Starting phenix.real_space_refine on Sun May 18 15:03:48 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/9dpb_47101/05_2025/9dpb_47101.cif Found real_map, /net/cci-nas-00/data/ceres_data/9dpb_47101/05_2025/9dpb_47101.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/9dpb_47101/05_2025/9dpb_47101.map" default_real_map = "/net/cci-nas-00/data/ceres_data/9dpb_47101/05_2025/9dpb_47101.map" model { file = "/net/cci-nas-00/data/ceres_data/9dpb_47101/05_2025/9dpb_47101.cif" } default_model = "/net/cci-nas-00/data/ceres_data/9dpb_47101/05_2025/9dpb_47101.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.007 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 9120 atoms to isotropic. 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: 7 Type Number sf(0) Gaussians P 79 5.49 5 Mg 4 5.21 5 S 56 5.16 5 Na 1 4.78 5 C 5970 2.51 5 N 1680 2.21 5 O 2046 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 7 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 9836 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 4100 Number of conformers: 1 Conformer: "" Number of residues, atoms: 506, 4100 Classifications: {'peptide': 506} Link IDs: {'PTRANS': 29, 'TRANS': 476} Chain: "B" Number of atoms: 4092 Number of conformers: 1 Conformer: "" Number of residues, atoms: 505, 4092 Classifications: {'peptide': 505} Link IDs: {'PTRANS': 29, 'TRANS': 475} Chain: "C" Number of atoms: 1557 Number of conformers: 1 Conformer: "" Number of residues, atoms: 73, 1557 Classifications: {'RNA': 73} Modifications used: {'rna2p_pur': 8, 'rna2p_pyr': 4, 'rna3p_pur': 29, 'rna3p_pyr': 32} Link IDs: {'rna2p': 11, 'rna3p': 61} Chain: "A" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "A" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'APC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "B" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 10 Classifications: {'peptide': 1} Modifications used: {'COO': 1} Chain: "B" Number of atoms: 33 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 33 Unusual residues: {' MG': 2, 'APC': 1} Classifications: {'undetermined': 3} Link IDs: {None: 2} Chain: "C" Number of atoms: 1 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 1 Unusual residues: {' NA': 1} Classifications: {'undetermined': 1} Time building chain proxies: 6.74, per 1000 atoms: 0.69 Number of scatterers: 9836 At special positions: 0 Unit cell: (85.6, 103.79, 141.24, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 7 Type Number sf(0) S 56 16.00 P 79 15.00 Mg 4 11.99 Na 1 11.00 O 2046 8.00 N 1680 7.00 C 5970 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: 2.62 Conformation dependent library (CDL) restraints added in 1.2 seconds 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1898 Finding SS restraints... Secondary structure from input PDB file: 33 helices and 10 sheets defined 38.7% alpha, 24.1% beta 26 base pairs and 36 stacking pairs defined. Time for finding SS restraints: 3.64 Creating SS restraints... Processing helix chain 'A' and resid 75 through 90 Processing helix chain 'A' and resid 104 through 113 Processing helix chain 'A' and resid 161 through 163 No H-bonds generated for 'chain 'A' and resid 161 through 163' Processing helix chain 'A' and resid 165 through 174 Processing helix chain 'A' and resid 224 through 229 Processing helix chain 'A' and resid 229 through 237 Processing helix chain 'A' and resid 238 through 261 removed outlier: 3.782A pdb=" N GLN A 242 " --> pdb=" O ASP A 238 " (cutoff:3.500A) Processing helix chain 'A' and resid 300 through 311 Processing helix chain 'A' and resid 346 through 367 removed outlier: 4.300A pdb=" N GLU A 352 " --> pdb=" O HIS A 348 " (cutoff:3.500A) removed outlier: 3.845A pdb=" N ILE A 353 " --> pdb=" O ASP A 349 " (cutoff:3.500A) Processing helix chain 'A' and resid 395 through 405 Processing helix chain 'A' and resid 410 through 415 removed outlier: 4.466A pdb=" N GLU A 415 " --> pdb=" O ASN A 412 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 430 Processing helix chain 'A' and resid 439 through 452 Processing helix chain 'A' and resid 453 through 456 Processing helix chain 'A' and resid 504 through 521 Processing helix chain 'A' and resid 530 through 538 removed outlier: 3.724A pdb=" N GLU A 538 " --> pdb=" O CYS A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 559 Processing helix chain 'A' and resid 563 through 567 Processing helix chain 'B' and resid 73 through 90 removed outlier: 3.533A pdb=" N ASN B 90 " --> pdb=" O GLN B 86 " (cutoff:3.500A) Processing helix chain 'B' and resid 104 through 112 Processing helix chain 'B' and resid 165 through 174 removed outlier: 3.669A pdb=" N ASN B 174 " --> pdb=" O ILE B 170 " (cutoff:3.500A) Processing helix chain 'B' and resid 222 through 229 Processing helix chain 'B' and resid 229 through 237 Processing helix chain 'B' and resid 238 through 261 removed outlier: 3.614A pdb=" N GLN B 242 " --> pdb=" O ASP B 238 " (cutoff:3.500A) Processing helix chain 'B' and resid 300 through 311 Processing helix chain 'B' and resid 348 through 367 removed outlier: 4.435A pdb=" N GLU B 352 " --> pdb=" O HIS B 348 " (cutoff:3.500A) removed outlier: 4.036A pdb=" N ILE B 353 " --> pdb=" O ASP B 349 " (cutoff:3.500A) Processing helix chain 'B' and resid 397 through 405 Processing helix chain 'B' and resid 416 through 430 removed outlier: 3.538A pdb=" N ARG B 420 " --> pdb=" O THR B 416 " (cutoff:3.500A) Processing helix chain 'B' and resid 439 through 452 Processing helix chain 'B' and resid 468 through 470 No H-bonds generated for 'chain 'B' and resid 468 through 470' Processing helix chain 'B' and resid 504 through 522 Processing helix chain 'B' and resid 530 through 539 Processing helix chain 'B' and resid 551 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 126 through 137 removed outlier: 5.862A pdb=" N ILE A 132 " --> pdb=" O ARG A 148 " (cutoff:3.500A) removed outlier: 6.364A pdb=" N ARG A 148 " --> pdb=" O ILE A 132 " (cutoff:3.500A) removed outlier: 4.143A pdb=" N ALA A 134 " --> pdb=" O ASP A 146 " (cutoff:3.500A) removed outlier: 8.613A pdb=" N LYS A 153 " --> pdb=" O LEU A 196 " (cutoff:3.500A) removed outlier: 9.049A pdb=" N ILE A 198 " --> pdb=" O LYS A 153 " (cutoff:3.500A) removed outlier: 7.076A pdb=" N GLN A 155 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 7.564A pdb=" N MET A 157 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 8.983A pdb=" N GLU A 202 " --> pdb=" O MET A 157 " (cutoff:3.500A) removed outlier: 10.160A pdb=" N ASN A 159 " --> pdb=" O GLU A 202 " (cutoff:3.500A) removed outlier: 12.610A pdb=" N THR A 204 " --> pdb=" O ASN A 159 " (cutoff:3.500A) removed outlier: 4.874A pdb=" N ILE A 198 " --> pdb=" O GLY A 189 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N GLY A 189 " --> pdb=" O ILE A 198 " (cutoff:3.500A) removed outlier: 6.438A pdb=" N ASN A 187 " --> pdb=" O PRO A 200 " (cutoff:3.500A) removed outlier: 6.686A pdb=" N ILE A 181 " --> pdb=" O LEU A 206 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 264 through 265 removed outlier: 5.932A pdb=" N LEU A 264 " --> pdb=" O TYR A 316 " (cutoff:3.500A) removed outlier: 8.251A pdb=" N ILE A 318 " --> pdb=" O LEU A 264 " (cutoff:3.500A) removed outlier: 6.705A pdb=" N ILE A 495 " --> pdb=" O GLY A 550 " (cutoff:3.500A) removed outlier: 4.977A pdb=" N GLU A 494 " --> pdb=" O VAL A 490 " (cutoff:3.500A) removed outlier: 6.367A pdb=" N VAL A 490 " --> pdb=" O GLU A 494 " (cutoff:3.500A) removed outlier: 3.728A pdb=" N CYS A 496 " --> pdb=" O LEU A 488 " (cutoff:3.500A) removed outlier: 6.972A pdb=" N ARG A 392 " --> pdb=" O PHE A 461 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 271 through 272 Processing sheet with id=AA4, first strand: chain 'A' and resid 370 through 373 Processing sheet with id=AA5, first strand: chain 'A' and resid 465 through 466 removed outlier: 3.889A pdb=" N HIS A 465 " --> pdb=" O THR A 483 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 156 through 159 removed outlier: 3.919A pdb=" N ALA B 134 " --> pdb=" O ASP B 146 " (cutoff:3.500A) removed outlier: 6.891A pdb=" N ARG B 148 " --> pdb=" O ILE B 132 " (cutoff:3.500A) removed outlier: 5.753A pdb=" N ILE B 132 " --> pdb=" O ARG B 148 " (cutoff:3.500A) removed outlier: 7.568A pdb=" N ILE B 181 " --> pdb=" O LEU B 205 " (cutoff:3.500A) removed outlier: 5.321A pdb=" N LEU B 205 " --> pdb=" O ILE B 181 " (cutoff:3.500A) removed outlier: 6.675A pdb=" N GLY B 183 " --> pdb=" O ILE B 203 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ILE B 203 " --> pdb=" O GLY B 183 " (cutoff:3.500A) removed outlier: 7.067A pdb=" N GLN B 185 " --> pdb=" O TYR B 201 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 264 through 265 removed outlier: 5.854A pdb=" N LEU B 264 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE B 318 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 495 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 490 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS B 496 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU B 484 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 6.712A pdb=" N ARG B 392 " --> pdb=" O PHE B 461 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'B' and resid 264 through 265 removed outlier: 5.854A pdb=" N LEU B 264 " --> pdb=" O TYR B 316 " (cutoff:3.500A) removed outlier: 8.132A pdb=" N ILE B 318 " --> pdb=" O LEU B 264 " (cutoff:3.500A) removed outlier: 6.545A pdb=" N ILE B 495 " --> pdb=" O GLY B 550 " (cutoff:3.500A) removed outlier: 4.975A pdb=" N GLU B 494 " --> pdb=" O VAL B 490 " (cutoff:3.500A) removed outlier: 6.405A pdb=" N VAL B 490 " --> pdb=" O GLU B 494 " (cutoff:3.500A) removed outlier: 3.874A pdb=" N CYS B 496 " --> pdb=" O LEU B 488 " (cutoff:3.500A) removed outlier: 5.657A pdb=" N GLU B 484 " --> pdb=" O THR B 500 " (cutoff:3.500A) removed outlier: 3.855A pdb=" N HIS B 465 " --> pdb=" O THR B 483 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'B' and resid 271 through 272 Processing sheet with id=AB1, first strand: chain 'B' and resid 370 through 373 388 hydrogen bonds defined for protein. 1119 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 66 hydrogen bonds 108 hydrogen bond angles 0 basepair planarities 26 basepair parallelities 36 stacking parallelities Total time for adding SS restraints: 3.44 Time building geometry restraints manager: 2.96 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: 2116 1.33 - 1.45: 2612 1.45 - 1.58: 5230 1.58 - 1.70: 151 1.70 - 1.82: 100 Bond restraints: 10209 Sorted by residual: bond pdb=" C PRO B 375 " pdb=" N ASP B 376 " ideal model delta sigma weight residual 1.332 1.207 0.125 1.40e-02 5.10e+03 7.99e+01 bond pdb=" C GLY B 405 " pdb=" N MET B 406 " ideal model delta sigma weight residual 1.330 1.407 -0.077 1.53e-02 4.27e+03 2.56e+01 bond pdb=" C THR B 191 " pdb=" N LYS B 192 " ideal model delta sigma weight residual 1.335 1.401 -0.066 1.31e-02 5.83e+03 2.56e+01 bond pdb=" C GLY A 405 " pdb=" N MET A 406 " ideal model delta sigma weight residual 1.329 1.398 -0.068 1.36e-02 5.41e+03 2.51e+01 bond pdb=" C LYS B 135 " pdb=" N ARG B 136 " ideal model delta sigma weight residual 1.330 1.396 -0.065 1.45e-02 4.76e+03 2.03e+01 ... (remaining 10204 not shown) Histogram of bond angle deviations from ideal: 0.00 - 5.27: 14139 5.27 - 10.54: 17 10.54 - 15.81: 2 15.81 - 21.08: 0 21.08 - 26.35: 2 Bond angle restraints: 14160 Sorted by residual: angle pdb=" PB APC B 602 " pdb=" O3B APC B 602 " pdb=" PG APC B 602 " ideal model delta sigma weight residual 106.84 133.19 -26.35 3.00e+00 1.11e-01 7.72e+01 angle pdb=" PB APC A 602 " pdb=" O3B APC A 602 " pdb=" PG APC A 602 " ideal model delta sigma weight residual 106.84 131.47 -24.63 3.00e+00 1.11e-01 6.74e+01 angle pdb=" O PRO B 375 " pdb=" C PRO B 375 " pdb=" N ASP B 376 " ideal model delta sigma weight residual 122.38 115.08 7.30 1.39e+00 5.18e-01 2.76e+01 angle pdb=" C5' APC B 602 " pdb=" O5' APC B 602 " pdb=" PA APC B 602 " ideal model delta sigma weight residual 106.85 122.55 -15.70 3.00e+00 1.11e-01 2.74e+01 angle pdb=" C5' APC A 602 " pdb=" O5' APC A 602 " pdb=" PA APC A 602 " ideal model delta sigma weight residual 106.85 122.21 -15.36 3.00e+00 1.11e-01 2.62e+01 ... (remaining 14155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 32.38: 5881 32.38 - 64.76: 412 64.76 - 97.14: 40 97.14 - 129.52: 2 129.52 - 161.90: 1 Dihedral angle restraints: 6336 sinusoidal: 3385 harmonic: 2951 Sorted by residual: dihedral pdb=" O4' U C 20 " pdb=" C1' U C 20 " pdb=" N1 U C 20 " pdb=" C2 U C 20 " ideal model delta sinusoidal sigma weight residual 200.00 38.10 161.90 1 1.50e+01 4.44e-03 8.32e+01 dihedral pdb=" CA ILE A 462 " pdb=" C ILE A 462 " pdb=" N CYS A 463 " pdb=" CA CYS A 463 " ideal model delta harmonic sigma weight residual 180.00 -156.15 -23.85 0 5.00e+00 4.00e-02 2.27e+01 dihedral pdb=" CA TYR B 499 " pdb=" C TYR B 499 " pdb=" N THR B 500 " pdb=" CA THR B 500 " ideal model delta harmonic sigma weight residual 180.00 156.70 23.30 0 5.00e+00 4.00e-02 2.17e+01 ... (remaining 6333 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 1316 0.050 - 0.100: 228 0.100 - 0.150: 44 0.150 - 0.200: 8 0.200 - 0.250: 2 Chirality restraints: 1598 Sorted by residual: chirality pdb=" CG LEU B 329 " pdb=" CB LEU B 329 " pdb=" CD1 LEU B 329 " pdb=" CD2 LEU B 329 " both_signs ideal model delta sigma weight residual False -2.59 -2.34 -0.25 2.00e-01 2.50e+01 1.56e+00 chirality pdb=" CG LEU A 444 " pdb=" CB LEU A 444 " pdb=" CD1 LEU A 444 " pdb=" CD2 LEU A 444 " both_signs ideal model delta sigma weight residual False -2.59 -2.38 -0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE B 462 " pdb=" N ILE B 462 " pdb=" C ILE B 462 " pdb=" CB ILE B 462 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.79e-01 ... (remaining 1595 not shown) Planarity restraints: 1549 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ASP B 376 " -0.015 2.00e-02 2.50e+03 3.01e-02 9.03e+00 pdb=" C ASP B 376 " 0.052 2.00e-02 2.50e+03 pdb=" O ASP B 376 " -0.019 2.00e-02 2.50e+03 pdb=" N GLY B 377 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR A 388 " -0.032 5.00e-02 4.00e+02 4.79e-02 3.67e+00 pdb=" N PRO A 389 " 0.083 5.00e-02 4.00e+02 pdb=" CA PRO A 389 " -0.025 5.00e-02 4.00e+02 pdb=" CD PRO A 389 " -0.026 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ILE B 468 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.18e+00 pdb=" C ILE B 468 " -0.031 2.00e-02 2.50e+03 pdb=" O ILE B 468 " 0.012 2.00e-02 2.50e+03 pdb=" N MET B 469 " 0.010 2.00e-02 2.50e+03 ... (remaining 1546 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.76: 1668 2.76 - 3.30: 9423 3.30 - 3.83: 17982 3.83 - 4.37: 21263 4.37 - 4.90: 34339 Nonbonded interactions: 84675 Sorted by model distance: nonbonded pdb=" N GLU B 195 " pdb=" OE1 GLU B 195 " model vdw 2.231 3.120 nonbonded pdb=" N GLU A 453 " pdb=" OE1 GLU A 453 " model vdw 2.252 3.120 nonbonded pdb=" OD2 ASP B 222 " pdb=" OG1 THR B 225 " model vdw 2.258 3.040 nonbonded pdb=" OE2 GLU A 494 " pdb="MG MG A 603 " model vdw 2.258 2.170 nonbonded pdb=" OH TYR B 286 " pdb=" OD1 ASP B 291 " model vdw 2.279 3.040 ... (remaining 84670 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 72 through 576 or resid 601 or resid 602 through 604)) selection = chain 'B' } 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: 0.930 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.120 Construct map_model_manager: 0.010 Extract box with map and model: 0.400 Check model and map are aligned: 0.070 Set scattering table: 0.100 Process input model: 28.240 Find NCS groups from input model: 0.350 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:10.680 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7366 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 0.125 10209 Z= 0.318 Angle : 0.770 26.351 14160 Z= 0.437 Chirality : 0.041 0.250 1598 Planarity : 0.005 0.048 1549 Dihedral : 19.843 161.904 4438 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 9.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 1.45 % Allowed : 22.19 % Favored : 76.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.31 (0.27), residues: 1007 helix: 0.88 (0.27), residues: 366 sheet: -0.28 (0.36), residues: 211 loop : -1.06 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 547 HIS 0.011 0.001 HIS B 465 PHE 0.026 0.001 PHE B 340 TYR 0.010 0.001 TYR A 316 ARG 0.006 0.000 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.11241 ( 431) hydrogen bonds : angle 6.44685 ( 1227) covalent geometry : bond 0.00504 (10209) covalent geometry : angle 0.76951 (14160) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 74 time to evaluate : 1.103 Fit side-chains revert: symmetry clash REVERT: A 469 MET cc_start: 0.8014 (mpt) cc_final: 0.7776 (mpt) outliers start: 13 outliers final: 10 residues processed: 87 average time/residue: 1.3375 time to fit residues: 124.9435 Evaluate side-chains 71 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.947 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 318 ILE Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 484 GLU Chi-restraints excluded: chain B residue 529 ILE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 8.9990 chunk 81 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 2.9990 chunk 83 optimal weight: 5.9990 chunk 32 optimal weight: 5.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.7980 chunk 97 optimal weight: 3.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 75 GLN A 229 GLN A 288 ASN ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 229 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3923 r_free = 0.3923 target = 0.114206 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3134 r_free = 0.3134 target = 0.069029 restraints weight = 18366.396| |-----------------------------------------------------------------------------| r_work (start): 0.3085 rms_B_bonded: 2.69 r_work: 0.2881 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2881 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8260 moved from start: 0.0939 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.055 10209 Z= 0.229 Angle : 0.581 8.737 14160 Z= 0.295 Chirality : 0.040 0.297 1598 Planarity : 0.005 0.051 1549 Dihedral : 19.473 161.880 2350 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 8.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.34 % Allowed : 20.51 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.05 (0.27), residues: 1007 helix: 1.19 (0.27), residues: 370 sheet: -0.36 (0.37), residues: 217 loop : -0.89 (0.31), residues: 420 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP A 547 HIS 0.004 0.001 HIS A 215 PHE 0.032 0.002 PHE A 340 TYR 0.012 0.002 TYR A 316 ARG 0.004 0.001 ARG B 161 Details of bonding type rmsd hydrogen bonds : bond 0.04726 ( 431) hydrogen bonds : angle 5.12167 ( 1227) covalent geometry : bond 0.00543 (10209) covalent geometry : angle 0.58141 (14160) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 70 time to evaluate : 1.052 Fit side-chains revert: symmetry clash REVERT: A 301 GLU cc_start: 0.8773 (tt0) cc_final: 0.8289 (tp30) REVERT: A 453 GLU cc_start: 0.7995 (mp0) cc_final: 0.7763 (mp0) REVERT: A 499 TYR cc_start: 0.8276 (m-80) cc_final: 0.7996 (m-80) REVERT: B 161 ARG cc_start: 0.8797 (mtm-85) cc_final: 0.8558 (mtm-85) REVERT: B 192 LYS cc_start: 0.9138 (ttpp) cc_final: 0.8778 (tmmt) outliers start: 30 outliers final: 11 residues processed: 93 average time/residue: 1.2435 time to fit residues: 125.1093 Evaluate side-chains 75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 64 time to evaluate : 1.037 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 385 VAL Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 469 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 4 optimal weight: 0.2980 chunk 89 optimal weight: 4.9990 chunk 78 optimal weight: 0.6980 chunk 97 optimal weight: 0.0770 chunk 48 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 9 optimal weight: 0.6980 chunk 57 optimal weight: 0.8980 chunk 23 optimal weight: 0.9980 chunk 14 optimal weight: 4.9990 overall best weight: 0.5338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3958 r_free = 0.3958 target = 0.116458 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3194 r_free = 0.3194 target = 0.071673 restraints weight = 18635.401| |-----------------------------------------------------------------------------| r_work (start): 0.3140 rms_B_bonded: 2.73 r_work: 0.2935 rms_B_bonded: 3.66 restraints_weight: 0.5000 r_work (final): 0.2935 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8226 moved from start: 0.1032 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.034 10209 Z= 0.107 Angle : 0.518 8.312 14160 Z= 0.258 Chirality : 0.036 0.148 1598 Planarity : 0.004 0.048 1549 Dihedral : 19.223 163.110 2336 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % Rotamer: Outliers : 3.34 % Allowed : 20.51 % Favored : 76.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.12 (0.27), residues: 1007 helix: 1.38 (0.27), residues: 371 sheet: -0.28 (0.37), residues: 215 loop : -0.84 (0.31), residues: 421 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP B 547 HIS 0.002 0.000 HIS A 465 PHE 0.027 0.001 PHE B 340 TYR 0.014 0.001 TYR A 499 ARG 0.003 0.000 ARG A 442 Details of bonding type rmsd hydrogen bonds : bond 0.04038 ( 431) hydrogen bonds : angle 4.75629 ( 1227) covalent geometry : bond 0.00249 (10209) covalent geometry : angle 0.51773 (14160) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 69 time to evaluate : 1.058 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8719 (OUTLIER) cc_final: 0.8189 (m-30) REVERT: A 301 GLU cc_start: 0.8767 (tt0) cc_final: 0.8248 (tp30) REVERT: A 450 GLU cc_start: 0.8687 (OUTLIER) cc_final: 0.8316 (mp0) REVERT: A 453 GLU cc_start: 0.7910 (mp0) cc_final: 0.7483 (OUTLIER) REVERT: A 499 TYR cc_start: 0.8270 (m-80) cc_final: 0.7973 (m-80) REVERT: B 161 ARG cc_start: 0.8782 (mtm-85) cc_final: 0.8403 (mtm-85) REVERT: B 162 ASN cc_start: 0.9072 (m110) cc_final: 0.8217 (m110) REVERT: B 192 LYS cc_start: 0.9118 (ttpp) cc_final: 0.8806 (tmmt) REVERT: B 406 MET cc_start: 0.7346 (pp-130) cc_final: 0.6401 (pmm) outliers start: 30 outliers final: 12 residues processed: 92 average time/residue: 1.2419 time to fit residues: 123.0103 Evaluate side-chains 74 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 61 time to evaluate : 1.122 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain A residue 544 THR Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 232 LEU Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 61 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 35 optimal weight: 2.9990 chunk 67 optimal weight: 1.9990 chunk 97 optimal weight: 1.9990 chunk 41 optimal weight: 2.9990 chunk 65 optimal weight: 3.9990 chunk 28 optimal weight: 0.5980 chunk 98 optimal weight: 0.6980 chunk 46 optimal weight: 0.8980 chunk 4 optimal weight: 0.5980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 515 GLN B 465 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4016 r_free = 0.4016 target = 0.117260 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3281 r_free = 0.3281 target = 0.073386 restraints weight = 18314.193| |-----------------------------------------------------------------------------| r_work (start): 0.3216 rms_B_bonded: 2.58 r_work: 0.3015 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.3015 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1156 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 10209 Z= 0.120 Angle : 0.524 9.141 14160 Z= 0.260 Chirality : 0.036 0.145 1598 Planarity : 0.004 0.048 1549 Dihedral : 19.110 162.576 2336 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.46 % Allowed : 21.18 % Favored : 75.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.20 (0.27), residues: 1007 helix: 1.48 (0.27), residues: 369 sheet: -0.24 (0.37), residues: 214 loop : -0.83 (0.31), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP B 547 HIS 0.002 0.000 HIS A 215 PHE 0.028 0.001 PHE A 340 TYR 0.014 0.001 TYR A 499 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 431) hydrogen bonds : angle 4.64342 ( 1227) covalent geometry : bond 0.00284 (10209) covalent geometry : angle 0.52395 (14160) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 1.088 Fit side-chains revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8582 (OUTLIER) cc_final: 0.8220 (m-30) REVERT: A 301 GLU cc_start: 0.8728 (tt0) cc_final: 0.8296 (tp30) REVERT: A 453 GLU cc_start: 0.8004 (OUTLIER) cc_final: 0.7589 (mp0) REVERT: A 499 TYR cc_start: 0.8209 (m-80) cc_final: 0.7950 (m-80) REVERT: B 161 ARG cc_start: 0.8730 (mtm-85) cc_final: 0.8482 (mpp80) REVERT: B 162 ASN cc_start: 0.9144 (m110) cc_final: 0.8713 (m110) REVERT: B 192 LYS cc_start: 0.9101 (ttpp) cc_final: 0.8805 (tmmt) REVERT: B 406 MET cc_start: 0.7304 (pp-130) cc_final: 0.6551 (pmm) outliers start: 31 outliers final: 11 residues processed: 87 average time/residue: 1.1669 time to fit residues: 109.8155 Evaluate side-chains 75 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.967 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 2 optimal weight: 0.0010 chunk 34 optimal weight: 1.9990 chunk 22 optimal weight: 0.7980 chunk 36 optimal weight: 7.9990 chunk 45 optimal weight: 0.9980 chunk 101 optimal weight: 20.0000 chunk 103 optimal weight: 5.9990 chunk 5 optimal weight: 2.9990 chunk 84 optimal weight: 6.9990 chunk 74 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 overall best weight: 0.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4010 r_free = 0.4010 target = 0.116831 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 29)----------------| | r_work = 0.3277 r_free = 0.3277 target = 0.073209 restraints weight = 18341.985| |-----------------------------------------------------------------------------| r_work (start): 0.3212 rms_B_bonded: 2.57 r_work: 0.3010 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.3010 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1239 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 10209 Z= 0.133 Angle : 0.530 10.756 14160 Z= 0.262 Chirality : 0.037 0.148 1598 Planarity : 0.004 0.048 1549 Dihedral : 19.019 162.456 2333 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.43 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 3.46 % Allowed : 20.74 % Favored : 75.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.23 (0.27), residues: 1007 helix: 1.51 (0.27), residues: 369 sheet: -0.19 (0.37), residues: 213 loop : -0.83 (0.31), residues: 425 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.003 TRP B 547 HIS 0.004 0.001 HIS B 465 PHE 0.028 0.001 PHE A 340 TYR 0.016 0.001 TYR A 499 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.04039 ( 431) hydrogen bonds : angle 4.57788 ( 1227) covalent geometry : bond 0.00315 (10209) covalent geometry : angle 0.52961 (14160) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 96 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 65 time to evaluate : 1.135 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8606 (OUTLIER) cc_final: 0.8211 (m-30) REVERT: A 301 GLU cc_start: 0.8714 (tt0) cc_final: 0.8224 (tp30) REVERT: A 450 GLU cc_start: 0.8673 (OUTLIER) cc_final: 0.8272 (mp0) REVERT: A 453 GLU cc_start: 0.8048 (OUTLIER) cc_final: 0.7674 (mp0) REVERT: A 499 TYR cc_start: 0.8218 (m-80) cc_final: 0.7944 (m-80) REVERT: B 161 ARG cc_start: 0.8708 (mtm-85) cc_final: 0.8287 (mtm-85) REVERT: B 162 ASN cc_start: 0.9195 (m110) cc_final: 0.8320 (m110) REVERT: B 192 LYS cc_start: 0.9100 (ttpp) cc_final: 0.8796 (tmmt) REVERT: B 212 MET cc_start: 0.8884 (ttp) cc_final: 0.8570 (ttm) REVERT: B 406 MET cc_start: 0.7070 (pp-130) cc_final: 0.6580 (pp-130) REVERT: B 499 TYR cc_start: 0.8507 (m-10) cc_final: 0.8080 (m-80) outliers start: 31 outliers final: 13 residues processed: 88 average time/residue: 1.2379 time to fit residues: 117.6037 Evaluate side-chains 77 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 61 time to evaluate : 0.993 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 412 ASN Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 42 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 95 optimal weight: 6.9990 chunk 43 optimal weight: 3.9990 chunk 79 optimal weight: 2.9990 chunk 86 optimal weight: 0.0270 chunk 96 optimal weight: 2.9990 chunk 85 optimal weight: 0.6980 chunk 65 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 50 optimal weight: 1.9990 overall best weight: 1.7444 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3986 r_free = 0.3986 target = 0.115374 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.3230 r_free = 0.3230 target = 0.071118 restraints weight = 18494.068| |-----------------------------------------------------------------------------| r_work (start): 0.3169 rms_B_bonded: 2.58 r_work: 0.2970 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2970 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8415 moved from start: 0.1355 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 10209 Z= 0.203 Angle : 0.565 12.230 14160 Z= 0.282 Chirality : 0.038 0.189 1598 Planarity : 0.005 0.049 1549 Dihedral : 19.021 162.390 2333 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 8.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.46 % Allowed : 20.96 % Favored : 75.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.14 (0.27), residues: 1007 helix: 1.36 (0.27), residues: 371 sheet: -0.25 (0.37), residues: 213 loop : -0.82 (0.30), residues: 423 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP A 547 HIS 0.004 0.001 HIS A 215 PHE 0.033 0.002 PHE A 340 TYR 0.018 0.001 TYR A 499 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.04394 ( 431) hydrogen bonds : angle 4.69304 ( 1227) covalent geometry : bond 0.00483 (10209) covalent geometry : angle 0.56477 (14160) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 31 poor density : 62 time to evaluate : 1.000 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 301 GLU cc_start: 0.8731 (tt0) cc_final: 0.8221 (tp30) REVERT: A 450 GLU cc_start: 0.8668 (OUTLIER) cc_final: 0.8280 (mp0) REVERT: A 453 GLU cc_start: 0.8112 (OUTLIER) cc_final: 0.7776 (mp0) REVERT: A 499 TYR cc_start: 0.8273 (m-80) cc_final: 0.8009 (m-80) REVERT: B 161 ARG cc_start: 0.8742 (mtm-85) cc_final: 0.8499 (mpp80) REVERT: B 162 ASN cc_start: 0.9129 (m110) cc_final: 0.8660 (m110) REVERT: B 192 LYS cc_start: 0.9112 (ttpp) cc_final: 0.8793 (tmmt) REVERT: B 406 MET cc_start: 0.7208 (pp-130) cc_final: 0.6623 (pp-130) REVERT: B 499 TYR cc_start: 0.8581 (m-10) cc_final: 0.8266 (m-80) outliers start: 31 outliers final: 16 residues processed: 84 average time/residue: 1.3201 time to fit residues: 118.9000 Evaluate side-chains 79 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 61 time to evaluate : 1.083 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 329 LEU Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 193 LYS Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 80 optimal weight: 3.9990 chunk 93 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 96 optimal weight: 0.9990 chunk 15 optimal weight: 2.9990 chunk 2 optimal weight: 0.8980 chunk 77 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 45 optimal weight: 10.0000 overall best weight: 1.0984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3998 r_free = 0.3998 target = 0.116181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3252 r_free = 0.3252 target = 0.072103 restraints weight = 18509.105| |-----------------------------------------------------------------------------| r_work (start): 0.3191 rms_B_bonded: 2.58 r_work: 0.2987 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2987 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.1368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 10209 Z= 0.144 Angle : 0.549 13.129 14160 Z= 0.270 Chirality : 0.037 0.176 1598 Planarity : 0.004 0.049 1549 Dihedral : 18.962 163.137 2333 Min Nonbonded Distance : 2.296 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.38 % Favored : 96.62 % Rotamer: Outliers : 3.34 % Allowed : 21.74 % Favored : 74.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.15 (0.27), residues: 1007 helix: 1.47 (0.27), residues: 369 sheet: -0.34 (0.37), residues: 216 loop : -0.83 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.003 TRP B 547 HIS 0.004 0.001 HIS B 465 PHE 0.029 0.002 PHE A 340 TYR 0.019 0.001 TYR A 499 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.04098 ( 431) hydrogen bonds : angle 4.59036 ( 1227) covalent geometry : bond 0.00342 (10209) covalent geometry : angle 0.54917 (14160) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 64 time to evaluate : 1.011 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8623 (OUTLIER) cc_final: 0.8233 (m-30) REVERT: A 301 GLU cc_start: 0.8681 (tt0) cc_final: 0.8231 (tp30) REVERT: A 450 GLU cc_start: 0.8664 (OUTLIER) cc_final: 0.8257 (mp0) REVERT: A 453 GLU cc_start: 0.8080 (OUTLIER) cc_final: 0.7774 (mp0) REVERT: A 499 TYR cc_start: 0.8229 (m-80) cc_final: 0.7996 (m-80) REVERT: B 161 ARG cc_start: 0.8737 (mtm-85) cc_final: 0.8475 (mpp80) REVERT: B 162 ASN cc_start: 0.9175 (m110) cc_final: 0.8727 (m110) REVERT: B 192 LYS cc_start: 0.9118 (ttpp) cc_final: 0.8807 (tmmt) REVERT: B 406 MET cc_start: 0.7044 (pp-130) cc_final: 0.6396 (pp-130) REVERT: B 499 TYR cc_start: 0.8511 (m-10) cc_final: 0.8165 (m-80) outliers start: 30 outliers final: 17 residues processed: 87 average time/residue: 1.2691 time to fit residues: 118.7160 Evaluate side-chains 81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 20 poor density : 61 time to evaluate : 0.974 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 406 MET Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 450 GLU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 87 LEU Chi-restraints excluded: chain B residue 126 LEU Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 272 ASN Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 485 ARG Chi-restraints excluded: chain B residue 490 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 0.8980 chunk 5 optimal weight: 1.9990 chunk 2 optimal weight: 0.7980 chunk 87 optimal weight: 3.9990 chunk 91 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 chunk 98 optimal weight: 0.7980 chunk 65 optimal weight: 3.9990 chunk 76 optimal weight: 0.9990 chunk 22 optimal weight: 0.9980 chunk 71 optimal weight: 2.9990 overall best weight: 0.8982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4007 r_free = 0.4007 target = 0.117417 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3263 r_free = 0.3263 target = 0.073453 restraints weight = 18581.504| |-----------------------------------------------------------------------------| r_work (start): 0.3200 rms_B_bonded: 2.60 r_work: 0.2995 rms_B_bonded: 3.57 restraints_weight: 0.5000 r_work (final): 0.2995 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 10209 Z= 0.132 Angle : 0.558 13.537 14160 Z= 0.273 Chirality : 0.037 0.198 1598 Planarity : 0.004 0.048 1549 Dihedral : 18.909 163.056 2333 Min Nonbonded Distance : 2.285 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.77 % Favored : 96.23 % Rotamer: Outliers : 3.01 % Allowed : 22.41 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.19 (0.27), residues: 1007 helix: 1.51 (0.27), residues: 369 sheet: -0.32 (0.37), residues: 216 loop : -0.83 (0.30), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.003 TRP B 547 HIS 0.004 0.001 HIS A 465 PHE 0.027 0.001 PHE B 340 TYR 0.019 0.001 TYR A 499 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.04034 ( 431) hydrogen bonds : angle 4.55065 ( 1227) covalent geometry : bond 0.00314 (10209) covalent geometry : angle 0.55804 (14160) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 64 time to evaluate : 1.010 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8603 (OUTLIER) cc_final: 0.8206 (m-30) REVERT: A 292 MET cc_start: 0.8365 (ptt) cc_final: 0.8070 (pmt) REVERT: A 301 GLU cc_start: 0.8696 (tt0) cc_final: 0.8260 (tp30) REVERT: A 453 GLU cc_start: 0.8090 (OUTLIER) cc_final: 0.7784 (mp0) REVERT: A 499 TYR cc_start: 0.8223 (m-80) cc_final: 0.7962 (m-80) REVERT: B 161 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8282 (mpp80) REVERT: B 162 ASN cc_start: 0.9196 (m110) cc_final: 0.8816 (m110) REVERT: B 192 LYS cc_start: 0.9149 (ttpp) cc_final: 0.8818 (tmmt) REVERT: B 406 MET cc_start: 0.6992 (pp-130) cc_final: 0.6282 (pp-130) REVERT: B 499 TYR cc_start: 0.8477 (m-10) cc_final: 0.8195 (m-80) outliers start: 27 outliers final: 16 residues processed: 86 average time/residue: 1.2701 time to fit residues: 117.6531 Evaluate side-chains 80 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 62 time to evaluate : 1.031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 274 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 483 THR Chi-restraints excluded: chain A residue 494 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 157 MET Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 601 LYS Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 22 optimal weight: 0.9980 chunk 40 optimal weight: 9.9990 chunk 23 optimal weight: 0.5980 chunk 103 optimal weight: 5.9990 chunk 36 optimal weight: 5.9990 chunk 29 optimal weight: 0.0980 chunk 45 optimal weight: 10.0000 chunk 20 optimal weight: 0.5980 chunk 55 optimal weight: 0.9980 chunk 62 optimal weight: 2.9990 chunk 1 optimal weight: 3.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4014 r_free = 0.4014 target = 0.117188 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3283 r_free = 0.3283 target = 0.073576 restraints weight = 18526.390| |-----------------------------------------------------------------------------| r_work (start): 0.3218 rms_B_bonded: 2.58 r_work: 0.3014 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.3014 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8398 moved from start: 0.1501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 10209 Z= 0.115 Angle : 0.563 13.512 14160 Z= 0.276 Chirality : 0.037 0.199 1598 Planarity : 0.004 0.050 1549 Dihedral : 18.839 162.996 2333 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 2.34 % Allowed : 23.30 % Favored : 74.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.27), residues: 1007 helix: 1.59 (0.27), residues: 369 sheet: -0.17 (0.37), residues: 211 loop : -0.89 (0.30), residues: 427 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.003 TRP B 547 HIS 0.004 0.000 HIS A 465 PHE 0.026 0.001 PHE B 340 TYR 0.020 0.001 TYR A 499 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.03915 ( 431) hydrogen bonds : angle 4.47075 ( 1227) covalent geometry : bond 0.00272 (10209) covalent geometry : angle 0.56340 (14160) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 68 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8590 (OUTLIER) cc_final: 0.8219 (m-30) REVERT: A 292 MET cc_start: 0.8379 (ptt) cc_final: 0.8077 (pmt) REVERT: A 301 GLU cc_start: 0.8678 (tt0) cc_final: 0.8268 (tp30) REVERT: A 453 GLU cc_start: 0.8164 (OUTLIER) cc_final: 0.7891 (mp0) REVERT: A 499 TYR cc_start: 0.8166 (m-80) cc_final: 0.7959 (m-80) REVERT: B 161 ARG cc_start: 0.8716 (mtm-85) cc_final: 0.8267 (mpp80) REVERT: B 162 ASN cc_start: 0.9188 (m110) cc_final: 0.8806 (m110) REVERT: B 192 LYS cc_start: 0.9128 (ttpp) cc_final: 0.8797 (tmmt) REVERT: B 406 MET cc_start: 0.6810 (pp-130) cc_final: 0.6205 (pp-130) REVERT: B 499 TYR cc_start: 0.8410 (m-10) cc_final: 0.8070 (m-80) outliers start: 21 outliers final: 12 residues processed: 84 average time/residue: 1.2920 time to fit residues: 116.6035 Evaluate side-chains 80 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.046 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 447 LEU Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 601 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 93 optimal weight: 0.0870 chunk 94 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 36 optimal weight: 7.9990 chunk 77 optimal weight: 0.0970 chunk 58 optimal weight: 2.9990 chunk 99 optimal weight: 0.6980 chunk 85 optimal weight: 5.9990 chunk 96 optimal weight: 0.9980 overall best weight: 0.7758 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4011 r_free = 0.4011 target = 0.117015 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 55)----------------| | r_work = 0.3280 r_free = 0.3280 target = 0.073366 restraints weight = 18476.964| |-----------------------------------------------------------------------------| r_work (start): 0.3214 rms_B_bonded: 2.59 r_work: 0.3012 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.3012 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8377 moved from start: 0.1521 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 10209 Z= 0.123 Angle : 0.565 13.489 14160 Z= 0.275 Chirality : 0.037 0.309 1598 Planarity : 0.004 0.050 1549 Dihedral : 18.800 162.651 2333 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 7.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.56 % Allowed : 24.19 % Favored : 74.25 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1007 helix: 1.63 (0.27), residues: 369 sheet: -0.09 (0.37), residues: 208 loop : -0.91 (0.30), residues: 430 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.003 TRP A 475 HIS 0.004 0.001 HIS A 465 PHE 0.028 0.001 PHE A 340 TYR 0.018 0.001 TYR A 499 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.03962 ( 431) hydrogen bonds : angle 4.46776 ( 1227) covalent geometry : bond 0.00293 (10209) covalent geometry : angle 0.56479 (14160) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2014 Ramachandran restraints generated. 1007 Oldfield, 0 Emsley, 1007 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 67 time to evaluate : 1.063 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 119 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8207 (m-30) REVERT: A 292 MET cc_start: 0.8378 (ptt) cc_final: 0.8044 (pmt) REVERT: A 301 GLU cc_start: 0.8693 (tt0) cc_final: 0.8260 (tp30) REVERT: A 402 LYS cc_start: 0.9290 (mttp) cc_final: 0.8961 (mtmm) REVERT: A 453 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7770 (mp0) REVERT: B 107 ASP cc_start: 0.8575 (m-30) cc_final: 0.8104 (m-30) REVERT: B 161 ARG cc_start: 0.8727 (mtm-85) cc_final: 0.8426 (mpp80) REVERT: B 162 ASN cc_start: 0.9165 (m110) cc_final: 0.8780 (m110) REVERT: B 192 LYS cc_start: 0.9133 (ttpp) cc_final: 0.8806 (tmmt) REVERT: B 406 MET cc_start: 0.6811 (pp-130) cc_final: 0.6202 (pp-130) REVERT: B 499 TYR cc_start: 0.8415 (m-10) cc_final: 0.8103 (m-80) outliers start: 14 outliers final: 12 residues processed: 78 average time/residue: 1.2773 time to fit residues: 107.2744 Evaluate side-chains 80 residues out of total 897 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 66 time to evaluate : 1.041 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 119 ASP Chi-restraints excluded: chain A residue 153 LYS Chi-restraints excluded: chain A residue 198 ILE Chi-restraints excluded: chain A residue 439 THR Chi-restraints excluded: chain A residue 453 GLU Chi-restraints excluded: chain A residue 512 PHE Chi-restraints excluded: chain B residue 153 LYS Chi-restraints excluded: chain B residue 397 VAL Chi-restraints excluded: chain B residue 411 THR Chi-restraints excluded: chain B residue 447 LEU Chi-restraints excluded: chain B residue 450 GLU Chi-restraints excluded: chain B residue 452 LEU Chi-restraints excluded: chain B residue 490 VAL Chi-restraints excluded: chain B residue 601 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 0.4980 chunk 38 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 80 optimal weight: 1.9990 chunk 59 optimal weight: 1.9990 chunk 39 optimal weight: 0.9980 chunk 5 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 67 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 465 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4012 r_free = 0.4012 target = 0.117062 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3275 r_free = 0.3275 target = 0.073132 restraints weight = 18400.858| |-----------------------------------------------------------------------------| r_work (start): 0.3215 rms_B_bonded: 2.59 r_work: 0.3017 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.3017 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8373 moved from start: 0.1563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 10209 Z= 0.122 Angle : 0.564 13.444 14160 Z= 0.274 Chirality : 0.037 0.289 1598 Planarity : 0.004 0.051 1549 Dihedral : 18.766 162.535 2333 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % Rotamer: Outliers : 1.56 % Allowed : 23.86 % Favored : 74.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.27), residues: 1007 helix: 1.65 (0.27), residues: 369 sheet: -0.16 (0.37), residues: 210 loop : -0.88 (0.30), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.004 TRP A 475 HIS 0.005 0.001 HIS A 465 PHE 0.027 0.001 PHE A 340 TYR 0.010 0.001 TYR A 316 ARG 0.002 0.000 ARG B 247 Details of bonding type rmsd hydrogen bonds : bond 0.03957 ( 431) hydrogen bonds : angle 4.45648 ( 1227) covalent geometry : bond 0.00290 (10209) covalent geometry : angle 0.56365 (14160) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 6277.49 seconds wall clock time: 109 minutes 5.99 seconds (6545.99 seconds total)