Starting phenix.real_space_refine on Wed Sep 17 11:44:41 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8zkz_60213/09_2025/8zkz_60213.cif Found real_map, /net/cci-nas-00/data/ceres_data/8zkz_60213/09_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 { model { file = "/net/cci-nas-00/data/ceres_data/8zkz_60213/09_2025/8zkz_60213.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8zkz_60213/09_2025/8zkz_60213.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/8zkz_60213/09_2025/8zkz_60213.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8zkz_60213/09_2025/8zkz_60213.map" } resolution = 2.7 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.003 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): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-2.0-5805/lib/python3.9/site-packages/chem_data/mon_lib" Total number of atoms: 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: {'ARG:plan': 3, 'GLU:plan': 1} 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: 2.01, per 1000 atoms: 0.24 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: 0.56 Conformation dependent library (CDL) restraints added in 274.2 milliseconds Enol-peptide restraints added in 476.8 nanoseconds 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: 0.26 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: 0.85 Time building geometry restraints manager: 0.73 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 601)) 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 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: 1.030 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: 0.000 Extract box with map and model: 0.150 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 7.910 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.010 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:6.070 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 15.330 ------------------------------------------------------------------------------- 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= 0.402 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.23 (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 ARG 0.006 0.001 ARG A 66 TYR 0.028 0.002 TYR A 282 PHE 0.028 0.002 PHE B 251 TRP 0.012 0.001 TRP B 576 HIS 0.015 0.002 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00777 ( 8712) covalent geometry : angle 0.82431 (11842) hydrogen bonds : bond 0.16324 ( 550) hydrogen bonds : angle 5.22768 ( 1626) *********************** 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 : 0.229 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: 0.6349 time to fit residues: 53.1085 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 : 0.345 ------------------------------------------------------------------------------- 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 49 optimal weight: 2.9990 chunk 97 optimal weight: 1.9990 chunk 53 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 chunk 33 optimal weight: 0.0980 chunk 65 optimal weight: 3.9990 chunk 62 optimal weight: 0.9980 chunk 51 optimal weight: 1.9990 chunk 100 optimal weight: 0.8980 chunk 106 optimal weight: 10.0000 chunk 38 optimal weight: 0.9980 overall best weight: 0.9982 ------------------------------------------------------------------------------- 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 = 0.3128 r_free = 0.3128 target = 0.066877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2735 r_free = 0.2735 target = 0.049289 restraints weight = 23121.845| |-----------------------------------------------------------------------------| r_work (start): 0.2715 rms_B_bonded: 2.89 r_work: 0.2589 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2589 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8552 moved from start: 0.1041 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 8712 Z= 0.139 Angle : 0.570 7.248 11842 Z= 0.307 Chirality : 0.041 0.169 1382 Planarity : 0.005 0.049 1442 Dihedral : 8.628 105.588 1251 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 3.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.55 % Allowed : 5.41 % Favored : 94.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.48 (0.26), residues: 1072 helix: 1.76 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -1.33 (0.37), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 399 TYR 0.028 0.001 TYR B 282 PHE 0.036 0.001 PHE A 251 TRP 0.010 0.001 TRP A 414 HIS 0.008 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00279 ( 8712) covalent geometry : angle 0.56989 (11842) hydrogen bonds : bond 0.05700 ( 550) hydrogen bonds : angle 4.15573 ( 1626) *********************** 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 77 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.392 Fit side-chains REVERT: A 323 ASP cc_start: 0.8807 (p0) cc_final: 0.8525 (p0) outliers start: 5 outliers final: 1 residues processed: 73 average time/residue: 0.6557 time to fit residues: 51.0491 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 : 0.331 ------------------------------------------------------------------------------- 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 91 optimal weight: 1.9990 chunk 56 optimal weight: 0.9990 chunk 69 optimal weight: 0.6980 chunk 18 optimal weight: 7.9990 chunk 83 optimal weight: 0.9990 chunk 64 optimal weight: 4.9990 chunk 49 optimal weight: 1.9990 chunk 10 optimal weight: 5.9990 chunk 77 optimal weight: 1.9990 chunk 30 optimal weight: 0.9990 chunk 104 optimal weight: 0.9990 overall best weight: 0.9388 ------------------------------------------------------------------------------- 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 = 0.3167 r_free = 0.3167 target = 0.068928 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.2787 r_free = 0.2787 target = 0.051471 restraints weight = 22769.634| |-----------------------------------------------------------------------------| r_work (start): 0.2764 rms_B_bonded: 2.87 r_work: 0.2642 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2642 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8506 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 : 0.002 0.030 8712 Z= 0.116 Angle : 0.516 6.157 11842 Z= 0.272 Chirality : 0.040 0.166 1382 Planarity : 0.005 0.046 1442 Dihedral : 7.775 88.454 1251 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.77 % Favored : 98.23 % Rotamer: Outliers : 0.88 % Allowed : 6.96 % Favored : 92.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.73 (0.26), residues: 1072 helix: 1.96 (0.18), residues: 794 sheet: None (None), residues: 0 loop : -1.30 (0.37), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG B 399 TYR 0.028 0.001 TYR B 282 PHE 0.031 0.001 PHE A 251 TRP 0.009 0.001 TRP A 414 HIS 0.007 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00244 ( 8712) covalent geometry : angle 0.51551 (11842) hydrogen bonds : bond 0.04413 ( 550) hydrogen bonds : angle 3.86164 ( 1626) *********************** 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 82 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 74 time to evaluate : 0.361 Fit side-chains REVERT: A 323 ASP cc_start: 0.8775 (p0) cc_final: 0.8463 (p0) outliers start: 8 outliers final: 2 residues processed: 75 average time/residue: 0.6236 time to fit residues: 49.9097 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 : 0.339 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 220 THR Chi-restraints excluded: chain A residue 316 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 21 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 57 optimal weight: 0.8980 chunk 4 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 88 optimal weight: 5.9990 chunk 16 optimal weight: 7.9990 chunk 80 optimal weight: 10.0000 chunk 70 optimal weight: 0.8980 chunk 36 optimal weight: 6.9990 chunk 63 optimal weight: 6.9990 overall best weight: 2.7586 ------------------------------------------------------------------------------- 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 = 0.3109 r_free = 0.3109 target = 0.065814 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2712 r_free = 0.2712 target = 0.048222 restraints weight = 23760.459| |-----------------------------------------------------------------------------| r_work (start): 0.2694 rms_B_bonded: 2.89 r_work: 0.2570 rms_B_bonded: 3.46 restraints_weight: 0.5000 r_work (final): 0.2570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8565 moved from start: 0.1404 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 8712 Z= 0.182 Angle : 0.563 6.847 11842 Z= 0.298 Chirality : 0.041 0.182 1382 Planarity : 0.005 0.047 1442 Dihedral : 7.891 81.943 1250 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 3.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.24 % Favored : 97.76 % Rotamer: Outliers : 0.55 % Allowed : 8.51 % Favored : 90.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.76 (0.26), residues: 1072 helix: 2.02 (0.18), residues: 793 sheet: None (None), residues: 0 loop : -1.39 (0.36), residues: 279 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.003 0.000 ARG A 66 TYR 0.024 0.001 TYR B 282 PHE 0.029 0.001 PHE A 251 TRP 0.012 0.001 TRP A 414 HIS 0.008 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00441 ( 8712) covalent geometry : angle 0.56289 (11842) hydrogen bonds : bond 0.05627 ( 550) hydrogen bonds : angle 3.95986 ( 1626) *********************** 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 76 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 71 time to evaluate : 0.378 Fit side-chains REVERT: A 323 ASP cc_start: 0.8767 (p0) cc_final: 0.8462 (p0) REVERT: B 68 MET cc_start: 0.9246 (OUTLIER) cc_final: 0.8830 (ttm) outliers start: 5 outliers final: 1 residues processed: 72 average time/residue: 0.6490 time to fit residues: 49.7402 Evaluate side-chains 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.349 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 316 ASP Chi-restraints excluded: chain B residue 68 MET Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 20 optimal weight: 1.9990 chunk 63 optimal weight: 5.9990 chunk 104 optimal weight: 0.9990 chunk 95 optimal weight: 0.2980 chunk 4 optimal weight: 1.9990 chunk 73 optimal weight: 8.9990 chunk 8 optimal weight: 0.8980 chunk 13 optimal weight: 6.9990 chunk 77 optimal weight: 1.9990 chunk 79 optimal weight: 0.5980 chunk 97 optimal weight: 0.8980 overall best weight: 0.7382 ------------------------------------------------------------------------------- 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 = 0.3161 r_free = 0.3161 target = 0.068607 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2776 r_free = 0.2776 target = 0.051078 restraints weight = 23152.898| |-----------------------------------------------------------------------------| r_work (start): 0.2751 rms_B_bonded: 2.90 r_work: 0.2627 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2627 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8516 moved from start: 0.1736 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= 0.109 Angle : 0.505 6.160 11842 Z= 0.266 Chirality : 0.039 0.164 1382 Planarity : 0.004 0.044 1442 Dihedral : 7.625 78.746 1250 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.59 % Favored : 98.41 % Rotamer: Outliers : 0.66 % Allowed : 9.28 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 1.84 (0.26), residues: 1072 helix: 2.08 (0.18), residues: 792 sheet: None (None), residues: 0 loop : -1.37 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG B 137 TYR 0.024 0.001 TYR B 282 PHE 0.025 0.001 PHE A 251 TRP 0.008 0.001 TRP A 414 HIS 0.004 0.001 HIS B 335 Details of bonding type rmsd covalent geometry : bond 0.00220 ( 8712) covalent geometry : angle 0.50524 (11842) hydrogen bonds : bond 0.04222 ( 550) hydrogen bonds : angle 3.75558 ( 1626) *********************** 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 79 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 73 time to evaluate : 0.343 Fit side-chains revert: symmetry clash REVERT: A 323 ASP cc_start: 0.8764 (p0) cc_final: 0.8445 (p0) outliers start: 6 outliers final: 1 residues processed: 77 average time/residue: 0.6341 time to fit residues: 52.1058 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 : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 22 optimal weight: 0.9980 chunk 74 optimal weight: 0.9990 chunk 93 optimal weight: 6.9990 chunk 31 optimal weight: 0.9980 chunk 57 optimal weight: 0.9980 chunk 47 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 58 optimal weight: 0.6980 chunk 98 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 55 optimal weight: 0.8980 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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 = 0.3163 r_free = 0.3163 target = 0.068715 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2780 r_free = 0.2780 target = 0.051204 restraints weight = 23110.683| |-----------------------------------------------------------------------------| r_work (start): 0.2752 rms_B_bonded: 2.88 r_work: 0.2630 rms_B_bonded: 3.50 restraints_weight: 0.5000 r_work (final): 0.2630 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8518 moved from start: 0.1843 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= 0.112 Angle : 0.510 8.242 11842 Z= 0.268 Chirality : 0.039 0.166 1382 Planarity : 0.004 0.044 1442 Dihedral : 7.456 77.986 1250 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 3.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.55 % Allowed : 10.17 % Favored : 89.28 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.01 (0.26), residues: 1072 helix: 2.19 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.16 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 66 TYR 0.024 0.001 TYR B 282 PHE 0.023 0.001 PHE A 251 TRP 0.008 0.001 TRP A 414 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00236 ( 8712) covalent geometry : angle 0.50974 (11842) hydrogen bonds : bond 0.04153 ( 550) hydrogen bonds : angle 3.70232 ( 1626) *********************** 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 77 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 72 time to evaluate : 0.328 Fit side-chains REVERT: A 323 ASP cc_start: 0.8755 (p0) cc_final: 0.8430 (p0) outliers start: 5 outliers final: 1 residues processed: 73 average time/residue: 0.6551 time to fit residues: 50.9512 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 : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 42 optimal weight: 5.9990 chunk 70 optimal weight: 0.0870 chunk 64 optimal weight: 7.9990 chunk 85 optimal weight: 0.1980 chunk 61 optimal weight: 5.9990 chunk 33 optimal weight: 0.6980 chunk 56 optimal weight: 0.8980 chunk 20 optimal weight: 6.9990 chunk 49 optimal weight: 0.7980 chunk 59 optimal weight: 7.9990 chunk 91 optimal weight: 1.9990 overall best weight: 0.5358 ------------------------------------------------------------------------------- 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 = 0.3198 r_free = 0.3198 target = 0.070486 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.053008 restraints weight = 23171.088| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 2.92 r_work: 0.2679 rms_B_bonded: 3.54 restraints_weight: 0.5000 r_work (final): 0.2679 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8474 moved from start: 0.2105 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= 0.102 Angle : 0.504 12.246 11842 Z= 0.260 Chirality : 0.038 0.158 1382 Planarity : 0.004 0.045 1442 Dihedral : 7.116 77.626 1250 Min Nonbonded Distance : 2.535 Molprobity Statistics. All-atom Clashscore : 4.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.66 % Allowed : 11.05 % 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 values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.10 (0.26), residues: 1072 helix: 2.25 (0.18), residues: 782 sheet: None (None), residues: 0 loop : -1.06 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.001 0.000 ARG A 353 TYR 0.025 0.001 TYR B 282 PHE 0.019 0.001 PHE A 251 TRP 0.006 0.001 TRP A 414 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00207 ( 8712) covalent geometry : angle 0.50413 (11842) hydrogen bonds : bond 0.03580 ( 550) hydrogen bonds : angle 3.59705 ( 1626) *********************** 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 81 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 0.342 Fit side-chains REVERT: A 323 ASP cc_start: 0.8707 (p0) cc_final: 0.8386 (p0) REVERT: A 340 MET cc_start: 0.8966 (ttm) cc_final: 0.8721 (ptt) outliers start: 6 outliers final: 3 residues processed: 78 average time/residue: 0.6042 time to fit residues: 50.3791 Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.345 ------------------------------------------------------------------------------- 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 70 optimal weight: 3.9990 chunk 103 optimal weight: 8.9990 chunk 102 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 25 optimal weight: 3.9990 chunk 22 optimal weight: 0.7980 chunk 43 optimal weight: 6.9990 chunk 24 optimal weight: 0.9990 chunk 34 optimal weight: 0.8980 chunk 68 optimal weight: 20.0000 chunk 4 optimal weight: 0.9990 overall best weight: 0.9386 ------------------------------------------------------------------------------- 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 = 0.3189 r_free = 0.3189 target = 0.069974 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2812 r_free = 0.2812 target = 0.052484 restraints weight = 22954.115| |-----------------------------------------------------------------------------| r_work (start): 0.2787 rms_B_bonded: 2.90 r_work: 0.2667 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8488 moved from start: 0.2098 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= 0.108 Angle : 0.515 12.442 11842 Z= 0.263 Chirality : 0.038 0.165 1382 Planarity : 0.004 0.045 1442 Dihedral : 7.057 77.445 1250 Min Nonbonded Distance : 2.531 Molprobity Statistics. All-atom Clashscore : 4.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.55 % Allowed : 11.71 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.12 (0.26), residues: 1072 helix: 2.25 (0.18), residues: 785 sheet: None (None), residues: 0 loop : -1.06 (0.37), residues: 287 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.004 0.000 ARG A 151 TYR 0.025 0.001 TYR B 282 PHE 0.020 0.001 PHE A 251 TRP 0.009 0.001 TRP A 298 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00234 ( 8712) covalent geometry : angle 0.51502 (11842) hydrogen bonds : bond 0.03763 ( 550) hydrogen bonds : angle 3.59496 ( 1626) *********************** 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 74 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 69 time to evaluate : 0.281 Fit side-chains REVERT: A 323 ASP cc_start: 0.8727 (p0) cc_final: 0.8426 (p0) REVERT: A 340 MET cc_start: 0.8857 (ttm) cc_final: 0.8594 (ptt) outliers start: 5 outliers final: 2 residues processed: 73 average time/residue: 0.6473 time to fit residues: 50.3090 Evaluate side-chains 71 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.332 ------------------------------------------------------------------------------- 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 60 optimal weight: 0.9990 chunk 23 optimal weight: 0.0170 chunk 34 optimal weight: 0.9990 chunk 90 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 54 optimal weight: 0.4980 chunk 93 optimal weight: 4.9990 chunk 105 optimal weight: 6.9990 chunk 29 optimal weight: 0.9990 chunk 74 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 overall best weight: 0.5618 ------------------------------------------------------------------------------- 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 = 0.3210 r_free = 0.3210 target = 0.071089 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 37)----------------| | r_work = 0.2840 r_free = 0.2840 target = 0.053641 restraints weight = 22709.795| |-----------------------------------------------------------------------------| r_work (start): 0.2812 rms_B_bonded: 2.89 r_work: 0.2693 rms_B_bonded: 3.52 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8471 moved from start: 0.2272 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= 0.101 Angle : 0.508 12.847 11842 Z= 0.259 Chirality : 0.038 0.160 1382 Planarity : 0.004 0.045 1442 Dihedral : 6.862 78.133 1250 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.68 % Favored : 98.32 % Rotamer: Outliers : 0.22 % Allowed : 12.15 % Favored : 87.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.26), residues: 1072 helix: 2.35 (0.18), residues: 776 sheet: None (None), residues: 0 loop : -1.05 (0.37), residues: 296 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.026 0.001 TYR B 282 PHE 0.017 0.001 PHE B 251 TRP 0.017 0.001 TRP A 298 HIS 0.004 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00209 ( 8712) covalent geometry : angle 0.50751 (11842) hydrogen bonds : bond 0.03449 ( 550) hydrogen bonds : angle 3.53724 ( 1626) *********************** 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 73 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 71 time to evaluate : 0.340 Fit side-chains REVERT: A 323 ASP cc_start: 0.8708 (p0) cc_final: 0.8389 (OUTLIER) REVERT: A 340 MET cc_start: 0.8827 (ttm) cc_final: 0.8543 (ptt) REVERT: A 363 ASP cc_start: 0.8812 (m-30) cc_final: 0.8609 (m-30) outliers start: 2 outliers final: 4 residues processed: 73 average time/residue: 0.6293 time to fit residues: 48.9571 Evaluate side-chains 72 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 69 time to evaluate : 0.347 ------------------------------------------------------------------------------- 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 92 optimal weight: 3.9990 chunk 39 optimal weight: 4.9990 chunk 91 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 97 optimal weight: 6.9990 chunk 14 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 9 optimal weight: 2.9990 chunk 16 optimal weight: 9.9990 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 2.9990 overall best weight: 2.1586 ------------------------------------------------------------------------------- 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 = 0.3144 r_free = 0.3144 target = 0.067562 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2751 r_free = 0.2751 target = 0.049946 restraints weight = 23078.267| |-----------------------------------------------------------------------------| r_work (start): 0.2727 rms_B_bonded: 2.89 r_work: 0.2603 rms_B_bonded: 3.48 restraints_weight: 0.5000 r_work (final): 0.2603 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8548 moved from start: 0.1953 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.060 8712 Z= 0.155 Angle : 0.553 12.857 11842 Z= 0.286 Chirality : 0.040 0.181 1382 Planarity : 0.004 0.045 1442 Dihedral : 6.969 76.853 1250 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 3.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.96 % Favored : 98.04 % Rotamer: Outliers : 0.44 % Allowed : 11.82 % Favored : 87.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.09 (0.26), residues: 1072 helix: 2.22 (0.18), residues: 798 sheet: None (None), residues: 0 loop : -1.19 (0.37), residues: 274 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.023 0.001 TYR A 282 PHE 0.024 0.001 PHE B 251 TRP 0.011 0.001 TRP A 298 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00371 ( 8712) covalent geometry : angle 0.55306 (11842) hydrogen bonds : bond 0.04791 ( 550) hydrogen bonds : angle 3.70532 ( 1626) ********************** 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: 4 poor density : 69 time to evaluate : 0.383 Fit side-chains REVERT: A 323 ASP cc_start: 0.8711 (p0) cc_final: 0.8379 (OUTLIER) outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.6406 time to fit residues: 48.4721 Evaluate side-chains 71 residues out of total 916 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 69 time to evaluate : 0.328 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 220 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 107 random chunks: chunk 63 optimal weight: 5.9990 chunk 52 optimal weight: 0.0770 chunk 74 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 7.9990 chunk 80 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 83 optimal weight: 4.9990 chunk 70 optimal weight: 0.0670 chunk 79 optimal weight: 3.9990 overall best weight: 1.1480 ------------------------------------------------------------------------------- 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 = 0.068828 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.2782 r_free = 0.2782 target = 0.051242 restraints weight = 22915.113| |-----------------------------------------------------------------------------| r_work (start): 0.2757 rms_B_bonded: 2.90 r_work: 0.2634 rms_B_bonded: 3.51 restraints_weight: 0.5000 r_work (final): 0.2634 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8520 moved from start: 0.2043 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= 0.115 Angle : 0.525 12.648 11842 Z= 0.270 Chirality : 0.039 0.170 1382 Planarity : 0.004 0.044 1442 Dihedral : 6.935 78.029 1250 Min Nonbonded Distance : 2.538 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.87 % Favored : 98.13 % Rotamer: Outliers : 0.55 % Allowed : 11.49 % Favored : 87.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z values with (uncertainties): Interpretation: poor |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores below are scaled independently, so they aren not related in a simple way. whole: 2.21 (0.26), residues: 1072 helix: 2.28 (0.18), residues: 791 sheet: None (None), residues: 0 loop : -0.99 (0.38), residues: 281 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.002 0.000 ARG A 151 TYR 0.024 0.001 TYR B 282 PHE 0.020 0.001 PHE B 251 TRP 0.011 0.001 TRP A 298 HIS 0.005 0.001 HIS A 335 Details of bonding type rmsd covalent geometry : bond 0.00255 ( 8712) covalent geometry : angle 0.52480 (11842) hydrogen bonds : bond 0.04143 ( 550) hydrogen bonds : angle 3.62622 ( 1626) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2452.12 seconds wall clock time: 42 minutes 41.17 seconds (2561.17 seconds total)