Starting phenix.real_space_refine on Thu Sep 18 10:20:12 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9jnz_61632/09_2025/9jnz_61632.cif Found real_map, /net/cci-nas-00/data/ceres_data/9jnz_61632/09_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_61632/09_2025/9jnz_61632.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9jnz_61632/09_2025/9jnz_61632.map" model { file = "/net/cci-nas-00/data/ceres_data/9jnz_61632/09_2025/9jnz_61632.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9jnz_61632/09_2025/9jnz_61632.cif" } resolution = 3.0 write_initial_geo_file = False refinement { macro_cycles = 10 } 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/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: 3.87, per 1000 atoms: 0.24 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: 1.45 Conformation dependent library (CDL) restraints added in 525.7 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 2.46 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: 4.34 Time building geometry restraints manager: 1.83 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: 1.310 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: 0.010 Extract box with map and model: 0.250 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 18.570 Find NCS groups from input model: 0.130 Set up NCS constraints: 0.030 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:8.050 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.420 ------------------------------------------------------------------------------- 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 : 12.20 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. 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 ARG 0.006 0.001 ARG H 83 TYR 0.016 0.002 TYR K 441 PHE 0.019 0.002 PHE C 25 TRP 0.037 0.002 TRP K 267 HIS 0.005 0.001 HIS K 402 Details of bonding type rmsd covalent geometry : bond 0.00540 (17214) covalent geometry : angle 0.69354 (24507) hydrogen bonds : bond 0.09697 ( 940) hydrogen bonds : angle 4.21842 ( 2399) *********************** 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 : 0.565 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: 0.7625 time to fit residues: 179.4825 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 : 0.504 ------------------------------------------------------------------------------- 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 98 optimal weight: 4.9990 chunk 107 optimal weight: 0.9980 chunk 10 optimal weight: 0.9990 chunk 66 optimal weight: 0.8980 chunk 130 optimal weight: 8.9990 chunk 124 optimal weight: 5.9990 chunk 103 optimal weight: 8.9990 chunk 77 optimal weight: 6.9990 chunk 122 optimal weight: 0.9990 chunk 91 optimal weight: 4.9990 chunk 149 optimal weight: 10.0000 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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 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: 9 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3694 r_free = 0.3694 target = 0.086158 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 56)----------------| | r_work = 0.3173 r_free = 0.3173 target = 0.060336 restraints weight = 45271.996| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.19 r_work: 0.2929 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2929 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.1061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.067 17214 Z= 0.192 Angle : 0.631 9.991 24507 Z= 0.356 Chirality : 0.038 0.148 2781 Planarity : 0.005 0.098 2100 Dihedral : 30.300 175.963 4615 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 9.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.89 % Favored : 95.11 % Rotamer: Outliers : 1.63 % Allowed : 11.62 % Favored : 86.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.28 (0.24), residues: 1269 helix: 1.46 (0.19), residues: 778 sheet: -2.26 (0.66), residues: 64 loop : -1.86 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG K 134 TYR 0.017 0.001 TYR H 39 PHE 0.013 0.001 PHE K 183 TRP 0.019 0.001 TRP K 267 HIS 0.022 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00434 (17214) covalent geometry : angle 0.63132 (24507) hydrogen bonds : bond 0.04516 ( 940) hydrogen bonds : angle 3.49807 ( 2399) *********************** 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 204 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 186 time to evaluate : 0.535 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8848 (t0) cc_final: 0.8526 (t0) REVERT: F 68 ASP cc_start: 0.8594 (m-30) cc_final: 0.7975 (m-30) REVERT: F 92 ARG cc_start: 0.8650 (ttp80) cc_final: 0.8328 (ttp80) REVERT: H 65 ASP cc_start: 0.9034 (t0) cc_final: 0.8795 (t0) REVERT: K 120 LYS cc_start: 0.9161 (pttm) cc_final: 0.8953 (tmmt) REVERT: K 133 PHE cc_start: 0.9095 (m-80) cc_final: 0.8750 (m-80) REVERT: K 223 MET cc_start: 0.8503 (pp-130) cc_final: 0.8221 (ppp) REVERT: K 527 MET cc_start: 0.8813 (mtm) cc_final: 0.8434 (mtt) REVERT: K 638 GLU cc_start: 0.8776 (tm-30) cc_final: 0.8572 (tm-30) outliers start: 18 outliers final: 8 residues processed: 193 average time/residue: 0.7472 time to fit residues: 156.5083 Evaluate side-chains 176 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 168 time to evaluate : 0.376 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 87 SER 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 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 50 optimal weight: 1.9990 chunk 46 optimal weight: 0.6980 chunk 63 optimal weight: 4.9990 chunk 151 optimal weight: 8.9990 chunk 104 optimal weight: 20.0000 chunk 76 optimal weight: 5.9990 chunk 78 optimal weight: 5.9990 chunk 0 optimal weight: 2.9990 chunk 116 optimal weight: 6.9990 chunk 15 optimal weight: 0.5980 chunk 118 optimal weight: 6.9990 overall best weight: 2.2586 ------------------------------------------------------------------------------- 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 = 0.3682 r_free = 0.3682 target = 0.085989 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 49)----------------| | r_work = 0.3164 r_free = 0.3164 target = 0.059914 restraints weight = 46312.076| |-----------------------------------------------------------------------------| r_work (start): 0.3081 rms_B_bonded: 2.26 r_work: 0.2909 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2909 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8707 moved from start: 0.1307 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= 0.213 Angle : 0.626 11.179 24507 Z= 0.354 Chirality : 0.038 0.153 2781 Planarity : 0.005 0.088 2100 Dihedral : 30.395 176.738 4611 Min Nonbonded Distance : 2.461 Molprobity Statistics. All-atom Clashscore : 8.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.20 % Favored : 94.80 % Rotamer: Outliers : 2.81 % Allowed : 13.88 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.47 (0.24), residues: 1269 helix: 1.60 (0.19), residues: 778 sheet: -1.96 (0.66), residues: 64 loop : -1.81 (0.28), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG K 134 TYR 0.012 0.001 TYR K 191 PHE 0.013 0.001 PHE K 185 TRP 0.017 0.001 TRP K 267 HIS 0.016 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00488 (17214) covalent geometry : angle 0.62648 (24507) hydrogen bonds : bond 0.04563 ( 940) hydrogen bonds : angle 3.44235 ( 2399) *********************** 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 203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 172 time to evaluate : 0.424 Fit side-chains revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8899 (t0) cc_final: 0.8554 (t0) REVERT: D 102 GLU cc_start: 0.8064 (mm-30) cc_final: 0.7694 (tp30) REVERT: F 68 ASP cc_start: 0.8685 (m-30) cc_final: 0.7844 (m-30) REVERT: F 92 ARG cc_start: 0.8653 (ttp80) cc_final: 0.8178 (ttp80) REVERT: G 15 LYS cc_start: 0.8595 (tptm) cc_final: 0.8122 (tmtt) REVERT: H 65 ASP cc_start: 0.9067 (t0) cc_final: 0.8762 (t0) REVERT: K 133 PHE cc_start: 0.9105 (m-80) cc_final: 0.8776 (m-80) REVERT: K 527 MET cc_start: 0.8813 (mtm) cc_final: 0.8437 (mtt) REVERT: K 638 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8540 (tm-30) outliers start: 31 outliers final: 12 residues processed: 185 average time/residue: 0.7454 time to fit residues: 149.6643 Evaluate side-chains 177 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 165 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 64 GLU Chi-restraints excluded: chain C residue 113 SER Chi-restraints excluded: chain D residue 36 ILE Chi-restraints excluded: chain D residue 44 GLN Chi-restraints excluded: chain E residue 87 SER 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 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 95 optimal weight: 6.9990 chunk 69 optimal weight: 0.8980 chunk 91 optimal weight: 4.9990 chunk 104 optimal weight: 0.6980 chunk 108 optimal weight: 5.9990 chunk 76 optimal weight: 4.9990 chunk 109 optimal weight: 7.9990 chunk 19 optimal weight: 6.9990 chunk 110 optimal weight: 2.9990 chunk 140 optimal weight: 2.9990 chunk 129 optimal weight: 5.9990 overall best weight: 2.5186 ------------------------------------------------------------------------------- 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 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 = 0.3676 r_free = 0.3676 target = 0.085152 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3151 r_free = 0.3151 target = 0.059391 restraints weight = 45762.233| |-----------------------------------------------------------------------------| r_work (start): 0.3076 rms_B_bonded: 2.19 r_work: 0.2905 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8711 moved from start: 0.1536 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.084 17214 Z= 0.226 Angle : 0.628 9.512 24507 Z= 0.355 Chirality : 0.039 0.160 2781 Planarity : 0.004 0.076 2100 Dihedral : 30.467 177.407 4611 Min Nonbonded Distance : 2.419 Molprobity Statistics. All-atom Clashscore : 8.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 2.90 % Allowed : 16.24 % Favored : 80.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.55 (0.24), residues: 1269 helix: 1.60 (0.19), residues: 787 sheet: -1.72 (0.67), residues: 64 loop : -1.73 (0.29), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG K 134 TYR 0.016 0.001 TYR H 39 PHE 0.009 0.001 PHE C 25 TRP 0.018 0.002 TRP K 267 HIS 0.012 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00521 (17214) covalent geometry : angle 0.62848 (24507) hydrogen bonds : bond 0.04620 ( 940) hydrogen bonds : angle 3.42920 ( 2399) *********************** 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 206 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 32 poor density : 174 time to evaluate : 0.501 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 90 ASP cc_start: 0.8906 (t0) cc_final: 0.8567 (t0) REVERT: D 102 GLU cc_start: 0.8050 (mm-30) cc_final: 0.7668 (tp30) REVERT: F 92 ARG cc_start: 0.8660 (ttp80) cc_final: 0.8283 (ttp80) REVERT: G 15 LYS cc_start: 0.8568 (tptm) cc_final: 0.8157 (tmtt) REVERT: H 65 ASP cc_start: 0.9055 (t0) cc_final: 0.8744 (t0) REVERT: K 133 PHE cc_start: 0.9094 (m-80) cc_final: 0.8809 (m-80) REVERT: K 499 TYR cc_start: 0.8665 (OUTLIER) cc_final: 0.8445 (t80) REVERT: K 527 MET cc_start: 0.8830 (mtm) cc_final: 0.8545 (mtt) REVERT: K 638 GLU cc_start: 0.8768 (tm-30) cc_final: 0.8555 (tm-30) outliers start: 32 outliers final: 17 residues processed: 186 average time/residue: 0.7751 time to fit residues: 156.0433 Evaluate side-chains 180 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 162 time to evaluate : 0.473 ------------------------------------------------------------------------------- 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 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 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 86 ILE Chi-restraints excluded: chain K residue 137 LEU Chi-restraints excluded: chain K residue 207 LEU Chi-restraints excluded: chain K residue 335 MET 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 25 optimal weight: 0.7980 chunk 35 optimal weight: 4.9990 chunk 10 optimal weight: 0.7980 chunk 41 optimal weight: 0.5980 chunk 151 optimal weight: 6.9990 chunk 76 optimal weight: 5.9990 chunk 107 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 43 optimal weight: 1.9990 chunk 26 optimal weight: 0.0570 chunk 60 optimal weight: 0.9980 overall best weight: 0.6498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 81 ASN 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 = 0.3735 r_free = 0.3735 target = 0.088130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3233 r_free = 0.3233 target = 0.062752 restraints weight = 45483.043| |-----------------------------------------------------------------------------| r_work (start): 0.3162 rms_B_bonded: 2.20 r_work: 0.2999 rms_B_bonded: 3.42 restraints_weight: 0.5000 r_work (final): 0.2999 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8634 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 17214 Z= 0.142 Angle : 0.600 11.205 24507 Z= 0.337 Chirality : 0.036 0.152 2781 Planarity : 0.004 0.064 2100 Dihedral : 30.055 175.379 4611 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 8.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.57 % Favored : 95.43 % Rotamer: Outliers : 2.45 % Allowed : 18.15 % Favored : 79.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.93 (0.24), residues: 1269 helix: 1.91 (0.19), residues: 779 sheet: -1.45 (0.69), residues: 64 loop : -1.56 (0.29), residues: 426 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.012 0.000 ARG K 134 TYR 0.011 0.001 TYR C 57 PHE 0.009 0.001 PHE E 67 TRP 0.022 0.001 TRP K 267 HIS 0.010 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00309 (17214) covalent geometry : angle 0.60025 (24507) hydrogen bonds : bond 0.03669 ( 940) hydrogen bonds : angle 3.13283 ( 2399) *********************** 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 221 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 194 time to evaluate : 0.354 Fit side-chains revert: symmetry clash REVERT: A 125 GLN cc_start: 0.9165 (OUTLIER) cc_final: 0.8938 (mp10) REVERT: C 90 ASP cc_start: 0.8929 (t0) cc_final: 0.8581 (t0) REVERT: D 102 GLU cc_start: 0.7735 (mm-30) cc_final: 0.7457 (tp30) REVERT: F 68 ASP cc_start: 0.8527 (m-30) cc_final: 0.8185 (m-30) REVERT: G 15 LYS cc_start: 0.8572 (tptm) cc_final: 0.8324 (tmtt) REVERT: H 60 ASN cc_start: 0.8999 (t0) cc_final: 0.8786 (t160) REVERT: H 65 ASP cc_start: 0.8991 (t0) cc_final: 0.8745 (t0) REVERT: K 133 PHE cc_start: 0.8992 (m-80) cc_final: 0.8692 (m-80) REVERT: K 134 ARG cc_start: 0.9226 (ttp80) cc_final: 0.8968 (mtp180) REVERT: K 433 MET cc_start: 0.7882 (mmm) cc_final: 0.7590 (tpt) REVERT: K 527 MET cc_start: 0.8855 (mtm) cc_final: 0.8599 (mtt) REVERT: K 638 GLU cc_start: 0.8740 (tm-30) cc_final: 0.8533 (tm-30) outliers start: 27 outliers final: 10 residues processed: 206 average time/residue: 0.6842 time to fit residues: 153.3133 Evaluate side-chains 179 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 168 time to evaluate : 0.443 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 77 ASP Chi-restraints excluded: chain A residue 94 GLU Chi-restraints excluded: chain A residue 125 GLN Chi-restraints excluded: chain B residue 43 VAL Chi-restraints excluded: chain C residue 72 ASP Chi-restraints excluded: chain E residue 80 THR Chi-restraints excluded: chain E residue 124 ILE Chi-restraints excluded: chain G residue 113 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 47 optimal weight: 2.9990 chunk 17 optimal weight: 6.9990 chunk 16 optimal weight: 0.9980 chunk 95 optimal weight: 6.9990 chunk 58 optimal weight: 0.9980 chunk 128 optimal weight: 10.0000 chunk 13 optimal weight: 4.9990 chunk 15 optimal weight: 4.9990 chunk 36 optimal weight: 2.9990 chunk 7 optimal weight: 6.9990 chunk 127 optimal weight: 30.0000 overall best weight: 2.5986 ------------------------------------------------------------------------------- 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 ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3685 r_free = 0.3685 target = 0.085622 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3158 r_free = 0.3158 target = 0.059786 restraints weight = 45847.801| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.20 r_work: 0.2916 rms_B_bonded: 3.43 restraints_weight: 0.5000 r_work (final): 0.2916 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8704 moved from start: 0.1924 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.080 17214 Z= 0.233 Angle : 0.645 14.638 24507 Z= 0.359 Chirality : 0.039 0.204 2781 Planarity : 0.004 0.057 2100 Dihedral : 30.317 177.332 4611 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 9.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.65 % Favored : 95.35 % Rotamer: Outliers : 2.81 % Allowed : 18.97 % Favored : 78.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 2.38 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.83 (0.25), residues: 1269 helix: 1.77 (0.19), residues: 785 sheet: -1.42 (0.63), residues: 79 loop : -1.51 (0.31), residues: 405 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG D 83 TYR 0.011 0.001 TYR H 39 PHE 0.018 0.001 PHE A 78 TRP 0.017 0.002 TRP K 267 HIS 0.009 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00540 (17214) covalent geometry : angle 0.64535 (24507) hydrogen bonds : bond 0.04594 ( 940) hydrogen bonds : angle 3.41873 ( 2399) *********************** 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 198 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 167 time to evaluate : 0.445 Fit side-chains REVERT: C 90 ASP cc_start: 0.8907 (t0) cc_final: 0.8553 (t0) REVERT: C 91 GLU cc_start: 0.8341 (tp30) cc_final: 0.8022 (tp30) REVERT: F 68 ASP cc_start: 0.8524 (m-30) cc_final: 0.7908 (m-30) REVERT: F 92 ARG cc_start: 0.8646 (ttp80) cc_final: 0.8341 (ttp80) REVERT: G 15 LYS cc_start: 0.8606 (tptm) cc_final: 0.8189 (tmtt) REVERT: H 65 ASP cc_start: 0.9045 (t0) cc_final: 0.8732 (t0) REVERT: K 133 PHE cc_start: 0.9009 (m-80) cc_final: 0.8710 (m-80) REVERT: K 134 ARG cc_start: 0.9254 (ttp80) cc_final: 0.8927 (mtp180) REVERT: K 436 MET cc_start: 0.7850 (tpp) cc_final: 0.7380 (tpt) REVERT: K 527 MET cc_start: 0.8893 (mtm) cc_final: 0.8599 (mtt) REVERT: K 638 GLU cc_start: 0.8764 (tm-30) cc_final: 0.8551 (tm-30) outliers start: 31 outliers final: 11 residues processed: 185 average time/residue: 0.6941 time to fit residues: 139.5526 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 162 time to evaluate : 0.299 ------------------------------------------------------------------------------- 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 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 17 optimal weight: 0.9990 chunk 106 optimal weight: 0.4980 chunk 24 optimal weight: 0.9980 chunk 52 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 75 optimal weight: 6.9990 chunk 107 optimal weight: 6.9990 chunk 124 optimal weight: 0.1980 chunk 25 optimal weight: 0.9990 chunk 45 optimal weight: 10.0000 chunk 103 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3739 r_free = 0.3739 target = 0.088900 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.3244 r_free = 0.3244 target = 0.063309 restraints weight = 45829.852| |-----------------------------------------------------------------------------| r_work (start): 0.3159 rms_B_bonded: 2.22 r_work: 0.2995 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8640 moved from start: 0.2297 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 : 0.618 12.403 24507 Z= 0.343 Chirality : 0.036 0.183 2781 Planarity : 0.004 0.054 2100 Dihedral : 29.978 176.070 4611 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 8.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.81 % Allowed : 21.05 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.00 (0.24), residues: 1269 helix: 1.92 (0.19), residues: 778 sheet: -1.30 (0.64), residues: 79 loop : -1.42 (0.30), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG G 99 TYR 0.010 0.001 TYR C 57 PHE 0.008 0.001 PHE A 67 TRP 0.017 0.001 TRP K 267 HIS 0.008 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00322 (17214) covalent geometry : angle 0.61822 (24507) hydrogen bonds : bond 0.03720 ( 940) hydrogen bonds : angle 3.19054 ( 2399) *********************** 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 203 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 183 time to evaluate : 0.324 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8176 (mm-30) cc_final: 0.7887 (mm-30) REVERT: C 90 ASP cc_start: 0.8901 (t0) cc_final: 0.8606 (t0) REVERT: C 91 GLU cc_start: 0.8304 (tp30) cc_final: 0.8036 (tp30) REVERT: F 68 ASP cc_start: 0.8561 (m-30) cc_final: 0.7892 (m-30) REVERT: F 92 ARG cc_start: 0.8642 (ttp80) cc_final: 0.8273 (ttp80) REVERT: G 15 LYS cc_start: 0.8538 (tptm) cc_final: 0.8144 (tmtt) REVERT: H 60 ASN cc_start: 0.8987 (t0) cc_final: 0.8778 (t0) REVERT: H 65 ASP cc_start: 0.8990 (t0) cc_final: 0.8737 (t0) REVERT: K 133 PHE cc_start: 0.8957 (m-80) cc_final: 0.8629 (m-80) REVERT: K 134 ARG cc_start: 0.9307 (ttp80) cc_final: 0.8965 (mtp180) REVERT: K 433 MET cc_start: 0.7953 (mmm) cc_final: 0.7661 (tpt) REVERT: K 436 MET cc_start: 0.7885 (tpp) cc_final: 0.7388 (tpt) REVERT: K 527 MET cc_start: 0.8895 (mtm) cc_final: 0.8686 (mtm) outliers start: 20 outliers final: 10 residues processed: 196 average time/residue: 0.6800 time to fit residues: 144.9871 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.399 ------------------------------------------------------------------------------- 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 87 SER Chi-restraints excluded: chain F residue 30 THR Chi-restraints excluded: chain G residue 113 SER Chi-restraints excluded: chain H residue 57 SER Chi-restraints excluded: chain K residue 287 ILE 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 152 random chunks: chunk 120 optimal weight: 10.0000 chunk 62 optimal weight: 5.9990 chunk 93 optimal weight: 5.9990 chunk 143 optimal weight: 4.9990 chunk 49 optimal weight: 4.9990 chunk 71 optimal weight: 0.9980 chunk 33 optimal weight: 2.9990 chunk 102 optimal weight: 3.9990 chunk 148 optimal weight: 8.9990 chunk 51 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 overall best weight: 2.5988 ------------------------------------------------------------------------------- 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 ** K 648 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.085712 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 61)----------------| | r_work = 0.3157 r_free = 0.3157 target = 0.059845 restraints weight = 45594.430| |-----------------------------------------------------------------------------| r_work (start): 0.3083 rms_B_bonded: 2.21 r_work: 0.2914 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2914 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8706 moved from start: 0.2161 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.076 17214 Z= 0.234 Angle : 0.664 11.799 24507 Z= 0.365 Chirality : 0.039 0.174 2781 Planarity : 0.004 0.053 2100 Dihedral : 30.294 177.844 4611 Min Nonbonded Distance : 2.430 Molprobity Statistics. All-atom Clashscore : 9.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 2.36 % Allowed : 21.69 % Favored : 75.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 0.95 (0.24), residues: 1269 helix: 1.82 (0.19), residues: 783 sheet: -0.96 (0.70), residues: 66 loop : -1.43 (0.30), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG G 99 TYR 0.011 0.001 TYR F 51 PHE 0.011 0.001 PHE B 61 TRP 0.014 0.002 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00541 (17214) covalent geometry : angle 0.66448 (24507) hydrogen bonds : bond 0.04605 ( 940) hydrogen bonds : angle 3.38224 ( 2399) *********************** 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 191 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 165 time to evaluate : 0.483 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8339 (mm-30) cc_final: 0.8081 (mm-30) REVERT: C 90 ASP cc_start: 0.8920 (t0) cc_final: 0.8621 (t0) REVERT: C 91 GLU cc_start: 0.8443 (tp30) cc_final: 0.8228 (tp30) REVERT: F 68 ASP cc_start: 0.8648 (m-30) cc_final: 0.7844 (m-30) REVERT: F 92 ARG cc_start: 0.8618 (ttp80) cc_final: 0.8186 (ttp80) REVERT: G 115 LEU cc_start: 0.9526 (OUTLIER) cc_final: 0.9245 (mt) REVERT: H 65 ASP cc_start: 0.9071 (t0) cc_final: 0.8747 (OUTLIER) REVERT: K 133 PHE cc_start: 0.8988 (m-80) cc_final: 0.8632 (m-80) REVERT: K 134 ARG cc_start: 0.9238 (ttp80) cc_final: 0.8945 (mtp180) REVERT: K 433 MET cc_start: 0.8135 (mmm) cc_final: 0.7922 (tpt) REVERT: K 436 MET cc_start: 0.7945 (tpp) cc_final: 0.7513 (tpt) REVERT: K 527 MET cc_start: 0.8940 (mtm) cc_final: 0.8664 (mtm) outliers start: 26 outliers final: 14 residues processed: 182 average time/residue: 0.7250 time to fit residues: 143.0414 Evaluate side-chains 172 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 158 time to evaluate : 0.454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 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 E residue 87 SER Chi-restraints excluded: chain E residue 124 ILE 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 57 SER Chi-restraints excluded: chain H residue 98 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 50 optimal weight: 0.5980 chunk 15 optimal weight: 0.8980 chunk 62 optimal weight: 5.9990 chunk 27 optimal weight: 0.8980 chunk 8 optimal weight: 0.9990 chunk 105 optimal weight: 9.9990 chunk 114 optimal weight: 1.9990 chunk 138 optimal weight: 7.9990 chunk 13 optimal weight: 1.9990 chunk 68 optimal weight: 4.9990 chunk 144 optimal weight: 3.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3725 r_free = 0.3725 target = 0.087596 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3213 r_free = 0.3213 target = 0.062020 restraints weight = 45407.714| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.22 r_work: 0.2975 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2975 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8657 moved from start: 0.2377 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= 0.158 Angle : 0.647 14.181 24507 Z= 0.354 Chirality : 0.037 0.179 2781 Planarity : 0.004 0.052 2100 Dihedral : 30.024 176.800 4611 Min Nonbonded Distance : 2.470 Molprobity Statistics. All-atom Clashscore : 8.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.33 % Favored : 95.67 % Rotamer: Outliers : 1.45 % Allowed : 22.96 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.08 (0.24), residues: 1269 helix: 1.93 (0.19), residues: 781 sheet: -1.07 (0.71), residues: 64 loop : -1.36 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG G 99 TYR 0.010 0.001 TYR C 57 PHE 0.013 0.001 PHE K 119 TRP 0.014 0.001 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00356 (17214) covalent geometry : angle 0.64677 (24507) hydrogen bonds : bond 0.03847 ( 940) hydrogen bonds : angle 3.20516 ( 2399) *********************** 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 186 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 170 time to evaluate : 0.514 Fit side-chains revert: symmetry clash REVERT: B 53 GLU cc_start: 0.8201 (mm-30) cc_final: 0.7908 (mm-30) REVERT: C 90 ASP cc_start: 0.8939 (t0) cc_final: 0.8641 (t0) REVERT: C 91 GLU cc_start: 0.8412 (tp30) cc_final: 0.8207 (tp30) REVERT: F 68 ASP cc_start: 0.8549 (m-30) cc_final: 0.7700 (m-30) REVERT: F 92 ARG cc_start: 0.8648 (ttp80) cc_final: 0.8205 (ttp80) REVERT: G 15 LYS cc_start: 0.8553 (tptm) cc_final: 0.8090 (tmtt) REVERT: G 115 LEU cc_start: 0.9504 (OUTLIER) cc_final: 0.9232 (mt) REVERT: H 60 ASN cc_start: 0.8995 (t0) cc_final: 0.8788 (t0) REVERT: H 65 ASP cc_start: 0.9003 (t0) cc_final: 0.8739 (t0) REVERT: K 133 PHE cc_start: 0.8975 (m-80) cc_final: 0.8646 (m-80) REVERT: K 134 ARG cc_start: 0.9317 (ttp80) cc_final: 0.8976 (mtp180) REVERT: K 436 MET cc_start: 0.8042 (tpp) cc_final: 0.7588 (tpt) REVERT: K 527 MET cc_start: 0.8935 (mtm) cc_final: 0.8626 (mtt) outliers start: 16 outliers final: 9 residues processed: 181 average time/residue: 0.7282 time to fit residues: 142.6596 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 163 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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 87 SER 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 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 105 optimal weight: 9.9990 chunk 48 optimal weight: 0.8980 chunk 97 optimal weight: 6.9990 chunk 43 optimal weight: 0.8980 chunk 102 optimal weight: 4.9990 chunk 67 optimal weight: 2.9990 chunk 135 optimal weight: 8.9990 chunk 116 optimal weight: 5.9990 chunk 142 optimal weight: 6.9990 chunk 35 optimal weight: 0.8980 chunk 80 optimal weight: 5.9990 overall best weight: 2.1384 ------------------------------------------------------------------------------- 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 Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3700 r_free = 0.3700 target = 0.086313 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3177 r_free = 0.3177 target = 0.060606 restraints weight = 45397.932| |-----------------------------------------------------------------------------| r_work (start): 0.3102 rms_B_bonded: 2.20 r_work: 0.2935 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8690 moved from start: 0.2312 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= 0.208 Angle : 0.677 13.471 24507 Z= 0.367 Chirality : 0.038 0.170 2781 Planarity : 0.004 0.052 2100 Dihedral : 30.173 177.776 4611 Min Nonbonded Distance : 2.448 Molprobity Statistics. All-atom Clashscore : 9.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.96 % Favored : 95.04 % Rotamer: Outliers : 1.81 % Allowed : 22.69 % Favored : 75.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.03 (0.24), residues: 1269 helix: 1.89 (0.19), residues: 781 sheet: -0.86 (0.71), residues: 66 loop : -1.41 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.014 0.001 TYR H 39 PHE 0.014 0.001 PHE K 119 TRP 0.022 0.002 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00480 (17214) covalent geometry : angle 0.67663 (24507) hydrogen bonds : bond 0.04338 ( 940) hydrogen bonds : angle 3.33189 ( 2399) ********************** 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: 20 poor density : 165 time to evaluate : 0.363 Fit side-chains REVERT: B 53 GLU cc_start: 0.8268 (mm-30) cc_final: 0.7981 (mm-30) REVERT: C 90 ASP cc_start: 0.8938 (t0) cc_final: 0.8648 (t0) REVERT: E 105 GLU cc_start: 0.8604 (tp30) cc_final: 0.8272 (tp30) REVERT: F 92 ARG cc_start: 0.8626 (ttp80) cc_final: 0.8176 (ttp80) REVERT: G 15 LYS cc_start: 0.8601 (tptm) cc_final: 0.8122 (tmtt) REVERT: G 115 LEU cc_start: 0.9517 (OUTLIER) cc_final: 0.9234 (mt) REVERT: H 65 ASP cc_start: 0.9066 (t0) cc_final: 0.8759 (t0) REVERT: K 133 PHE cc_start: 0.8967 (m-80) cc_final: 0.8639 (m-80) REVERT: K 134 ARG cc_start: 0.9307 (ttp80) cc_final: 0.8969 (mtp180) REVERT: K 265 ASN cc_start: 0.8936 (m-40) cc_final: 0.8727 (p0) REVERT: K 436 MET cc_start: 0.7881 (tpp) cc_final: 0.7480 (tpt) REVERT: K 527 MET cc_start: 0.8969 (mtm) cc_final: 0.8682 (mtm) REVERT: K 648 GLN cc_start: 0.8927 (tp40) cc_final: 0.8598 (tp-100) outliers start: 20 outliers final: 14 residues processed: 178 average time/residue: 0.7219 time to fit residues: 139.1371 Evaluate side-chains 173 residues out of total 1116 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 158 time to evaluate : 0.427 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 133 GLU 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 E residue 80 THR Chi-restraints excluded: chain E residue 87 SER 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 K residue 207 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 82 optimal weight: 6.9990 chunk 107 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 40 optimal weight: 4.9990 chunk 109 optimal weight: 0.9990 chunk 39 optimal weight: 0.8980 chunk 91 optimal weight: 5.9990 chunk 108 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 146 optimal weight: 6.9990 overall best weight: 1.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 84 GLN G 73 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3690 r_free = 0.3690 target = 0.087247 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3174 r_free = 0.3174 target = 0.061352 restraints weight = 45276.812| |-----------------------------------------------------------------------------| r_work (start): 0.3079 rms_B_bonded: 2.22 r_work: 0.2905 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2905 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8680 moved from start: 0.2349 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.056 17214 Z= 0.200 Angle : 0.682 13.175 24507 Z= 0.370 Chirality : 0.038 0.165 2781 Planarity : 0.004 0.051 2100 Dihedral : 30.139 177.738 4611 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.81 % Favored : 95.19 % Rotamer: Outliers : 1.81 % Allowed : 23.23 % Favored : 74.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.08 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.02 (0.24), residues: 1269 helix: 1.89 (0.19), residues: 781 sheet: -1.05 (0.71), residues: 64 loop : -1.39 (0.30), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG H 76 TYR 0.010 0.001 TYR B 51 PHE 0.009 0.001 PHE B 61 TRP 0.019 0.002 TRP K 267 HIS 0.007 0.001 HIS K 613 Details of bonding type rmsd covalent geometry : bond 0.00461 (17214) covalent geometry : angle 0.68244 (24507) hydrogen bonds : bond 0.04248 ( 940) hydrogen bonds : angle 3.27640 ( 2399) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4753.82 seconds wall clock time: 81 minutes 40.89 seconds (4900.89 seconds total)