (0.19), residues: 778 sheet: -2.32 (0.64), residues: 66 loop : -1.88 (0.28), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 267 HIS 0.023 0.002 HIS K 613 PHE 0.015 0.002 PHE C 25 TYR 0.016 0.002 TYR H 39 ARG 0.009 0.001 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.05022 ( 940) hydrogen bonds : angle 3.61394 ( 2399) covalent geometry : bond 0.00571 (17214) covalent geometry : angle 0.65357 (24507) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 199 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 180 time to evaluate : 1.453 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8848 (t0) cc_final: 0.8537 (t0) REVERT: F 68 ASP cc_start: 0.8631 (m-30) cc_final: 0.8047 (m-30) REVERT: F 92 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8292 (ttp80) REVERT: H 65 ASP cc_start: 0.9051 (t0) cc_final: 0.8810 (t0) REVERT: K 133 PHE cc_start: 0.9109 (m-80) cc_final: 0.8758 (m-80) REVERT: K 527 MET cc_start: 0.8841 (mtm) cc_final: 0.8518 (mtt) outliers start: 19 outliers final: 10 residues processed: 187 average time/residue: 1.8783 time to fit residues: 381.6721 Evaluate side-chains 171 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 161 time to evaluate : 1.172 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain G residue 62 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 538 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 35 optimal weight: 1.9990 chunk 82 optimal weight: 5.9990 chunk 127 optimal weight: 7.9990 chunk 118 optimal weight: 9.9990 chunk 65 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 84 optimal weight: 6.9990 chunk 10 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.9586 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 110 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.086259 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3176 r_free = 0.3176 target = 0.060663 restraints weight = 46285.999| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.17 r_work: 0.2915 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2915 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8699 moved from start: 0.1309 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 17214 Z= 0.197 Angle : 0.623 11.096 24507 Z= 0.353 Chirality : 0.038 0.158 2781 Planarity : 0.005 0.090 2100 Dihedral : 30.425 176.609 4611 Min Nonbonded Distance : 2.410 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.72 % Allowed : 14.16 % Favored : 83.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.44 (0.24), residues: 1269 helix: 1.57 (0.19), residues: 778 sheet: -1.96 (0.66), residues: 64 loop : -1.79 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP K 267 HIS 0.016 0.001 HIS K 613 PHE 0.011 0.001 PHE B 100 TYR 0.012 0.001 TYR K 191 ARG 0.007 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04459 ( 940) hydrogen bonds : angle 3.42337 ( 2399) covalent geometry : bond 0.00448 (17214) covalent geometry : angle 0.62326 (24507) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 202 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 172 time to evaluate : 1.696 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8902 (t0) cc_final: 0.8551 (t0) REVERT: D 102 GLU cc_start: 0.8078 (mm-30) cc_final: 0.7735 (tp30) REVERT: F 68 ASP cc_start: 0.8689 (m-30) cc_final: 0.7820 (m-30) REVERT: F 92 ARG cc_start: 0.8661 (ttp80) cc_final: 0.8175 (ttp80) REVERT: H 65 ASP cc_start: 0.9053 (t0) cc_final: 0.8769 (t0) REVERT: K 133 PHE cc_start: 0.9085 (m-80) cc_final: 0.8775 (m-80) REVERT: K 527 MET cc_start: 0.8799 (mtm) cc_final: 0.8484 (mtt) outliers start: 30 outliers final: 13 residues processed: 185 average time/residue: 1.7276 time to fit residues: 347.3538 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 164 time to evaluate : 1.549 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 139 optimal weight: 1.9990 chunk 92 optimal weight: 5.9990 chunk 25 optimal weight: 0.5980 chunk 118 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 chunk 143 optimal weight: 3.9990 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 4.9990 chunk 104 optimal weight: 0.5980 overall best weight: 1.0184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 93 GLN C 84 GLN C 104 GLN D 81 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3716 r_free = 0.3716 target = 0.087165 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3209 r_free = 0.3209 target = 0.061794 restraints weight = 45261.857| |-----------------------------------------------------------------------------| r_work (start): 0.3136 rms_B_bonded: 2.17 r_work: 0.2972 rms_B_bonded: 3.39 restraints_weight: 0.5000 r_work (final): 0.2972 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8656 moved from start: 0.1732 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17214 Z= 0.154 Angle : 0.596 10.160 24507 Z= 0.338 Chirality : 0.037 0.152 2781 Planarity : 0.004 0.075 2100 Dihedral : 30.197 175.700 4611 Min Nonbonded Distance : 2.469 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.41 % Favored : 95.59 % Rotamer: Outliers : 2.72 % Allowed : 15.52 % Favored : 81.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.77 (0.24), residues: 1269 helix: 1.82 (0.19), residues: 777 sheet: -1.63 (0.68), residues: 64 loop : -1.66 (0.29), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 267 HIS 0.012 0.001 HIS K 613 PHE 0.010 0.001 PHE A 67 TYR 0.016 0.001 TYR H 39 ARG 0.013 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.03864 ( 940) hydrogen bonds : angle 3.25761 ( 2399) covalent geometry : bond 0.00340 (17214) covalent geometry : angle 0.59627 (24507) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 221 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 191 time to evaluate : 1.516 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8941 (t0) cc_final: 0.8563 (t0) REVERT: D 102 GLU cc_start: 0.7852 (mm-30) cc_final: 0.7523 (tp30) REVERT: F 92 ARG cc_start: 0.8655 (ttp80) cc_final: 0.8282 (ttp80) REVERT: H 65 ASP cc_start: 0.8987 (t0) cc_final: 0.8729 (t0) REVERT: K 133 PHE cc_start: 0.9097 (m-80) cc_final: 0.8815 (m-80) REVERT: K 527 MET cc_start: 0.8806 (mtm) cc_final: 0.8489 (mtt) outliers start: 30 outliers final: 11 residues processed: 203 average time/residue: 1.7654 time to fit residues: 392.4322 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 70 ILE Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 38 optimal weight: 0.7980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 69 optimal weight: 0.7980 chunk 57 optimal weight: 0.9990 chunk 103 optimal weight: 6.9990 chunk 61 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 149 optimal weight: 10.0000 chunk 151 optimal weight: 6.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN G 73 ASN G 104 GLN H 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3709 r_free = 0.3709 target = 0.087346 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3195 r_free = 0.3195 target = 0.061413 restraints weight = 46574.524| |-----------------------------------------------------------------------------| r_work (start): 0.3111 rms_B_bonded: 2.22 r_work: 0.2942 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8682 moved from start: 0.1896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 17214 Z= 0.172 Angle : 0.611 10.593 24507 Z= 0.343 Chirality : 0.037 0.150 2781 Planarity : 0.004 0.063 2100 Dihedral : 30.212 176.502 4611 Min Nonbonded Distance : 2.484 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.72 % Allowed : 17.24 % Favored : 80.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % 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: 0.84 (0.25), residues: 1269 helix: 1.81 (0.19), residues: 786 sheet: -1.63 (0.62), residues: 79 loop : -1.54 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 267 HIS 0.010 0.001 HIS K 613 PHE 0.012 0.001 PHE H 67 TYR 0.010 0.001 TYR C 57 ARG 0.012 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04031 ( 940) hydrogen bonds : angle 3.21837 ( 2399) covalent geometry : bond 0.00387 (17214) covalent geometry : angle 0.61130 (24507) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 209 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 179 time to evaluate : 1.903 Fit side-chains REVERT: A 125 GLN cc_start: 0.9162 (OUTLIER) cc_final: 0.8946 (mp10) REVERT: C 90 ASP cc_start: 0.8948 (t0) cc_final: 0.8595 (t0) REVERT: D 102 GLU cc_start: 0.7856 (mm-30) cc_final: 0.7593 (tp30) REVERT: F 68 ASP cc_start: 0.8520 (m-30) cc_final: 0.7739 (m-30) REVERT: F 92 ARG cc_start: 0.8714 (ttp80) cc_final: 0.8423 (ttp80) REVERT: H 65 ASP cc_start: 0.8983 (t0) cc_final: 0.8742 (t0) REVERT: K 133 PHE cc_start: 0.8988 (m-80) cc_final: 0.8766 (m-80) REVERT: K 433 MET cc_start: 0.8066 (mmm) cc_final: 0.7736 (tpt) REVERT: K 499 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8461 (t80) REVERT: K 527 MET cc_start: 0.8837 (mtm) cc_final: 0.8515 (mtt) REVERT: K 638 GLU cc_start: 0.8791 (tm-30) cc_final: 0.8351 (tm-30) REVERT: K 642 GLN cc_start: 0.8938 (mt0) cc_final: 0.8462 (mt0) outliers start: 30 outliers final: 12 residues processed: 194 average time/residue: 2.0163 time to fit residues: 426.0824 Evaluate side-chains 184 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 170 time to evaluate : 2.169 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 499 TYR Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 119 optimal weight: 4.9990 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 6.9990 chunk 34 optimal weight: 0.3980 chunk 17 optimal weight: 4.9990 chunk 146 optimal weight: 2.9990 chunk 150 optimal weight: 2.9990 chunk 68 optimal weight: 0.0870 chunk 37 optimal weight: 0.9990 chunk 121 optimal weight: 5.9990 chunk 63 optimal weight: 4.9990 overall best weight: 1.2964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN G 73 ASN G 104 GLN H 60 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.087151 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3204 r_free = 0.3204 target = 0.061599 restraints weight = 45612.633| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.18 r_work: 0.2964 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8666 moved from start: 0.2031 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17214 Z= 0.163 Angle : 0.611 11.486 24507 Z= 0.341 Chirality : 0.037 0.163 2781 Planarity : 0.004 0.056 2100 Dihedral : 30.115 176.484 4611 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.54 % Allowed : 19.15 % Favored : 78.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 0.99 (0.24), residues: 1269 helix: 1.93 (0.19), residues: 782 sheet: -1.57 (0.61), residues: 79 loop : -1.46 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 267 HIS 0.008 0.001 HIS K 613 PHE 0.008 0.001 PHE B 61 TYR 0.014 0.001 TYR H 39 ARG 0.014 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.03928 ( 940) hydrogen bonds : angle 3.21790 ( 2399) covalent geometry : bond 0.00367 (17214) covalent geometry : angle 0.61081 (24507) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 201 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 28 poor density : 173 time to evaluate : 1.344 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8909 (t0) cc_final: 0.8555 (t0) REVERT: C 91 GLU cc_start: 0.8233 (tp30) cc_final: 0.7923 (tp30) REVERT: D 96 ARG cc_start: 0.8991 (ttp80) cc_final: 0.8742 (ttp-110) REVERT: F 68 ASP cc_start: 0.8542 (m-30) cc_final: 0.8098 (m-30) REVERT: F 92 ARG cc_start: 0.8685 (ttp80) cc_final: 0.8431 (ttp80) REVERT: H 65 ASP cc_start: 0.9001 (t0) cc_final: 0.8755 (t0) REVERT: K 133 PHE cc_start: 0.9049 (m-80) cc_final: 0.8758 (m-80) REVERT: K 134 ARG cc_start: 0.9219 (ttp80) cc_final: 0.8850 (mtp180) REVERT: K 436 MET cc_start: 0.7793 (tpp) cc_final: 0.7323 (tpt) REVERT: K 527 MET cc_start: 0.8894 (mtm) cc_final: 0.8619 (mtm) REVERT: K 638 GLU cc_start: 0.8836 (tm-30) cc_final: 0.8411 (tm-30) REVERT: K 642 GLN cc_start: 0.8957 (mt0) cc_final: 0.8372 (mt0) outliers start: 28 outliers final: 15 residues processed: 186 average time/residue: 1.6268 time to fit residues: 329.5028 Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 164 time to evaluate : 1.833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 18 optimal weight: 0.5980 chunk 117 optimal weight: 5.9990 chunk 34 optimal weight: 1.9990 chunk 151 optimal weight: 0.9990 chunk 42 optimal weight: 0.8980 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 8.9990 chunk 47 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 110 ASN G 73 ASN G 104 GLN H 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3714 r_free = 0.3714 target = 0.087117 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3199 r_free = 0.3199 target = 0.061511 restraints weight = 45561.466| |-----------------------------------------------------------------------------| r_work (start): 0.3126 rms_B_bonded: 2.19 r_work: 0.2960 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2960 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8668 moved from start: 0.2128 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.051 17214 Z= 0.172 Angle : 0.620 11.841 24507 Z= 0.346 Chirality : 0.037 0.184 2781 Planarity : 0.004 0.055 2100 Dihedral : 30.102 176.869 4611 Min Nonbonded Distance : 2.494 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.27 % Allowed : 20.05 % Favored : 77.68 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.04 (0.24), residues: 1269 helix: 1.94 (0.19), residues: 782 sheet: -1.40 (0.62), residues: 79 loop : -1.39 (0.30), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 267 HIS 0.008 0.001 HIS K 613 PHE 0.009 0.001 PHE B 61 TYR 0.010 0.001 TYR C 57 ARG 0.008 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04016 ( 940) hydrogen bonds : angle 3.22841 ( 2399) covalent geometry : bond 0.00391 (17214) covalent geometry : angle 0.62025 (24507) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 25 poor density : 175 time to evaluate : 1.488 Fit side-chains REVERT: B 53 GLU cc_start: 0.8250 (mm-30) cc_final: 0.7936 (mm-30) REVERT: C 90 ASP cc_start: 0.8915 (t0) cc_final: 0.8602 (t0) REVERT: C 91 GLU cc_start: 0.8281 (tp30) cc_final: 0.8012 (tp30) REVERT: F 92 ARG cc_start: 0.8694 (ttp80) cc_final: 0.8410 (ttp80) REVERT: H 65 ASP cc_start: 0.9028 (t0) cc_final: 0.8761 (t0) REVERT: K 133 PHE cc_start: 0.8959 (m-80) cc_final: 0.8649 (m-80) REVERT: K 134 ARG cc_start: 0.9209 (ttp80) cc_final: 0.8844 (mtp180) REVERT: K 433 MET cc_start: 0.7993 (mmm) cc_final: 0.7728 (tpt) REVERT: K 436 MET cc_start: 0.7877 (tpp) cc_final: 0.7442 (tpt) REVERT: K 527 MET cc_start: 0.8938 (mtm) cc_final: 0.8692 (mtm) REVERT: K 638 GLU cc_start: 0.8814 (tm-30) cc_final: 0.8451 (tm-30) REVERT: K 642 GLN cc_start: 0.8945 (mt0) cc_final: 0.8423 (mt0) outliers start: 25 outliers final: 16 residues processed: 187 average time/residue: 2.0584 time to fit residues: 418.1280 Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 164 time to evaluate : 1.590 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 48 ASP Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 36 optimal weight: 0.9990 chunk 84 optimal weight: 6.9990 chunk 144 optimal weight: 9.9990 chunk 148 optimal weight: 6.9990 chunk 14 optimal weight: 0.7980 chunk 113 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 131 optimal weight: 10.0000 chunk 46 optimal weight: 0.7980 chunk 140 optimal weight: 0.6980 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3743 r_free = 0.3743 target = 0.088574 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3242 r_free = 0.3242 target = 0.063198 restraints weight = 45385.516| |-----------------------------------------------------------------------------| r_work (start): 0.3167 rms_B_bonded: 2.22 r_work: 0.3003 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.3003 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8636 moved from start: 0.2383 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 17214 Z= 0.146 Angle : 0.623 12.803 24507 Z= 0.343 Chirality : 0.036 0.176 2781 Planarity : 0.004 0.053 2100 Dihedral : 29.930 176.473 4611 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 1.81 % Allowed : 21.14 % Favored : 77.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.15 (0.25), residues: 1269 helix: 2.01 (0.19), residues: 779 sheet: -1.40 (0.61), residues: 79 loop : -1.28 (0.30), residues: 411 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 PHE 0.013 0.001 PHE K 119 TYR 0.015 0.001 TYR H 39 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03714 ( 940) hydrogen bonds : angle 3.15415 ( 2399) covalent geometry : bond 0.00323 (17214) covalent geometry : angle 0.62263 (24507) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 200 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 180 time to evaluate : 1.523 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8100 (mm-30) cc_final: 0.7842 (mm-30) REVERT: C 90 ASP cc_start: 0.8937 (t0) cc_final: 0.8629 (t0) REVERT: F 68 ASP cc_start: 0.8459 (m-30) cc_final: 0.8253 (m-30) REVERT: G 41 GLU cc_start: 0.8680 (OUTLIER) cc_final: 0.8430 (tt0) REVERT: H 65 ASP cc_start: 0.8985 (t0) cc_final: 0.8733 (t0) REVERT: K 133 PHE cc_start: 0.8947 (m-80) cc_final: 0.8645 (m-80) REVERT: K 134 ARG cc_start: 0.9212 (ttp80) cc_final: 0.8944 (mtp180) REVERT: K 433 MET cc_start: 0.7764 (mmm) cc_final: 0.7446 (tpt) REVERT: K 436 MET cc_start: 0.8018 (tpp) cc_final: 0.7582 (tpt) REVERT: K 527 MET cc_start: 0.8922 (mtm) cc_final: 0.8622 (mtt) REVERT: K 648 GLN cc_start: 0.8886 (tp40) cc_final: 0.8553 (tp-100) outliers start: 20 outliers final: 11 residues processed: 191 average time/residue: 1.9062 time to fit residues: 403.1097 Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 167 time to evaluate : 1.899 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 41 GLU Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 7.9990 chunk 141 optimal weight: 0.3980 chunk 8 optimal weight: 0.9990 chunk 151 optimal weight: 1.9990 chunk 91 optimal weight: 5.9990 chunk 143 optimal weight: 0.0060 chunk 150 optimal weight: 3.9990 chunk 28 optimal weight: 3.9990 chunk 142 optimal weight: 5.9990 chunk 117 optimal weight: 6.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 110 ASN G 73 ASN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3749 r_free = 0.3749 target = 0.088847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3245 r_free = 0.3245 target = 0.063309 restraints weight = 45773.725| |-----------------------------------------------------------------------------| r_work (start): 0.3170 rms_B_bonded: 2.18 r_work: 0.3007 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.3007 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8630 moved from start: 0.2550 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 17214 Z= 0.151 Angle : 0.643 15.618 24507 Z= 0.351 Chirality : 0.036 0.177 2781 Planarity : 0.004 0.053 2100 Dihedral : 29.880 176.784 4611 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.72 % Allowed : 22.23 % Favored : 76.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.20 (0.25), residues: 1269 helix: 2.05 (0.19), residues: 778 sheet: -1.37 (0.61), residues: 79 loop : -1.24 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 PHE 0.008 0.001 PHE K 296 TYR 0.010 0.001 TYR B 51 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03724 ( 940) hydrogen bonds : angle 3.14706 ( 2399) covalent geometry : bond 0.00337 (17214) covalent geometry : angle 0.64283 (24507) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 194 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 175 time to evaluate : 2.021 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8099 (mm-30) cc_final: 0.7864 (mm-30) REVERT: C 90 ASP cc_start: 0.8936 (t0) cc_final: 0.8615 (t0) REVERT: C 91 GLU cc_start: 0.8331 (tp30) cc_final: 0.8073 (tp30) REVERT: G 115 LEU cc_start: 0.9445 (OUTLIER) cc_final: 0.9152 (mt) REVERT: H 65 ASP cc_start: 0.8995 (t0) cc_final: 0.8742 (t0) REVERT: K 133 PHE cc_start: 0.8864 (m-80) cc_final: 0.8591 (m-80) REVERT: K 134 ARG cc_start: 0.9211 (ttp80) cc_final: 0.8923 (mtp180) REVERT: K 433 MET cc_start: 0.7653 (mmm) cc_final: 0.7377 (tpt) REVERT: K 436 MET cc_start: 0.8031 (tpp) cc_final: 0.7588 (tpt) REVERT: K 527 MET cc_start: 0.8935 (mtm) cc_final: 0.8672 (mtt) REVERT: K 648 GLN cc_start: 0.8893 (tp40) cc_final: 0.8545 (tp-100) outliers start: 19 outliers final: 10 residues processed: 186 average time/residue: 1.5879 time to fit residues: 323.2312 Evaluate side-chains 178 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 167 time to evaluate : 1.609 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 115 optimal weight: 7.9990 chunk 67 optimal weight: 0.6980 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 49 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 114 optimal weight: 0.0170 chunk 100 optimal weight: 0.9990 chunk 126 optimal weight: 10.0000 chunk 147 optimal weight: 0.9980 overall best weight: 1.3422 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: G 73 ASN ** K 184 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3735 r_free = 0.3735 target = 0.088135 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3223 r_free = 0.3223 target = 0.062477 restraints weight = 45798.437| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.22 r_work: 0.2984 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8650 moved from start: 0.2539 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 17214 Z= 0.168 Angle : 0.661 14.272 24507 Z= 0.357 Chirality : 0.037 0.176 2781 Planarity : 0.004 0.052 2100 Dihedral : 29.922 177.217 4611 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.27 % Allowed : 22.87 % Favored : 75.86 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % 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: 1.18 (0.24), residues: 1269 helix: 2.02 (0.19), residues: 778 sheet: -1.28 (0.61), residues: 79 loop : -1.25 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 PHE 0.009 0.001 PHE B 61 TYR 0.015 0.001 TYR H 39 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03966 ( 940) hydrogen bonds : angle 3.20139 ( 2399) covalent geometry : bond 0.00382 (17214) covalent geometry : angle 0.66078 (24507) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2538 Ramachandran restraints generated. 1269 Oldfield, 0 Emsley, 1269 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 172 time to evaluate : 1.611 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8164 (mm-30) cc_final: 0.7908 (mm-30) REVERT: C 90 ASP cc_start: 0.8925 (t0) cc_final: 0.8639 (t0) REVERT: C 91 GLU cc_start: 0.8404 (tp30) cc_final: 0.8179 (tp30) REVERT: F 68 ASP cc_start: 0.8441 (m-30) cc_final: 0.8159 (m-30) REVERT: F 92 ARG cc_start: 0.8588 (ttp80) cc_final: 0.8353 (ttp80) REVERT: G 115 LEU cc_start: 0.9466 (OUTLIER) cc_final: 0.9177 (mt) REVERT: H 65 ASP cc_start: 0.9052 (t0) cc_final: 0.8788 (t0) REVERT: K 133 PHE cc_start: 0.8930 (m-80) cc_final: 0.8631 (m-80) REVERT: K 134 ARG cc_start: 0.9295 (ttp80) cc_final: 0.8971 (mtp180) REVERT: K 433 MET cc_start: 0.7672 (mmm) cc_final: 0.7393 (tpt) REVERT: K 436 MET cc_start: 0.8081 (tpp) cc_final: 0.7623 (tpt) REVERT: K 527 MET cc_start: 0.8952 (mtm) cc_final: 0.8619 (mtt) REVERT: K 648 GLN cc_start: 0.8893 (tp40) cc_final: 0.8536 (tp-100) outliers start: 14 outliers final: 12 residues processed: 182 average time/residue: 2.1872 time to fit residues: 432.5781 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 163 time to evaluate : 1.384 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 18 HIS Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 49 LEU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 65 ASP Chi-restraints excluded: chain E residue 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain K residue 320 TYR Chi-restraints excluded: chain K residue 404 VAL Chi-restraints excluded: chain K residue 538 CYS Chi-restraints excluded: chain K residue 546 CYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 55 optimal weight: 6.9990 chunk 87 optimal weight: 8.9990 chunk 54 optimal weight: 4.9990 chunk 68 optimal weight: 0.9980 chunk 72 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 5.9990 chunk 141 optimal weight: 1.9990 chunk 29 optimal weight: 0.9990 chunk 61 optimal weight: 4.9990 chunk 20 optimal weight: 0.8980 overall best weight: 1.3786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 110 ASN G 73 ASN ** K 184 GLN ** 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 = 0.3734 r_free = 0.3734 target = 0.088088 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3227 r_free = 0.3227 target = 0.062687 restraints weight = 45537.990| |-----------------------------------------------------------------------------| r_work (start): 0.3149 rms_B_bonded: 2.18 r_work: 0.2985 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2985 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8649 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.047 17214 Z= 0.170 Angle : 0.665 14.052 24507 Z= 0.358 Chirality : 0.037 0.163 2781 Planarity : 0.004 0.052 2100 Dihedral : 29.920 177.315 4611 Min Nonbonded Distance : 2.465 Molprobity Statistics. All-atom Clashscore : 9.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.54 % Allowed : 22.50 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 1.16 (0.24), residues: 1269 helix: 1.98 (0.19), residues: 778 sheet: -1.18 (0.61), residues: 81 loop : -1.23 (0.30), residues: 410 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 PHE 0.009 0.001 PHE B 61 TYR 0.010 0.001 TYR F 88 ARG 0.007 0.000 ARG G 99 Details of bonding type rmsd hydrogen bonds : bond 0.03974 ( 940) hydrogen bonds : angle 3.24581 ( 2399) covalent geometry : bond 0.00388 (17214) covalent geometry : angle 0.66459 (24507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 12033.40 seconds wall clock time: 214 minutes 23.79 seconds (12863.79 seconds total)