Starting phenix.real_space_refine on Sat May 17 18:41:07 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnz_61632/05_2025/9jnz_61632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnz_61632/05_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_61632/05_2025/9jnz_61632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnz_61632/05_2025/9jnz_61632.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnz_61632/05_2025/9jnz_61632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnz_61632/05_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-5687/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: 9.00, per 1000 atoms: 0.55 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: 3.85 Conformation dependent library (CDL) restraints added in 1.3 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: 7.21 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: 7.66 Time building geometry restraints manager: 4.58 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: 1.050 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 0.580 Check model and map are aligned: 0.120 Set scattering table: 0.140 Process input model: 42.340 Find NCS groups from input model: 0.450 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.110 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 55.870 ------------------------------------------------------------------------------- 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 : 1.332 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: 1.5015 time to fit residues: 354.7581 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 : 1.414 ------------------------------------------------------------------------------- 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): 0.3069 rms_B_bonded: 2.21 r_work: 0.2895 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2895 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8723 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 : 1.312 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8845 (t0) cc_final: 0.8541 (t0) REVERT: F 68 ASP cc_start: 0.8618 (m-30) cc_final: 0.8034 (m-30) REVERT: F 92 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8288 (ttp80) REVERT: H 65 ASP cc_start: 0.9041 (t0) cc_final: 0.8804 (t0) REVERT: K 133 PHE cc_start: 0.9106 (m-80) cc_final: 0.8753 (m-80) REVERT: K 527 MET cc_start: 0.8842 (mtm) cc_final: 0.8519 (mtt) outliers start: 19 outliers final: 10 residues processed: 187 average time/residue: 1.4924 time to fit residues: 304.1533 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 : 1.443 ------------------------------------------------------------------------------- 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: 5.9990 chunk 118 optimal weight: 10.0000 chunk 65 optimal weight: 4.9990 chunk 149 optimal weight: 2.9990 chunk 18 optimal weight: 4.9990 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 = 0.086290 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3178 r_free = 0.3178 target = 0.060693 restraints weight = 46288.493| |-----------------------------------------------------------------------------| r_work (start): 0.3086 rms_B_bonded: 2.18 r_work: 0.2916 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8700 moved from start: 0.1324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 17214 Z= 0.196 Angle : 0.624 11.173 24507 Z= 0.353 Chirality : 0.038 0.164 2781 Planarity : 0.005 0.089 2100 Dihedral : 30.421 176.586 4611 Min Nonbonded Distance : 2.440 Molprobity Statistics. All-atom Clashscore : 8.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.90 % Allowed : 13.79 % Favored : 83.30 % 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: 0.46 (0.24), residues: 1269 helix: 1.57 (0.19), residues: 781 sheet: -1.97 (0.66), residues: 64 loop : -1.77 (0.28), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP K 267 HIS 0.016 0.001 HIS K 613 PHE 0.009 0.001 PHE C 25 TYR 0.013 0.001 TYR K 199 ARG 0.010 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04439 ( 940) hydrogen bonds : angle 3.42520 ( 2399) covalent geometry : bond 0.00447 (17214) covalent geometry : angle 0.62382 (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 207 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 175 time to evaluate : 1.318 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8897 (t0) cc_final: 0.8534 (t0) REVERT: D 102 GLU cc_start: 0.8069 (mm-30) cc_final: 0.7730 (tp30) REVERT: F 68 ASP cc_start: 0.8683 (m-30) cc_final: 0.7816 (m-30) REVERT: F 92 ARG cc_start: 0.8662 (ttp80) cc_final: 0.8179 (ttp80) REVERT: H 65 ASP cc_start: 0.9053 (t0) cc_final: 0.8768 (t0) REVERT: K 133 PHE cc_start: 0.9106 (m-80) cc_final: 0.8793 (m-80) REVERT: K 527 MET cc_start: 0.8795 (mtm) cc_final: 0.8435 (mtt) outliers start: 32 outliers final: 13 residues processed: 188 average time/residue: 1.5022 time to fit residues: 307.9001 Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 166 time to evaluate : 1.374 ------------------------------------------------------------------------------- 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: 5.9990 chunk 92 optimal weight: 5.9990 chunk 25 optimal weight: 0.0030 chunk 118 optimal weight: 10.0000 chunk 14 optimal weight: 0.9980 chunk 3 optimal weight: 1.9990 chunk 15 optimal weight: 0.5980 chunk 143 optimal weight: 0.8980 chunk 43 optimal weight: 0.8980 chunk 47 optimal weight: 0.0980 chunk 104 optimal weight: 1.9990 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN C 104 GLN D 81 ASN G 73 ASN G 104 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.088421 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063322 restraints weight = 45419.962| |-----------------------------------------------------------------------------| r_work (start): 0.3174 rms_B_bonded: 2.16 r_work: 0.3011 rms_B_bonded: 3.40 restraints_weight: 0.5000 r_work (final): 0.3011 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8626 moved from start: 0.1932 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= 0.141 Angle : 0.591 10.425 24507 Z= 0.335 Chirality : 0.036 0.151 2781 Planarity : 0.004 0.073 2100 Dihedral : 30.060 174.965 4611 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.09 % Allowed : 16.24 % Favored : 81.67 % 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: 0.90 (0.25), residues: 1269 helix: 1.91 (0.19), residues: 774 sheet: -1.61 (0.68), residues: 64 loop : -1.56 (0.29), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.001 TRP K 267 HIS 0.011 0.001 HIS K 613 PHE 0.008 0.001 PHE E 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 0.03671 ( 940) hydrogen bonds : angle 3.19832 ( 2399) covalent geometry : bond 0.00306 (17214) covalent geometry : angle 0.59126 (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 216 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 193 time to evaluate : 1.355 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8929 (t0) cc_final: 0.8604 (t0) REVERT: D 102 GLU cc_start: 0.7698 (mm-30) cc_final: 0.7456 (tp30) REVERT: F 68 ASP cc_start: 0.8536 (m-30) cc_final: 0.7965 (m-30) REVERT: F 92 ARG cc_start: 0.8635 (ttp80) cc_final: 0.8261 (ttp80) REVERT: H 60 ASN cc_start: 0.8990 (t0) cc_final: 0.8778 (t0) REVERT: K 133 PHE cc_start: 0.9010 (m-80) cc_final: 0.8726 (m-80) REVERT: K 134 ARG cc_start: 0.9185 (ttp80) cc_final: 0.8813 (mtp180) REVERT: K 433 MET cc_start: 0.7782 (mmm) cc_final: 0.7509 (tpt) REVERT: K 527 MET cc_start: 0.8828 (mtm) cc_final: 0.8528 (mtt) outliers start: 23 outliers final: 10 residues processed: 203 average time/residue: 1.5232 time to fit residues: 338.9828 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 166 time to evaluate : 1.337 ------------------------------------------------------------------------------- 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 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: 0.4980 chunk 66 optimal weight: 3.9990 chunk 53 optimal weight: 7.9990 chunk 19 optimal weight: 7.9990 chunk 69 optimal weight: 3.9990 chunk 57 optimal weight: 0.7980 chunk 103 optimal weight: 2.9990 chunk 61 optimal weight: 5.9990 chunk 10 optimal weight: 1.9990 chunk 149 optimal weight: 5.9990 chunk 151 optimal weight: 6.9990 overall best weight: 2.0586 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3695 r_free = 0.3695 target = 0.086173 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.060193 restraints weight = 46039.585| |-----------------------------------------------------------------------------| r_work (start): 0.3096 rms_B_bonded: 2.23 r_work: 0.2926 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2926 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8694 moved from start: 0.1880 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.070 17214 Z= 0.202 Angle : 0.621 10.294 24507 Z= 0.348 Chirality : 0.038 0.154 2781 Planarity : 0.004 0.060 2100 Dihedral : 30.287 177.031 4611 Min Nonbonded Distance : 2.483 Molprobity Statistics. All-atom Clashscore : 8.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 3.18 % Allowed : 17.79 % Favored : 79.04 % 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: 0.85 (0.25), residues: 1269 helix: 1.81 (0.19), residues: 787 sheet: -1.58 (0.61), residues: 81 loop : -1.54 (0.31), residues: 401 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP K 267 HIS 0.010 0.001 HIS K 613 PHE 0.011 0.001 PHE H 67 TYR 0.010 0.001 TYR C 57 ARG 0.008 0.001 ARG K 266 Details of bonding type rmsd hydrogen bonds : bond 0.04397 ( 940) hydrogen bonds : angle 3.28490 ( 2399) covalent geometry : bond 0.00463 (17214) covalent geometry : angle 0.62066 (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 207 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 172 time to evaluate : 1.421 Fit side-chains REVERT: C 90 ASP cc_start: 0.8921 (t0) cc_final: 0.8591 (t0) REVERT: D 102 GLU cc_start: 0.8013 (mm-30) cc_final: 0.7693 (tp30) REVERT: F 92 ARG cc_start: 0.8666 (ttp80) cc_final: 0.8235 (ttp80) REVERT: K 133 PHE cc_start: 0.9040 (m-80) cc_final: 0.8771 (m-80) REVERT: K 499 TYR cc_start: 0.8656 (OUTLIER) cc_final: 0.8450 (t80) REVERT: K 527 MET cc_start: 0.8857 (mtm) cc_final: 0.8526 (mtt) REVERT: K 638 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8368 (tm-30) REVERT: K 642 GLN cc_start: 0.8984 (mt0) cc_final: 0.8530 (mt0) outliers start: 35 outliers final: 13 residues processed: 192 average time/residue: 1.4680 time to fit residues: 308.1758 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 162 time to evaluate : 1.452 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 F residue 30 THR 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 523 ILE 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: 0.0570 chunk 33 optimal weight: 1.9990 chunk 76 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 17 optimal weight: 7.9990 chunk 146 optimal weight: 3.9990 chunk 150 optimal weight: 6.9990 chunk 68 optimal weight: 7.9990 chunk 37 optimal weight: 1.9990 chunk 121 optimal weight: 0.7980 chunk 63 optimal weight: 3.9990 overall best weight: 1.7704 ------------------------------------------------------------------------------- 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 = 0.3704 r_free = 0.3704 target = 0.086575 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3181 r_free = 0.3181 target = 0.060792 restraints weight = 45728.448| |-----------------------------------------------------------------------------| r_work (start): 0.3108 rms_B_bonded: 2.17 r_work: 0.2941 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2941 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.056 17214 Z= 0.185 Angle : 0.617 11.340 24507 Z= 0.345 Chirality : 0.037 0.168 2781 Planarity : 0.004 0.056 2100 Dihedral : 30.192 176.932 4611 Min Nonbonded Distance : 2.490 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.81 % Allowed : 19.69 % Favored : 77.50 % 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: 0.87 (0.24), residues: 1269 helix: 1.81 (0.19), residues: 786 sheet: -1.53 (0.62), residues: 79 loop : -1.50 (0.30), residues: 404 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP K 267 HIS 0.009 0.001 HIS K 613 PHE 0.009 0.001 PHE B 61 TYR 0.015 0.001 TYR H 39 ARG 0.012 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04125 ( 940) hydrogen bonds : angle 3.27610 ( 2399) covalent geometry : bond 0.00419 (17214) covalent geometry : angle 0.61699 (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 208 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 177 time to evaluate : 1.542 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8905 (t0) cc_final: 0.8553 (t0) REVERT: C 91 GLU cc_start: 0.8269 (tp30) cc_final: 0.7958 (tp30) REVERT: F 68 ASP cc_start: 0.8566 (m-30) cc_final: 0.7712 (m-30) REVERT: F 92 ARG cc_start: 0.8688 (ttp80) cc_final: 0.8383 (ttp80) REVERT: K 527 MET cc_start: 0.8878 (mtm) cc_final: 0.8587 (mtm) REVERT: K 638 GLU cc_start: 0.8811 (tm-30) cc_final: 0.8405 (tm-30) REVERT: K 642 GLN cc_start: 0.8992 (mt0) cc_final: 0.8570 (mt0) outliers start: 31 outliers final: 14 residues processed: 192 average time/residue: 1.5542 time to fit residues: 325.6187 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.400 ------------------------------------------------------------------------------- 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 57 SER 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: 0.9980 chunk 117 optimal weight: 5.9990 chunk 34 optimal weight: 4.9990 chunk 151 optimal weight: 1.9990 chunk 42 optimal weight: 2.9990 chunk 72 optimal weight: 8.9990 chunk 30 optimal weight: 3.9990 chunk 123 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 95 optimal weight: 6.9990 overall best weight: 1.9988 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3697 r_free = 0.3697 target = 0.086248 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060571 restraints weight = 45518.642| |-----------------------------------------------------------------------------| r_work (start): 0.3101 rms_B_bonded: 2.16 r_work: 0.2934 rms_B_bonded: 3.41 restraints_weight: 0.5000 r_work (final): 0.2934 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8688 moved from start: 0.2081 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.063 17214 Z= 0.199 Angle : 0.647 15.433 24507 Z= 0.357 Chirality : 0.038 0.192 2781 Planarity : 0.004 0.054 2100 Dihedral : 30.222 177.323 4611 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 2.36 % Allowed : 20.78 % Favored : 76.86 % 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: 0.90 (0.25), residues: 1269 helix: 1.83 (0.19), residues: 785 sheet: -1.37 (0.64), residues: 79 loop : -1.48 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.002 TRP K 267 HIS 0.008 0.001 HIS K 613 PHE 0.009 0.001 PHE B 61 TYR 0.009 0.001 TYR C 57 ARG 0.015 0.001 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04280 ( 940) hydrogen bonds : angle 3.32531 ( 2399) covalent geometry : bond 0.00457 (17214) covalent geometry : angle 0.64687 (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 193 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 2.092 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8351 (mm-30) cc_final: 0.8110 (mm-30) REVERT: C 90 ASP cc_start: 0.8917 (t0) cc_final: 0.8602 (t0) REVERT: C 91 GLU cc_start: 0.8316 (tp30) cc_final: 0.8039 (tp30) REVERT: F 92 ARG cc_start: 0.8686 (ttp80) cc_final: 0.8333 (ttp80) REVERT: G 13 LYS cc_start: 0.8954 (tppp) cc_final: 0.8661 (tmtt) REVERT: K 134 ARG cc_start: 0.9277 (ttp80) cc_final: 0.8957 (mtp180) REVERT: K 433 MET cc_start: 0.8102 (mmm) cc_final: 0.7869 (tpt) REVERT: K 527 MET cc_start: 0.8899 (mtm) cc_final: 0.8623 (mtt) outliers start: 26 outliers final: 17 residues processed: 183 average time/residue: 1.5964 time to fit residues: 317.5060 Evaluate side-chains 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 155 time to evaluate : 1.333 ------------------------------------------------------------------------------- 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 53 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 223 MET Chi-restraints excluded: chain K residue 287 ILE Chi-restraints excluded: chain K residue 320 TYR 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: 0.7980 chunk 84 optimal weight: 6.9990 chunk 144 optimal weight: 7.9990 chunk 148 optimal weight: 10.0000 chunk 14 optimal weight: 0.9990 chunk 113 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 99 optimal weight: 6.9990 chunk 131 optimal weight: 7.9990 chunk 46 optimal weight: 0.5980 chunk 140 optimal weight: 1.9990 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 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 = 0.3730 r_free = 0.3730 target = 0.087855 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3222 r_free = 0.3222 target = 0.062490 restraints weight = 45333.901| |-----------------------------------------------------------------------------| r_work (start): 0.3148 rms_B_bonded: 2.18 r_work: 0.2984 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2984 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8648 moved from start: 0.2342 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17214 Z= 0.157 Angle : 0.638 13.457 24507 Z= 0.350 Chirality : 0.037 0.181 2781 Planarity : 0.004 0.053 2100 Dihedral : 30.014 176.687 4611 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 8.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.09 % Allowed : 21.69 % Favored : 76.23 % 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: 1.07 (0.25), residues: 1269 helix: 1.96 (0.19), residues: 778 sheet: -1.35 (0.64), residues: 79 loop : -1.34 (0.31), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 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 0.011 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.03838 ( 940) hydrogen bonds : angle 3.22643 ( 2399) covalent geometry : bond 0.00354 (17214) covalent geometry : angle 0.63795 (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 192 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 169 time to evaluate : 1.267 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8931 (t0) cc_final: 0.8628 (t0) REVERT: F 68 ASP cc_start: 0.8462 (m-30) cc_final: 0.7709 (m-30) REVERT: F 92 ARG cc_start: 0.8697 (ttp80) cc_final: 0.8388 (ttp80) REVERT: G 13 LYS cc_start: 0.9019 (tppp) cc_final: 0.8749 (tptp) REVERT: G 115 LEU cc_start: 0.9497 (OUTLIER) cc_final: 0.9230 (mt) REVERT: H 60 ASN cc_start: 0.8980 (t0) cc_final: 0.8780 (t0) REVERT: K 433 MET cc_start: 0.7880 (mmm) cc_final: 0.7637 (tpt) REVERT: K 527 MET cc_start: 0.8936 (mtm) cc_final: 0.8635 (mtt) outliers start: 23 outliers final: 13 residues processed: 182 average time/residue: 1.5528 time to fit residues: 309.3482 Evaluate side-chains 174 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 160 time to evaluate : 1.553 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 82 LEU 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 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 H residue 57 SER Chi-restraints excluded: chain H residue 98 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 132 optimal weight: 6.9990 chunk 141 optimal weight: 2.9990 chunk 8 optimal weight: 0.7980 chunk 151 optimal weight: 5.9990 chunk 91 optimal weight: 4.9990 chunk 143 optimal weight: 3.9990 chunk 150 optimal weight: 5.9990 chunk 28 optimal weight: 0.9990 chunk 142 optimal weight: 5.9990 chunk 117 optimal weight: 7.9990 chunk 67 optimal weight: 0.8980 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 84 GLN C 110 ASN G 73 ASN G 104 GLN ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3705 r_free = 0.3705 target = 0.086536 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3182 r_free = 0.3182 target = 0.060732 restraints weight = 45574.488| |-----------------------------------------------------------------------------| r_work (start): 0.3109 rms_B_bonded: 2.20 r_work: 0.2942 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2942 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8684 moved from start: 0.2298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.057 17214 Z= 0.198 Angle : 0.659 12.749 24507 Z= 0.361 Chirality : 0.038 0.174 2781 Planarity : 0.004 0.054 2100 Dihedral : 30.149 177.663 4611 Min Nonbonded Distance : 2.444 Molprobity Statistics. All-atom Clashscore : 9.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 2.36 % Allowed : 21.87 % Favored : 75.77 % 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 (0.25), residues: 1269 helix: 1.91 (0.19), residues: 782 sheet: -1.29 (0.62), residues: 81 loop : -1.35 (0.31), residues: 406 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 0.015 0.001 PHE K 119 TYR 0.009 0.001 TYR F 51 ARG 0.020 0.001 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04262 ( 940) hydrogen bonds : angle 3.30421 ( 2399) covalent geometry : bond 0.00454 (17214) covalent geometry : angle 0.65883 (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 193 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 167 time to evaluate : 1.308 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8951 (t0) cc_final: 0.8647 (t0) REVERT: C 91 GLU cc_start: 0.8390 (tp30) cc_final: 0.8149 (tp30) REVERT: F 68 ASP cc_start: 0.8540 (m-30) cc_final: 0.8180 (m-30) REVERT: F 92 ARG cc_start: 0.8705 (ttp80) cc_final: 0.8468 (ttp80) REVERT: G 115 LEU cc_start: 0.9528 (OUTLIER) cc_final: 0.9257 (mt) REVERT: K 433 MET cc_start: 0.8011 (mmm) cc_final: 0.7771 (tpt) REVERT: K 436 MET cc_start: 0.8155 (tpp) cc_final: 0.7797 (tpt) outliers start: 26 outliers final: 19 residues processed: 183 average time/residue: 1.5491 time to fit residues: 308.2374 Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 162 time to evaluate : 1.313 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU 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 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 104 GLN Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 98 LEU Chi-restraints excluded: chain K residue 223 MET 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 115 optimal weight: 5.9990 chunk 67 optimal weight: 0.9980 chunk 54 optimal weight: 4.9990 chunk 99 optimal weight: 6.9990 chunk 72 optimal weight: 8.9990 chunk 49 optimal weight: 2.9990 chunk 15 optimal weight: 0.9990 chunk 114 optimal weight: 0.9990 chunk 100 optimal weight: 2.9990 chunk 126 optimal weight: 9.9990 chunk 147 optimal weight: 0.7980 overall best weight: 1.3586 ------------------------------------------------------------------------------- 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 = 0.3719 r_free = 0.3719 target = 0.087243 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3202 r_free = 0.3202 target = 0.061636 restraints weight = 45768.830| |-----------------------------------------------------------------------------| r_work (start): 0.3130 rms_B_bonded: 2.19 r_work: 0.2965 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2965 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8665 moved from start: 0.2393 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 17214 Z= 0.171 Angle : 0.662 12.633 24507 Z= 0.361 Chirality : 0.037 0.177 2781 Planarity : 0.004 0.060 2100 Dihedral : 30.045 177.317 4611 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 9.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.73 % Favored : 95.27 % Rotamer: Outliers : 1.63 % Allowed : 23.23 % Favored : 75.14 % 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: 1.02 (0.25), residues: 1269 helix: 1.90 (0.19), residues: 782 sheet: -1.40 (0.63), residues: 79 loop : -1.34 (0.31), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 PHE 0.009 0.001 PHE A 67 TYR 0.016 0.001 TYR H 39 ARG 0.021 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.04006 ( 940) hydrogen bonds : angle 3.27882 ( 2399) covalent geometry : bond 0.00389 (17214) covalent geometry : angle 0.66242 (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 185 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 167 time to evaluate : 1.276 Fit side-chains REVERT: C 90 ASP cc_start: 0.8943 (t0) cc_final: 0.8659 (t0) REVERT: C 91 GLU cc_start: 0.8379 (tp30) cc_final: 0.8155 (tp30) REVERT: F 68 ASP cc_start: 0.8547 (m-30) cc_final: 0.7789 (m-30) REVERT: F 92 ARG cc_start: 0.8734 (ttp80) cc_final: 0.8468 (ttp80) REVERT: G 115 LEU cc_start: 0.9511 (OUTLIER) cc_final: 0.9236 (mt) REVERT: K 265 ASN cc_start: 0.8925 (m-40) cc_final: 0.8685 (p0) REVERT: K 648 GLN cc_start: 0.8912 (tp40) cc_final: 0.8569 (tp-100) outliers start: 18 outliers final: 16 residues processed: 178 average time/residue: 1.6178 time to fit residues: 313.7374 Evaluate side-chains 182 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 165 time to evaluate : 1.343 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain B residue 84 MET Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE 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 113 SER Chi-restraints excluded: chain G residue 115 LEU Chi-restraints excluded: chain H residue 53 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain H residue 98 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: 3.9990 chunk 68 optimal weight: 0.0980 chunk 72 optimal weight: 8.9990 chunk 43 optimal weight: 1.9990 chunk 122 optimal weight: 0.8980 chunk 141 optimal weight: 3.9990 chunk 29 optimal weight: 0.9980 chunk 61 optimal weight: 0.9990 chunk 20 optimal weight: 0.3980 overall best weight: 0.6782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 125 GLN C 84 GLN C 110 ASN G 73 ASN H 60 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3752 r_free = 0.3752 target = 0.089042 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3255 r_free = 0.3255 target = 0.063786 restraints weight = 45612.122| |-----------------------------------------------------------------------------| r_work (start): 0.3182 rms_B_bonded: 2.18 r_work: 0.3021 rms_B_bonded: 3.45 restraints_weight: 0.5000 r_work (final): 0.3021 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8618 moved from start: 0.2714 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 17214 Z= 0.149 Angle : 0.649 12.448 24507 Z= 0.353 Chirality : 0.037 0.162 2781 Planarity : 0.004 0.051 2100 Dihedral : 29.821 176.879 4611 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.45 % Allowed : 23.14 % Favored : 75.41 % 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: 1.13 (0.25), residues: 1269 helix: 1.98 (0.19), residues: 782 sheet: -1.23 (0.64), residues: 77 loop : -1.31 (0.31), residues: 410 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 0.011 0.001 PHE K 133 TYR 0.011 0.001 TYR F 88 ARG 0.007 0.000 ARG K 134 Details of bonding type rmsd hydrogen bonds : bond 0.03715 ( 940) hydrogen bonds : angle 3.16376 ( 2399) covalent geometry : bond 0.00331 (17214) covalent geometry : angle 0.64881 (24507) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 9883.21 seconds wall clock time: 171 minutes 8.97 seconds (10268.97 seconds total)