Starting phenix.real_space_refine on Thu Mar 13 00:56:40 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkz_60213/03_2025/8zkz_60213.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkz_60213/03_2025/8zkz_60213.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.7 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8zkz_60213/03_2025/8zkz_60213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkz_60213/03_2025/8zkz_60213.map" model { file = "/net/cci-nas-00/data/ceres_data/8zkz_60213/03_2025/8zkz_60213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkz_60213/03_2025/8zkz_60213.cif" } resolution = 2.7 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= 0.003 sd= 0.018 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 87 5.16 5 C 5641 2.51 5 N 1335 2.21 5 O 1425 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 29 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5624/modules/chem_data/mon_lib" Total number of atoms: 8490 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 4186 Number of conformers: 1 Conformer: "" Number of residues, atoms: 541, 4186 Classifications: {'peptide': 541} Incomplete info: {'truncation_to_alanine': 7} Link IDs: {'PTRANS': 33, 'TRANS': 507} Chain breaks: 1 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 35 Unresolved non-hydrogen dihedrals: 27 Planarities with less than four sites: {'GLU:plan': 1, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 19 Chain: "B" Number of atoms: 4190 Number of conformers: 1 Conformer: "" Number of residues, atoms: 539, 4190 Classifications: {'peptide': 539} Incomplete info: {'truncation_to_alanine': 4} Link IDs: {'PTRANS': 33, 'TRANS': 505} Chain breaks: 1 Unresolved non-hydrogen bonds: 10 Unresolved non-hydrogen angles: 11 Unresolved non-hydrogen dihedrals: 9 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Chain: "A" Number of atoms: 50 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 50 Unusual residues: {'PTY': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 64 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 64 Unusual residues: {'NAG': 1, 'PTY': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen dihedrals: 3 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 5.35, per 1000 atoms: 0.63 Number of scatterers: 8490 At special positions: 0 Unit cell: (85.975, 100.446, 117.471, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 87 16.00 P 2 15.00 O 1425 8.00 N 1335 7.00 C 5641 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: 2.25 Conformation dependent library (CDL) restraints added in 958.9 milliseconds 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2016 Finding SS restraints... Secondary structure from input PDB file: 64 helices and 0 sheets defined 82.0% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 33 through 53 removed outlier: 4.035A pdb=" N PHE A 37 " --> pdb=" O CYS A 33 " (cutoff:3.500A) removed outlier: 3.780A pdb=" N TRP A 41 " --> pdb=" O PHE A 37 " (cutoff:3.500A) removed outlier: 7.204A pdb=" N LYS A 42 " --> pdb=" O ALA A 38 " (cutoff:3.500A) removed outlier: 6.395A pdb=" N GLY A 43 " --> pdb=" O ASN A 39 " (cutoff:3.500A) Proline residue: A 50 - end of helix Processing helix chain 'A' and resid 54 through 59 Processing helix chain 'A' and resid 62 through 81 removed outlier: 3.675A pdb=" N ARG A 66 " --> pdb=" O GLY A 62 " (cutoff:3.500A) Processing helix chain 'A' and resid 84 through 89 Processing helix chain 'A' and resid 90 through 100 removed outlier: 4.171A pdb=" N VAL A 94 " --> pdb=" O MET A 90 " (cutoff:3.500A) Proline residue: A 97 - end of helix Processing helix chain 'A' and resid 103 through 111 removed outlier: 3.599A pdb=" N TYR A 111 " --> pdb=" O THR A 107 " (cutoff:3.500A) Processing helix chain 'A' and resid 113 through 132 Processing helix chain 'A' and resid 133 through 147 removed outlier: 3.660A pdb=" N ARG A 137 " --> pdb=" O ASN A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 149 through 166 Processing helix chain 'A' and resid 169 through 191 Proline residue: A 179 - end of helix removed outlier: 3.667A pdb=" N GLN A 191 " --> pdb=" O GLU A 187 " (cutoff:3.500A) Processing helix chain 'A' and resid 220 through 238 Processing helix chain 'A' and resid 239 through 240 No H-bonds generated for 'chain 'A' and resid 239 through 240' Processing helix chain 'A' and resid 241 through 244 Processing helix chain 'A' and resid 245 through 259 removed outlier: 3.872A pdb=" N LEU A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 295 Proline residue: A 277 - end of helix Processing helix chain 'A' and resid 302 through 314 Processing helix chain 'A' and resid 314 through 329 removed outlier: 3.699A pdb=" N LYS A 320 " --> pdb=" O ASP A 316 " (cutoff:3.500A) removed outlier: 3.523A pdb=" N LEU A 329 " --> pdb=" O ARG A 325 " (cutoff:3.500A) Processing helix chain 'A' and resid 333 through 352 Processing helix chain 'A' and resid 360 through 365 removed outlier: 3.845A pdb=" N LEU A 364 " --> pdb=" O GLY A 360 " (cutoff:3.500A) Processing helix chain 'A' and resid 372 through 386 removed outlier: 3.808A pdb=" N THR A 376 " --> pdb=" O ASN A 372 " (cutoff:3.500A) removed outlier: 3.638A pdb=" N PHE A 384 " --> pdb=" O VAL A 380 " (cutoff:3.500A) Processing helix chain 'A' and resid 390 through 396 Processing helix chain 'A' and resid 413 through 421 Processing helix chain 'A' and resid 423 through 443 removed outlier: 4.394A pdb=" N PHE A 427 " --> pdb=" O TRP A 423 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N GLY A 443 " --> pdb=" O SER A 439 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 452 removed outlier: 3.733A pdb=" N LEU A 452 " --> pdb=" O ILE A 448 " (cutoff:3.500A) Processing helix chain 'A' and resid 453 through 458 removed outlier: 3.514A pdb=" N LYS A 456 " --> pdb=" O ILE A 453 " (cutoff:3.500A) removed outlier: 4.058A pdb=" N VAL A 457 " --> pdb=" O GLY A 454 " (cutoff:3.500A) removed outlier: 3.792A pdb=" N LEU A 458 " --> pdb=" O LEU A 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 453 through 458' Processing helix chain 'A' and resid 459 through 475 Processing helix chain 'A' and resid 476 through 478 No H-bonds generated for 'chain 'A' and resid 476 through 478' Processing helix chain 'A' and resid 479 through 499 Proline residue: A 489 - end of helix Processing helix chain 'A' and resid 501 through 513 removed outlier: 4.051A pdb=" N LEU A 505 " --> pdb=" O HIS A 501 " (cutoff:3.500A) Proline residue: A 508 - end of helix Processing helix chain 'A' and resid 523 through 533 removed outlier: 3.516A pdb=" N ALA A 527 " --> pdb=" O THR A 523 " (cutoff:3.500A) Processing helix chain 'A' and resid 536 through 544 Processing helix chain 'A' and resid 544 through 567 removed outlier: 3.568A pdb=" N THR A 548 " --> pdb=" O GLY A 544 " (cutoff:3.500A) removed outlier: 4.126A pdb=" N GLN A 560 " --> pdb=" O PHE A 556 " (cutoff:3.500A) removed outlier: 4.541A pdb=" N LEU A 564 " --> pdb=" O GLN A 560 " (cutoff:3.500A) removed outlier: 3.904A pdb=" N VAL A 565 " --> pdb=" O THR A 561 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 584 Processing helix chain 'B' and resid 33 through 53 removed outlier: 4.167A pdb=" N PHE B 37 " --> pdb=" O CYS B 33 " (cutoff:3.500A) removed outlier: 3.716A pdb=" N ALA B 38 " --> pdb=" O SER B 34 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N TRP B 41 " --> pdb=" O PHE B 37 " (cutoff:3.500A) removed outlier: 6.935A pdb=" N LYS B 42 " --> pdb=" O ALA B 38 " (cutoff:3.500A) removed outlier: 6.337A pdb=" N GLY B 43 " --> pdb=" O ASN B 39 " (cutoff:3.500A) Proline residue: B 50 - end of helix Processing helix chain 'B' and resid 53 through 60 removed outlier: 4.089A pdb=" N MET B 57 " --> pdb=" O CYS B 53 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN B 60 " --> pdb=" O VAL B 56 " (cutoff:3.500A) Processing helix chain 'B' and resid 62 through 81 removed outlier: 3.940A pdb=" N ARG B 66 " --> pdb=" O GLY B 62 " (cutoff:3.500A) Processing helix chain 'B' and resid 84 through 89 Processing helix chain 'B' and resid 90 through 99 removed outlier: 4.012A pdb=" N VAL B 94 " --> pdb=" O MET B 90 " (cutoff:3.500A) Proline residue: B 97 - end of helix Processing helix chain 'B' and resid 103 through 111 removed outlier: 3.662A pdb=" N TYR B 111 " --> pdb=" O THR B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 113 through 131 Processing helix chain 'B' and resid 134 through 146 Processing helix chain 'B' and resid 149 through 166 Processing helix chain 'B' and resid 169 through 192 Proline residue: B 179 - end of helix Processing helix chain 'B' and resid 220 through 239 removed outlier: 3.589A pdb=" N SER B 235 " --> pdb=" O ALA B 231 " (cutoff:3.500A) removed outlier: 3.937A pdb=" N CYS B 239 " --> pdb=" O SER B 235 " (cutoff:3.500A) Processing helix chain 'B' and resid 240 through 244 removed outlier: 7.126A pdb=" N ILE B 243 " --> pdb=" O GLY B 240 " (cutoff:3.500A) Processing helix chain 'B' and resid 245 through 259 removed outlier: 3.848A pdb=" N LEU B 249 " --> pdb=" O THR B 245 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 296 Proline residue: B 277 - end of helix removed outlier: 3.619A pdb=" N GLY B 296 " --> pdb=" O TRP B 292 " (cutoff:3.500A) Processing helix chain 'B' and resid 302 through 313 Processing helix chain 'B' and resid 315 through 327 Processing helix chain 'B' and resid 333 through 352 Processing helix chain 'B' and resid 372 through 386 removed outlier: 4.324A pdb=" N THR B 376 " --> pdb=" O ASN B 372 " (cutoff:3.500A) removed outlier: 3.573A pdb=" N PHE B 384 " --> pdb=" O VAL B 380 " (cutoff:3.500A) Processing helix chain 'B' and resid 390 through 395 removed outlier: 3.817A pdb=" N LEU B 393 " --> pdb=" O TYR B 390 " (cutoff:3.500A) Processing helix chain 'B' and resid 413 through 420 removed outlier: 3.533A pdb=" N ILE B 417 " --> pdb=" O THR B 413 " (cutoff:3.500A) Processing helix chain 'B' and resid 424 through 443 removed outlier: 3.650A pdb=" N GLY B 443 " --> pdb=" O SER B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 452 removed outlier: 3.632A pdb=" N LEU B 447 " --> pdb=" O GLY B 443 " (cutoff:3.500A) Processing helix chain 'B' and resid 453 through 458 removed outlier: 3.565A pdb=" N LYS B 456 " --> pdb=" O ILE B 453 " (cutoff:3.500A) removed outlier: 4.011A pdb=" N VAL B 457 " --> pdb=" O GLY B 454 " (cutoff:3.500A) removed outlier: 3.561A pdb=" N LEU B 458 " --> pdb=" O LEU B 455 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 453 through 458' Processing helix chain 'B' and resid 459 through 476 Processing helix chain 'B' and resid 479 through 498 Proline residue: B 489 - end of helix Processing helix chain 'B' and resid 501 through 513 removed outlier: 3.971A pdb=" N LEU B 505 " --> pdb=" O HIS B 501 " (cutoff:3.500A) Proline residue: B 508 - end of helix Processing helix chain 'B' and resid 523 through 534 Processing helix chain 'B' and resid 536 through 544 Processing helix chain 'B' and resid 544 through 562 removed outlier: 3.795A pdb=" N GLN B 560 " --> pdb=" O PHE B 556 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 567 Processing helix chain 'B' and resid 574 through 584 550 hydrogen bonds defined for protein. 1626 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 2.49 Time building geometry restraints manager: 2.65 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 1318 1.32 - 1.44: 2266 1.44 - 1.57: 4979 1.57 - 1.69: 4 1.69 - 1.81: 145 Bond restraints: 8712 Sorted by residual: bond pdb=" N THR A 405 " pdb=" CA THR A 405 " ideal model delta sigma weight residual 1.459 1.497 -0.038 1.32e-02 5.74e+03 8.49e+00 bond pdb=" N ILE A 123 " pdb=" CA ILE A 123 " ideal model delta sigma weight residual 1.461 1.494 -0.034 1.19e-02 7.06e+03 7.93e+00 bond pdb=" N VAL A 125 " pdb=" CA VAL A 125 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.89e+00 bond pdb=" N VAL B 308 " pdb=" CA VAL B 308 " ideal model delta sigma weight residual 1.461 1.494 -0.033 1.19e-02 7.06e+03 7.77e+00 bond pdb=" N VAL A 129 " pdb=" CA VAL A 129 " ideal model delta sigma weight residual 1.461 1.493 -0.033 1.19e-02 7.06e+03 7.51e+00 ... (remaining 8707 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.87: 11309 1.87 - 3.75: 461 3.75 - 5.62: 60 5.62 - 7.50: 8 7.50 - 9.37: 4 Bond angle restraints: 11842 Sorted by residual: angle pdb=" CA TYR A 282 " pdb=" CB TYR A 282 " pdb=" CG TYR A 282 " ideal model delta sigma weight residual 113.90 122.03 -8.13 1.80e+00 3.09e-01 2.04e+01 angle pdb=" C THR A 250 " pdb=" N PHE A 251 " pdb=" CA PHE A 251 " ideal model delta sigma weight residual 120.68 114.24 6.44 1.70e+00 3.46e-01 1.43e+01 angle pdb=" CA MET A 295 " pdb=" C MET A 295 " pdb=" O MET A 295 " ideal model delta sigma weight residual 121.82 117.63 4.19 1.21e+00 6.83e-01 1.20e+01 angle pdb=" N LEU A 134 " pdb=" CA LEU A 134 " pdb=" C LEU A 134 " ideal model delta sigma weight residual 111.28 107.56 3.72 1.09e+00 8.42e-01 1.17e+01 angle pdb=" C VAL B 281 " pdb=" N TYR B 282 " pdb=" CA TYR B 282 " ideal model delta sigma weight residual 121.14 115.23 5.91 1.75e+00 3.27e-01 1.14e+01 ... (remaining 11837 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 26.22: 5049 26.22 - 52.44: 115 52.44 - 78.65: 10 78.65 - 104.87: 1 104.87 - 131.09: 3 Dihedral angle restraints: 5178 sinusoidal: 2048 harmonic: 3130 Sorted by residual: dihedral pdb=" CA ARG B 371 " pdb=" C ARG B 371 " pdb=" N ASN B 372 " pdb=" CA ASN B 372 " ideal model delta harmonic sigma weight residual 180.00 157.11 22.89 0 5.00e+00 4.00e-02 2.10e+01 dihedral pdb=" CA PHE A 259 " pdb=" C PHE A 259 " pdb=" N LYS A 260 " pdb=" CA LYS A 260 " ideal model delta harmonic sigma weight residual 180.00 158.77 21.23 0 5.00e+00 4.00e-02 1.80e+01 dihedral pdb=" C3 PTY A 601 " pdb=" O11 PTY A 601 " pdb=" P1 PTY A 601 " pdb=" O12 PTY A 601 " ideal model delta sinusoidal sigma weight residual 300.23 169.14 131.09 1 3.00e+01 1.11e-03 1.77e+01 ... (remaining 5175 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 1026 0.053 - 0.105: 257 0.105 - 0.158: 80 0.158 - 0.211: 14 0.211 - 0.263: 5 Chirality restraints: 1382 Sorted by residual: chirality pdb=" CA THR A 397 " pdb=" N THR A 397 " pdb=" C THR A 397 " pdb=" CB THR A 397 " both_signs ideal model delta sigma weight residual False 2.53 2.26 0.26 2.00e-01 2.50e+01 1.74e+00 chirality pdb=" CA TYR A 395 " pdb=" N TYR A 395 " pdb=" C TYR A 395 " pdb=" CB TYR A 395 " both_signs ideal model delta sigma weight residual False 2.51 2.76 -0.25 2.00e-01 2.50e+01 1.62e+00 chirality pdb=" CB THR A 405 " pdb=" CA THR A 405 " pdb=" OG1 THR A 405 " pdb=" CG2 THR A 405 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.45e+00 ... (remaining 1379 not shown) Planarity restraints: 1442 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C2 NAG B 602 " 0.327 2.00e-02 2.50e+03 2.82e-01 9.94e+02 pdb=" C7 NAG B 602 " -0.073 2.00e-02 2.50e+03 pdb=" C8 NAG B 602 " 0.031 2.00e-02 2.50e+03 pdb=" N2 NAG B 602 " -0.492 2.00e-02 2.50e+03 pdb=" O7 NAG B 602 " 0.207 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C LEU A 386 " 0.052 5.00e-02 4.00e+02 7.85e-02 9.85e+00 pdb=" N PRO A 387 " -0.136 5.00e-02 4.00e+02 pdb=" CA PRO A 387 " 0.042 5.00e-02 4.00e+02 pdb=" CD PRO A 387 " 0.042 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA PRO A 387 " -0.013 2.00e-02 2.50e+03 2.53e-02 6.42e+00 pdb=" C PRO A 387 " 0.044 2.00e-02 2.50e+03 pdb=" O PRO A 387 " -0.017 2.00e-02 2.50e+03 pdb=" N ALA A 388 " -0.014 2.00e-02 2.50e+03 ... (remaining 1439 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 55 2.67 - 3.22: 8368 3.22 - 3.78: 12490 3.78 - 4.34: 16651 4.34 - 4.90: 28240 Nonbonded interactions: 65804 Sorted by model distance: nonbonded pdb=" OD1 ASP B 114 " pdb=" OG SER B 373 " model vdw 2.107 3.040 nonbonded pdb=" OH TYR A 350 " pdb=" OG1 THR A 376 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASP B 316 " pdb=" N VAL B 317 " model vdw 2.336 3.120 nonbonded pdb=" O LYS A 260 " pdb=" OH TYR A 580 " model vdw 2.359 3.040 nonbonded pdb=" OG SER A 410 " pdb=" N1 PTY A 601 " model vdw 2.412 3.120 ... (remaining 65799 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 32 through 147 or (resid 148 and (name N or name CA or nam \ e C or name O or name CB )) or resid 149 through 200 or (resid 213 and (name N o \ r name CA or name C or name O or name CB )) or resid 216 through 584 or resid 60 \ 1)) selection = (chain 'B' and (resid 32 through 298 or (resid 299 and (name N or name CA or nam \ e C or name O or name CB )) or resid 300 through 302 or (resid 303 through 305 a \ nd (name N or name CA or name C or name O or name CB )) or resid 306 through 397 \ or (resid 398 through 399 and (name N or name CA or name C or name O or name CB \ )) or resid 400 through 584 or resid 601)) } 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: 111.150 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.070 Process input model: 22.340 Find NCS groups from input model: 0.410 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:12.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 147.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8667 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 : 0.008 0.047 8712 Z= 0.511 Angle : 0.824 9.370 11842 Z= 0.512 Chirality : 0.054 0.263 1382 Planarity : 0.009 0.282 1442 Dihedral : 11.981 131.090 3162 Min Nonbonded Distance : 2.107 Molprobity Statistics. All-atom Clashscore : 3.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.22 % Allowed : 0.33 % Favored : 99.45 % 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: 1.23 (0.26), residues: 1072 helix: 1.59 (0.18), residues: 775 sheet: None (None), residues: 0 loop : -1.26 (0.35), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 576 HIS 0.015 0.002 HIS B 335 PHE 0.028 0.002 PHE B 251 TYR 0.028 0.002 TYR A 282 ARG 0.006 0.001 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 78 time to evaluate : 0.894 Fit side-chains REVERT: A 323 ASP cc_start: 0.8647 (p0) cc_final: 0.8411 (p0) outliers start: 2 outliers final: 1 residues processed: 79 average time/residue: 1.2693 time to fit residues: 107.0339 Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 1.009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 6.9990 chunk 81 optimal weight: 0.8980 chunk 45 optimal weight: 0.9990 chunk 27 optimal weight: 6.9990 chunk 54 optimal weight: 4.9990 chunk 43 optimal weight: 0.0270 chunk 83 optimal weight: 0.7980 chunk 32 optimal weight: 8.9990 chunk 50 optimal weight: 1.9990 chunk 62 optimal weight: 0.9980 chunk 97 optimal weight: 1.9990 overall best weight: 0.7440 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 306 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067795 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2758 r_free = 0.2758 target = 0.050253 restraints weight = 22868.265| |-----------------------------------------------------------------------------| r_work (start): 0.2732 rms_B_bonded: 2.86 r_work: 0.2608 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 8712 Z= 0.172 Angle : 0.567 7.003 11842 Z= 0.303 Chirality : 0.041 0.164 1382 Planarity : 0.005 0.048 1442 Dihedral : 8.520 102.488 1251 Min Nonbonded Distance : 2.546 Molprobity Statistics. All-atom Clashscore : 3.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.55 % Allowed : 5.30 % Favored : 94.14 % 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: 1.45 (0.26), residues: 1072 helix: 1.73 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -1.31 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 562 HIS 0.008 0.001 HIS B 335 PHE 0.037 0.001 PHE A 251 TYR 0.028 0.001 TYR B 282 ARG 0.003 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 73 time to evaluate : 0.975 Fit side-chains REVERT: A 323 ASP cc_start: 0.8815 (p0) cc_final: 0.8518 (p0) outliers start: 5 outliers final: 1 residues processed: 74 average time/residue: 1.6111 time to fit residues: 127.1482 Evaluate side-chains 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 72 time to evaluate : 0.931 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 403 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 90 optimal weight: 5.9990 chunk 98 optimal weight: 4.9990 chunk 28 optimal weight: 0.0770 chunk 79 optimal weight: 6.9990 chunk 82 optimal weight: 4.9990 chunk 8 optimal weight: 4.9990 chunk 96 optimal weight: 1.9990 chunk 77 optimal weight: 0.7980 chunk 20 optimal weight: 7.9990 chunk 13 optimal weight: 0.5980 chunk 69 optimal weight: 2.9990 overall best weight: 1.2942 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3143 r_free = 0.3143 target = 0.067671 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.050179 restraints weight = 23276.715| |-----------------------------------------------------------------------------| r_work (start): 0.2737 rms_B_bonded: 2.90 r_work: 0.2613 rms_B_bonded: 3.49 restraints_weight: 0.5000 r_work (final): 0.2613 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1378 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8712 Z= 0.182 Angle : 0.527 6.620 11842 Z= 0.280 Chirality : 0.040 0.171 1382 Planarity : 0.005 0.045 1442 Dihedral : 7.960 94.121 1251 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.77 % Allowed : 7.29 % Favored : 91.93 % 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: 1.63 (0.26), residues: 1072 helix: 1.89 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -1.34 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 414 HIS 0.006 0.001 HIS B 335 PHE 0.031 0.001 PHE A 251 TYR 0.026 0.001 TYR B 282 ARG 0.001 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.918 Fit side-chains REVERT: A 323 ASP cc_start: 0.8786 (p0) cc_final: 0.8478 (p0) outliers start: 7 outliers final: 1 residues processed: 71 average time/residue: 1.4180 time to fit residues: 107.1189 Evaluate side-chains 71 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 70 time to evaluate : 0.944 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 166 MET Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 96 optimal weight: 0.9980 chunk 40 optimal weight: 0.9990 chunk 52 optimal weight: 0.0670 chunk 101 optimal weight: 0.0970 chunk 94 optimal weight: 5.9990 chunk 17 optimal weight: 0.0040 chunk 103 optimal weight: 5.9990 chunk 79 optimal weight: 6.9990 chunk 106 optimal weight: 5.9990 chunk 6 optimal weight: 4.9990 chunk 102 optimal weight: 2.9990 overall best weight: 0.4330 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 534 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3197 r_free = 0.3197 target = 0.070495 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 31)----------------| | r_work = 0.2826 r_free = 0.2826 target = 0.053116 restraints weight = 22683.159| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 2.87 r_work: 0.2680 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2680 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.1864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 8712 Z= 0.132 Angle : 0.491 5.639 11842 Z= 0.258 Chirality : 0.039 0.155 1382 Planarity : 0.005 0.047 1442 Dihedral : 7.459 80.375 1250 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.66 % Allowed : 8.07 % Favored : 91.27 % 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: 1.90 (0.26), residues: 1072 helix: 2.09 (0.18), residues: 783 sheet: None (None), residues: 0 loop : -1.11 (0.36), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 292 HIS 0.005 0.001 HIS A 335 PHE 0.027 0.001 PHE A 251 TYR 0.026 0.001 TYR B 282 ARG 0.001 0.000 ARG B 399 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 76 time to evaluate : 0.871 Fit side-chains REVERT: A 323 ASP cc_start: 0.8774 (p0) cc_final: 0.8444 (p0) outliers start: 6 outliers final: 1 residues processed: 78 average time/residue: 1.2895 time to fit residues: 107.4720 Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 0.991 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 49 optimal weight: 5.9990 chunk 58 optimal weight: 0.8980 chunk 85 optimal weight: 1.9990 chunk 96 optimal weight: 2.9990 chunk 94 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 100 optimal weight: 1.9990 chunk 16 optimal weight: 4.9990 chunk 7 optimal weight: 2.9990 chunk 74 optimal weight: 0.7980 chunk 15 optimal weight: 2.9990 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3146 r_free = 0.3146 target = 0.067783 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.2757 r_free = 0.2757 target = 0.050195 restraints weight = 22936.916| |-----------------------------------------------------------------------------| r_work (start): 0.2733 rms_B_bonded: 2.88 r_work: 0.2608 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2608 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8535 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 8712 Z= 0.205 Angle : 0.522 6.196 11842 Z= 0.274 Chirality : 0.040 0.171 1382 Planarity : 0.004 0.045 1442 Dihedral : 7.364 77.638 1250 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.77 % Allowed : 9.17 % Favored : 90.06 % 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: 1.92 (0.26), residues: 1072 helix: 2.13 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -1.34 (0.36), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 414 HIS 0.006 0.001 HIS B 335 PHE 0.025 0.001 PHE A 251 TYR 0.024 0.001 TYR A 282 ARG 0.004 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 71 time to evaluate : 0.977 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8752 (p0) cc_final: 0.8416 (p0) outliers start: 7 outliers final: 2 residues processed: 76 average time/residue: 1.4057 time to fit residues: 114.5893 Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 1.002 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 220 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 72 optimal weight: 0.9990 chunk 87 optimal weight: 0.7980 chunk 34 optimal weight: 0.7980 chunk 103 optimal weight: 8.9990 chunk 50 optimal weight: 0.9980 chunk 6 optimal weight: 0.0570 chunk 57 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 11 optimal weight: 0.5980 chunk 60 optimal weight: 4.9990 chunk 95 optimal weight: 0.0070 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3203 r_free = 0.3203 target = 0.070720 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2831 r_free = 0.2831 target = 0.053287 restraints weight = 22609.703| |-----------------------------------------------------------------------------| r_work (start): 0.2805 rms_B_bonded: 2.89 r_work: 0.2684 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2684 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8467 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 8712 Z= 0.129 Angle : 0.486 7.283 11842 Z= 0.253 Chirality : 0.038 0.156 1382 Planarity : 0.004 0.047 1442 Dihedral : 7.078 77.475 1250 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 4.39 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.66 % Allowed : 9.83 % Favored : 89.50 % 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: 2.09 (0.26), residues: 1072 helix: 2.26 (0.18), residues: 779 sheet: None (None), residues: 0 loop : -1.08 (0.37), residues: 293 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 562 HIS 0.004 0.001 HIS B 335 PHE 0.021 0.001 PHE A 251 TYR 0.024 0.001 TYR B 282 ARG 0.003 0.000 ARG B 353 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.908 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8711 (p0) cc_final: 0.8368 (p0) outliers start: 6 outliers final: 2 residues processed: 77 average time/residue: 1.3929 time to fit residues: 114.4259 Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 220 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 1 optimal weight: 4.9990 chunk 29 optimal weight: 2.9990 chunk 51 optimal weight: 3.9990 chunk 70 optimal weight: 5.9990 chunk 88 optimal weight: 0.9990 chunk 106 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 84 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 11 optimal weight: 5.9990 overall best weight: 2.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.066571 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2727 r_free = 0.2727 target = 0.048898 restraints weight = 23062.167| |-----------------------------------------------------------------------------| r_work (start): 0.2704 rms_B_bonded: 2.89 r_work: 0.2577 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2577 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8571 moved from start: 0.1737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 8712 Z= 0.254 Angle : 0.553 8.631 11842 Z= 0.289 Chirality : 0.041 0.179 1382 Planarity : 0.004 0.045 1442 Dihedral : 7.222 76.373 1250 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.77 % Allowed : 10.39 % Favored : 88.84 % 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: 2.02 (0.26), residues: 1072 helix: 2.17 (0.19), residues: 798 sheet: None (None), residues: 0 loop : -1.24 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 414 HIS 0.006 0.001 HIS A 335 PHE 0.024 0.001 PHE B 251 TYR 0.024 0.001 TYR A 282 ARG 0.002 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.929 Fit side-chains REVERT: A 323 ASP cc_start: 0.8740 (p0) cc_final: 0.8412 (p0) REVERT: B 166 MET cc_start: 0.8721 (OUTLIER) cc_final: 0.8456 (ttm) outliers start: 7 outliers final: 3 residues processed: 72 average time/residue: 1.4083 time to fit residues: 108.0560 Evaluate side-chains 74 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 70 time to evaluate : 1.005 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 328 ASP Chi-restraints excluded: chain B residue 166 MET Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 39 optimal weight: 2.9990 chunk 63 optimal weight: 5.9990 chunk 25 optimal weight: 6.9990 chunk 53 optimal weight: 2.9990 chunk 43 optimal weight: 0.9980 chunk 92 optimal weight: 4.9990 chunk 54 optimal weight: 4.9990 chunk 93 optimal weight: 1.9990 chunk 60 optimal weight: 0.9990 chunk 62 optimal weight: 0.8980 chunk 90 optimal weight: 0.2980 overall best weight: 1.0384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.068176 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2766 r_free = 0.2766 target = 0.050553 restraints weight = 23226.244| |-----------------------------------------------------------------------------| r_work (start): 0.2742 rms_B_bonded: 2.92 r_work: 0.2618 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2618 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8532 moved from start: 0.1901 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 8712 Z= 0.159 Angle : 0.519 12.552 11842 Z= 0.270 Chirality : 0.039 0.168 1382 Planarity : 0.004 0.044 1442 Dihedral : 7.151 76.883 1250 Min Nonbonded Distance : 2.533 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.77 % Allowed : 10.94 % Favored : 88.29 % 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: 2.03 (0.26), residues: 1072 helix: 2.17 (0.18), residues: 798 sheet: None (None), residues: 0 loop : -1.22 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 414 HIS 0.004 0.001 HIS B 335 PHE 0.022 0.001 PHE B 251 TYR 0.022 0.001 TYR B 282 ARG 0.001 0.000 ARG A 66 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 70 time to evaluate : 0.931 Fit side-chains REVERT: A 323 ASP cc_start: 0.8749 (p0) cc_final: 0.8416 (p0) outliers start: 7 outliers final: 2 residues processed: 73 average time/residue: 1.3462 time to fit residues: 104.8577 Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 70 time to evaluate : 0.950 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 220 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 40 optimal weight: 4.9990 chunk 14 optimal weight: 0.8980 chunk 46 optimal weight: 1.9990 chunk 20 optimal weight: 6.9990 chunk 91 optimal weight: 0.6980 chunk 43 optimal weight: 2.9990 chunk 96 optimal weight: 2.9990 chunk 98 optimal weight: 1.9990 chunk 54 optimal weight: 0.3980 chunk 0 optimal weight: 10.0000 chunk 105 optimal weight: 0.2980 overall best weight: 0.8582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3179 r_free = 0.3179 target = 0.069442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2795 r_free = 0.2795 target = 0.051818 restraints weight = 22979.467| |-----------------------------------------------------------------------------| r_work (start): 0.2770 rms_B_bonded: 2.92 r_work: 0.2648 rms_B_bonded: 3.53 restraints_weight: 0.5000 r_work (final): 0.2648 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8505 moved from start: 0.2066 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 8712 Z= 0.149 Angle : 0.514 13.640 11842 Z= 0.265 Chirality : 0.038 0.160 1382 Planarity : 0.004 0.044 1442 Dihedral : 6.993 77.950 1250 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.88 % Allowed : 10.94 % Favored : 88.18 % 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: 2.14 (0.26), residues: 1072 helix: 2.26 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.04 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.005 0.001 HIS A 335 PHE 0.020 0.001 PHE B 251 TYR 0.024 0.001 TYR B 282 ARG 0.001 0.000 ARG A 353 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 71 time to evaluate : 0.987 Fit side-chains REVERT: A 323 ASP cc_start: 0.8716 (p0) cc_final: 0.8383 (OUTLIER) REVERT: B 166 MET cc_start: 0.8683 (ttt) cc_final: 0.8474 (ttm) outliers start: 8 outliers final: 4 residues processed: 74 average time/residue: 1.3280 time to fit residues: 104.9349 Evaluate side-chains 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.966 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 114 ASP Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 220 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 0 optimal weight: 10.0000 chunk 1 optimal weight: 0.9980 chunk 4 optimal weight: 0.9980 chunk 26 optimal weight: 6.9990 chunk 79 optimal weight: 0.7980 chunk 32 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 13 optimal weight: 7.9990 chunk 48 optimal weight: 2.9990 chunk 56 optimal weight: 2.9990 chunk 103 optimal weight: 4.9990 overall best weight: 1.1584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3175 r_free = 0.3175 target = 0.069195 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2792 r_free = 0.2792 target = 0.051625 restraints weight = 22775.800| |-----------------------------------------------------------------------------| r_work (start): 0.2772 rms_B_bonded: 2.87 r_work: 0.2652 rms_B_bonded: 3.47 restraints_weight: 0.5000 r_work (final): 0.2652 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8497 moved from start: 0.2083 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 8712 Z= 0.166 Angle : 0.521 13.021 11842 Z= 0.268 Chirality : 0.039 0.163 1382 Planarity : 0.004 0.044 1442 Dihedral : 6.973 78.364 1250 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 4.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.33 % Allowed : 11.49 % Favored : 88.18 % 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: 2.13 (0.26), residues: 1072 helix: 2.26 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.05 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 414 HIS 0.005 0.001 HIS A 335 PHE 0.021 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG A 66 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2144 Ramachandran restraints generated. 1072 Oldfield, 0 Emsley, 1072 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 1.868 Fit side-chains REVERT: A 323 ASP cc_start: 0.8718 (p0) cc_final: 0.8388 (OUTLIER) REVERT: B 166 MET cc_start: 0.8677 (ttt) cc_final: 0.8463 (ttm) outliers start: 3 outliers final: 4 residues processed: 72 average time/residue: 1.6504 time to fit residues: 126.7171 Evaluate side-chains 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 70 time to evaluate : 0.956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 328 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 85 optimal weight: 0.0070 chunk 28 optimal weight: 2.9990 chunk 34 optimal weight: 3.9990 chunk 78 optimal weight: 2.9990 chunk 64 optimal weight: 6.9990 chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 52 optimal weight: 8.9990 chunk 2 optimal weight: 2.9990 chunk 86 optimal weight: 5.9990 chunk 105 optimal weight: 0.7980 overall best weight: 1.3802 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3168 r_free = 0.3168 target = 0.068785 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.051125 restraints weight = 23171.255| |-----------------------------------------------------------------------------| r_work (start): 0.2755 rms_B_bonded: 2.90 r_work: 0.2633 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2633 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8522 moved from start: 0.2065 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 8712 Z= 0.178 Angle : 0.518 13.011 11842 Z= 0.267 Chirality : 0.039 0.165 1382 Planarity : 0.004 0.045 1442 Dihedral : 6.958 78.578 1250 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.05 % Favored : 97.95 % Rotamer: Outliers : 0.55 % Allowed : 11.38 % Favored : 88.07 % 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: 2.17 (0.26), residues: 1072 helix: 2.24 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -0.96 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 414 HIS 0.005 0.001 HIS A 335 PHE 0.021 0.001 PHE B 251 TYR 0.023 0.001 TYR B 282 ARG 0.001 0.000 ARG A 325 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 5288.44 seconds wall clock time: 94 minutes 15.84 seconds (5655.84 seconds total)