Starting phenix.real_space_refine on Fri Jul 3 04:52:13 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28pn_56718/07_2026/28pn_56718.cif Found real_map, /net/cci-nas-00/data/ceres_data/28pn_56718/07_2026/28pn_56718.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/28pn_56718/07_2026/28pn_56718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28pn_56718/07_2026/28pn_56718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28pn_56718/07_2026/28pn_56718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28pn_56718/07_2026/28pn_56718.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= 0.000 sd= 0.011 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 6 Type Number sf(0) Gaussians Ca 2 9.91 5 Fe 6 7.16 5 S 44 5.16 5 C 7461 2.51 5 N 1876 2.21 5 O 2441 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 5 residue(s): 0.01s Monomer Library directory: "/net/cci-filer3/home/dcliebschner/04_cryoem/Phenix-dev-6108/lib/python3.11/site-packages/chem_data/mon_lib" Total number of atoms: 11830 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 5578 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 703, 5567 Classifications: {'peptide': 703} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 669} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Conformer: "B" Number of residues, atoms: 703, 5567 Classifications: {'peptide': 703} Incomplete info: {'backbone_only': 1} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 669} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 bond proxies already assigned to first conformer: 5735 Chain: "B" Number of atoms: 5528 Number of conformers: 2 Conformer: "A" Number of residues, atoms: 697, 5517 Classifications: {'peptide': 697} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 663} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 Conformer: "B" Number of residues, atoms: 697, 5517 Classifications: {'peptide': 697} Incomplete info: {'backbone_only': 1, 'truncation_to_alanine': 3} Link IDs: {'PCIS': 1, 'PTRANS': 32, 'TRANS': 663} Chain breaks: 1 Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 15 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'GLU:plan': 1} Unresolved non-hydrogen planarities: 4 bond proxies already assigned to first conformer: 5684 Chain: "A" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 86 Ad-hoc single atom residues: {' CA': 1, ' FE': 1} Unusual residues: {'HEM': 2} Classifications: {'undetermined': 2} Chain breaks: 2 Chain: "A" Number of atoms: 270 Number of conformers: 1 Conformer: "" Number of residues, atoms: 270, 270 Classifications: {'water': 270} Link IDs: {None: 269} Chain: "B" Number of atoms: 278 Number of conformers: 1 Conformer: "" Number of residues, atoms: 278, 278 Classifications: {'water': 278} Link IDs: {None: 277} Time building chain proxies: 4.70, per 1000 atoms: 0.40 Number of scatterers: 11830 At special positions: 0 Unit cell: (116.18, 79.18, 108.04, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Fe 6 26.01 Ca 2 19.99 S 44 16.00 O 2441 8.00 N 1876 7.00 C 7461 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=4, symmetry=0 Number of additional bonds: simple=4, symmetry=0 Coordination: Other bonds: Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 872.7 milliseconds 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2538 Finding SS restraints... Secondary structure from input PDB file: 81 helices and 5 sheets defined 78.1% alpha, 1.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.36 Creating SS restraints... Processing helix chain 'A' and resid 17 through 33 removed outlier: 3.612A pdb=" N GLY A 27 " --> pdb=" O GLY A 23 " (cutoff:3.500A) removed outlier: 3.542A pdb=" N GLU A 28 " --> pdb=" O PHE A 24 " (cutoff:3.500A) Processing helix chain 'A' and resid 51 through 64 Processing helix chain 'A' and resid 65 through 69 Processing helix chain 'A' and resid 82 through 105 Processing helix chain 'A' and resid 107 through 111 removed outlier: 3.524A pdb=" N LEU A 111 " --> pdb=" O TYR A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 112 through 129 removed outlier: 3.931A pdb=" N ALA A 129 " --> pdb=" O ALA A 125 " (cutoff:3.500A) Processing helix chain 'A' and resid 133 through 137 removed outlier: 3.705A pdb=" N GLY A 137 " --> pdb=" O ALA A 134 " (cutoff:3.500A) Processing helix chain 'A' and resid 142 through 161 Processing helix chain 'A' and resid 163 through 165 No H-bonds generated for 'chain 'A' and resid 163 through 165' Processing helix chain 'A' and resid 166 through 174 Processing helix chain 'A' and resid 182 through 202 Processing helix chain 'A' and resid 218 through 222 Processing helix chain 'A' and resid 226 through 253 Processing helix chain 'A' and resid 268 through 272 Processing helix chain 'A' and resid 276 through 281 Processing helix chain 'A' and resid 282 through 307 removed outlier: 3.539A pdb=" N LEU A 286 " --> pdb=" O LEU A 282 " (cutoff:3.500A) Processing helix chain 'A' and resid 317 through 321 removed outlier: 3.784A pdb=" N GLN A 320 " --> pdb=" O ASP A 317 " (cutoff:3.500A) Processing helix chain 'A' and resid 323 through 355 Proline residue: A 352 - end of helix removed outlier: 3.578A pdb=" N ASN A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) Processing helix chain 'A' and resid 362 through 390 Processing helix chain 'A' and resid 394 through 396 No H-bonds generated for 'chain 'A' and resid 394 through 396' Processing helix chain 'A' and resid 397 through 402 Processing helix chain 'A' and resid 412 through 435 removed outlier: 3.537A pdb=" N GLY A 433 " --> pdb=" O LEU A 429 " (cutoff:3.500A) Processing helix chain 'A' and resid 473 through 488 Processing helix chain 'A' and resid 491 through 508 Processing helix chain 'A' and resid 512 through 530 Processing helix chain 'A' and resid 530 through 537 Processing helix chain 'A' and resid 546 through 554 removed outlier: 3.734A pdb=" N SER A 554 " --> pdb=" O ALA A 550 " (cutoff:3.500A) Processing helix chain 'A' and resid 560 through 570 Processing helix chain 'A' and resid 571 through 576 Processing helix chain 'A' and resid 580 through 585 Processing helix chain 'A' and resid 586 through 603 removed outlier: 3.607A pdb=" N LEU A 590 " --> pdb=" O LEU A 586 " (cutoff:3.500A) Processing helix chain 'A' and resid 605 through 610 Processing helix chain 'A' and resid 613 through 621 removed outlier: 4.066A pdb=" N TYR A 619 " --> pdb=" O VAL A 615 " (cutoff:3.500A) Processing helix chain 'A' and resid 624 through 654 removed outlier: 3.726A pdb=" N VAL A 628 " --> pdb=" O ASN A 624 " (cutoff:3.500A) removed outlier: 3.613A pdb=" N HIS A 629 " --> pdb=" O THR A 625 " (cutoff:3.500A) removed outlier: 4.681A pdb=" N PHE A 640 " --> pdb=" O GLY A 636 " (cutoff:3.500A) Processing helix chain 'A' and resid 660 through 682 removed outlier: 3.701A pdb=" N SER A 682 " --> pdb=" O MET A 678 " (cutoff:3.500A) Processing helix chain 'A' and resid 682 through 697 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 704 through 709 Processing helix chain 'A' and resid 710 through 719 Processing helix chain 'A' and resid 720 through 744 Processing helix chain 'B' and resid 25 through 32 Processing helix chain 'B' and resid 51 through 64 removed outlier: 3.600A pdb=" N ILE B 64 " --> pdb=" O ALA B 60 " (cutoff:3.500A) Processing helix chain 'B' and resid 65 through 69 Processing helix chain 'B' and resid 82 through 105 Processing helix chain 'B' and resid 107 through 111 removed outlier: 3.555A pdb=" N LEU B 111 " --> pdb=" O TYR B 108 " (cutoff:3.500A) Processing helix chain 'B' and resid 112 through 129 removed outlier: 4.027A pdb=" N ALA B 129 " --> pdb=" O ALA B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 142 through 161 Processing helix chain 'B' and resid 163 through 165 No H-bonds generated for 'chain 'B' and resid 163 through 165' Processing helix chain 'B' and resid 166 through 174 Processing helix chain 'B' and resid 182 through 202 Processing helix chain 'B' and resid 218 through 222 Processing helix chain 'B' and resid 226 through 254 Processing helix chain 'B' and resid 268 through 272 removed outlier: 3.688A pdb=" N THR B 271 " --> pdb=" O ASP B 268 " (cutoff:3.500A) Processing helix chain 'B' and resid 276 through 281 Processing helix chain 'B' and resid 282 through 307 Processing helix chain 'B' and resid 319 through 321 No H-bonds generated for 'chain 'B' and resid 319 through 321' Processing helix chain 'B' and resid 323 through 355 Proline residue: B 352 - end of helix removed outlier: 3.569A pdb=" N ASN B 355 " --> pdb=" O ALA B 351 " (cutoff:3.500A) Processing helix chain 'B' and resid 362 through 390 Processing helix chain 'B' and resid 394 through 396 No H-bonds generated for 'chain 'B' and resid 394 through 396' Processing helix chain 'B' and resid 397 through 402 Processing helix chain 'B' and resid 412 through 439 Proline residue: B 436 - end of helix Processing helix chain 'B' and resid 473 through 488 removed outlier: 3.831A pdb=" N ILE B 484 " --> pdb=" O TRP B 480 " (cutoff:3.500A) removed outlier: 3.585A pdb=" N HIS B 486 " --> pdb=" O TRP B 482 " (cutoff:3.500A) Processing helix chain 'B' and resid 491 through 505 Processing helix chain 'B' and resid 512 through 525 Processing helix chain 'B' and resid 528 through 530 No H-bonds generated for 'chain 'B' and resid 528 through 530' Processing helix chain 'B' and resid 531 through 536 Processing helix chain 'B' and resid 537 through 539 No H-bonds generated for 'chain 'B' and resid 537 through 539' Processing helix chain 'B' and resid 545 through 555 removed outlier: 4.004A pdb=" N MET B 549 " --> pdb=" O THR B 545 " (cutoff:3.500A) removed outlier: 3.637A pdb=" N PHE B 555 " --> pdb=" O VAL B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 560 through 570 removed outlier: 3.838A pdb=" N GLU B 569 " --> pdb=" O VAL B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 571 through 576 Processing helix chain 'B' and resid 583 through 585 No H-bonds generated for 'chain 'B' and resid 583 through 585' Processing helix chain 'B' and resid 586 through 603 removed outlier: 3.649A pdb=" N LEU B 590 " --> pdb=" O LEU B 586 " (cutoff:3.500A) Processing helix chain 'B' and resid 605 through 611 removed outlier: 3.560A pdb=" N ILE B 611 " --> pdb=" O PHE B 607 " (cutoff:3.500A) Processing helix chain 'B' and resid 613 through 621 removed outlier: 4.100A pdb=" N TYR B 619 " --> pdb=" O VAL B 615 " (cutoff:3.500A) Processing helix chain 'B' and resid 624 through 654 removed outlier: 3.621A pdb=" N VAL B 628 " --> pdb=" O ASN B 624 " (cutoff:3.500A) removed outlier: 4.304A pdb=" N PHE B 640 " --> pdb=" O GLY B 636 " (cutoff:3.500A) Processing helix chain 'B' and resid 660 through 682 removed outlier: 3.716A pdb=" N SER B 682 " --> pdb=" O MET B 678 " (cutoff:3.500A) Processing helix chain 'B' and resid 682 through 697 Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 704 through 709 Processing helix chain 'B' and resid 710 through 720 Processing helix chain 'B' and resid 720 through 744 Processing sheet with id=AA1, first strand: chain 'A' and resid 47 through 50 removed outlier: 6.744A pdb=" N ARG A 47 " --> pdb=" O SER A 42 " (cutoff:3.500A) removed outlier: 6.200A pdb=" N SER A 42 " --> pdb=" O ARG A 47 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 71 through 72 Processing sheet with id=AA3, first strand: chain 'B' and resid 47 through 50 removed outlier: 6.865A pdb=" N VAL B 40 " --> pdb=" O LEU B 48 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 71 through 72 Processing sheet with id=AA5, first strand: chain 'B' and resid 312 through 313 764 hydrogen bonds defined for protein. 2215 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: 2.02 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.37: 3730 1.37 - 1.54: 7802 1.54 - 1.72: 43 1.72 - 1.89: 84 1.89 - 2.06: 16 Bond restraints: 11675 Sorted by residual: bond pdb=" N THR B 546 " pdb=" CA THR B 546 " ideal model delta sigma weight residual 1.463 1.495 -0.031 6.90e-03 2.10e+04 2.08e+01 bond pdb=" N LEU B 510 " pdb=" CA LEU B 510 " ideal model delta sigma weight residual 1.457 1.498 -0.040 1.29e-02 6.01e+03 9.75e+00 bond pdb=" C PRO A 547 " pdb=" O PRO A 547 " ideal model delta sigma weight residual 1.235 1.196 0.039 1.30e-02 5.92e+03 8.88e+00 bond pdb=" C PRO B 547 " pdb=" O PRO B 547 " ideal model delta sigma weight residual 1.235 1.198 0.037 1.30e-02 5.92e+03 8.30e+00 bond pdb=" N VAL B 511 " pdb=" CA VAL B 511 " ideal model delta sigma weight residual 1.459 1.495 -0.036 1.25e-02 6.40e+03 8.14e+00 ... (remaining 11670 not shown) Histogram of bond angle deviations from ideal: 0.00 - 3.34: 15858 3.34 - 6.67: 119 6.67 - 10.01: 6 10.01 - 13.34: 5 13.34 - 16.68: 3 Bond angle restraints: 15991 Sorted by residual: angle pdb=" N THR B 507 " pdb=" CA THR B 507 " pdb=" C THR B 507 " ideal model delta sigma weight residual 113.20 105.30 7.90 1.21e+00 6.83e-01 4.26e+01 angle pdb=" N PHE B 503 " pdb=" CA PHE B 503 " pdb=" C PHE B 503 " ideal model delta sigma weight residual 111.36 106.33 5.03 1.09e+00 8.42e-01 2.13e+01 angle pdb=" C THR A 545 " pdb=" CA THR A 545 " pdb=" CB THR A 545 " ideal model delta sigma weight residual 109.66 117.57 -7.91 1.94e+00 2.66e-01 1.66e+01 angle pdb=" C VAL B 560 " pdb=" N VAL B 561 " pdb=" CA VAL B 561 " ideal model delta sigma weight residual 120.33 123.56 -3.23 8.00e-01 1.56e+00 1.63e+01 angle pdb=" CA GLY B 509 " pdb=" C GLY B 509 " pdb=" O GLY B 509 " ideal model delta sigma weight residual 120.53 117.07 3.46 9.00e-01 1.23e+00 1.48e+01 ... (remaining 15986 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.99: 5639 17.99 - 35.97: 612 35.97 - 53.96: 185 53.96 - 71.94: 28 71.94 - 89.93: 18 Dihedral angle restraints: 6482 sinusoidal: 2492 harmonic: 3990 Sorted by residual: dihedral pdb=" CA ILE B 679 " pdb=" C ILE B 679 " pdb=" N PHE B 680 " pdb=" CA PHE B 680 " ideal model delta harmonic sigma weight residual -180.00 -162.41 -17.59 0 5.00e+00 4.00e-02 1.24e+01 dihedral pdb=" CA ILE A 679 " pdb=" C ILE A 679 " pdb=" N PHE A 680 " pdb=" CA PHE A 680 " ideal model delta harmonic sigma weight residual 180.00 -162.44 -17.56 0 5.00e+00 4.00e-02 1.23e+01 dihedral pdb=" C2D HEM B 804 " pdb=" C3D HEM B 804 " pdb=" CAD HEM B 804 " pdb=" CBD HEM B 804 " ideal model delta sinusoidal sigma weight residual 180.00 92.93 87.07 2 2.00e+01 2.50e-03 1.20e+01 ... (remaining 6479 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.039: 1142 0.039 - 0.077: 407 0.077 - 0.116: 110 0.116 - 0.154: 13 0.154 - 0.193: 4 Chirality restraints: 1676 Sorted by residual: chirality pdb=" CA THR B 546 " pdb=" N THR B 546 " pdb=" C THR B 546 " pdb=" CB THR B 546 " both_signs ideal model delta sigma weight residual False 2.53 2.33 0.19 2.00e-01 2.50e+01 9.27e-01 chirality pdb=" CA ILE B 504 " pdb=" N ILE B 504 " pdb=" C ILE B 504 " pdb=" CB ILE B 504 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.18 2.00e-01 2.50e+01 8.50e-01 chirality pdb=" CA THR A 546 " pdb=" N THR A 546 " pdb=" C THR A 546 " pdb=" CB THR A 546 " both_signs ideal model delta sigma weight residual False 2.53 2.35 0.18 2.00e-01 2.50e+01 7.90e-01 ... (remaining 1673 not shown) Planarity restraints: 1991 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU B 501 " 0.014 2.00e-02 2.50e+03 2.72e-02 7.41e+00 pdb=" C LEU B 501 " -0.047 2.00e-02 2.50e+03 pdb=" O LEU B 501 " 0.018 2.00e-02 2.50e+03 pdb=" N ALA B 502 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C PRO B 613 " -0.029 5.00e-02 4.00e+02 4.35e-02 3.03e+00 pdb=" N PRO B 614 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 614 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 614 " -0.024 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C TRP B 588 " -0.029 5.00e-02 4.00e+02 4.33e-02 3.00e+00 pdb=" N PRO B 589 " 0.075 5.00e-02 4.00e+02 pdb=" CA PRO B 589 " -0.022 5.00e-02 4.00e+02 pdb=" CD PRO B 589 " -0.025 5.00e-02 4.00e+02 ... (remaining 1988 not shown) Histogram of nonbonded interaction distances: 1.94 - 2.53: 151 2.53 - 3.12: 8834 3.12 - 3.71: 19349 3.71 - 4.31: 27693 4.31 - 4.90: 45935 Nonbonded interactions: 101962 Sorted by model distance: nonbonded pdb="FE FE A 804 " pdb=" O HOH A1011 " model vdw 1.935 3.000 nonbonded pdb="FE FE B 803 " pdb=" O HOH B1000 " model vdw 1.936 3.000 nonbonded pdb=" O ASN A 214 " pdb=" OH TYR A 618 " model vdw 2.200 3.040 nonbonded pdb=" OE1 GLU B 470 " pdb=" O HOH B 901 " model vdw 2.203 3.040 nonbonded pdb=" OD1 ASP B 396 " pdb=" O HOH B 902 " model vdw 2.209 3.040 ... (remaining 101957 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 24 through 245 or (resid 246 and (name N or name CA or nam \ e C or name O or name CB )) or resid 247 through 258 or (resid 259 and (name N o \ r name CA or name C or name O or name CB )) or resid 260 through 576 or (resid 5 \ 77 and (name N or name CA or name C or name O or name CB )) or resid 578 through \ 717 or resid 719 through 802)) selection = (chain 'B' and (resid 24 through 438 or resid 465 through 717 or resid 719 throu \ gh 802)) } 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=0.47 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: 3.390 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: 0.230 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 14.300 Find NCS groups from input model: 0.400 Set up NCS constraints: 0.040 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:6.510 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.940 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8931 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.192 11679 Z= 0.227 Angle : 0.748 16.680 15991 Z= 0.388 Chirality : 0.042 0.193 1676 Planarity : 0.005 0.043 1991 Dihedral : 16.985 89.927 3944 Min Nonbonded Distance : 1.935 Molprobity Statistics. All-atom Clashscore : 6.45 Ramachandran Plot: Outliers : 0.29 % Allowed : 3.95 % Favored : 95.76 % Rotamer: Outliers : 1.54 % Allowed : 21.27 % Favored : 77.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 1.42 (0.23), residues: 1394 helix: 1.72 (0.17), residues: 971 sheet: -1.76 (1.55), residues: 10 loop : -0.84 (0.31), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 186 TYR 0.017 0.002 TYR B 386 PHE 0.018 0.002 PHE B 635 TRP 0.018 0.002 TRP B 215 HIS 0.011 0.002 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00444 / 0.23 (11675) covalent geometry : angle 0.74787 / 0.39 (15991) hydrogen bonds : bond 0.13909 / 9.18 ( 764) hydrogen bonds : angle 5.55990 / 4.11 ( 2215) Misc. bond : bond 0.13150 / 6.56 ( 4) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 156 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 139 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 112 ASP cc_start: 0.8385 (OUTLIER) cc_final: 0.8175 (p0) REVERT: A 314 TYR cc_start: 0.7961 (m-80) cc_final: 0.7499 (m-80) REVERT: B 314 TYR cc_start: 0.7842 (m-80) cc_final: 0.7423 (m-80) REVERT: B 510 LEU cc_start: 0.8395 (tp) cc_final: 0.8195 (mm) outliers start: 17 outliers final: 2 residues processed: 151 average time/residue: 0.6718 time to fit residues: 109.3087 Evaluate side-chains 105 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 102 time to evaluate : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 112 ASP Chi-restraints excluded: chain A residue 233 SER Chi-restraints excluded: chain B residue 512 SER Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 98 optimal weight: 0.6980 chunk 107 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 66 optimal weight: 3.9990 chunk 130 optimal weight: 1.9990 chunk 124 optimal weight: 0.5980 chunk 103 optimal weight: 0.0030 chunk 77 optimal weight: 0.8980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS ** A 737 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 32 GLN B 537 HIS B 737 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.101809 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.072186 restraints weight = 29834.325| |-----------------------------------------------------------------------------| r_work (start): 0.2832 rms_B_bonded: 3.21 r_work: 0.2695 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2668 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2668 r_free = 0.2668 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2668 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8308 moved from start: 0.1318 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.119 11679 Z= 0.131 Angle : 0.668 16.135 15991 Z= 0.300 Chirality : 0.039 0.182 1676 Planarity : 0.004 0.039 1991 Dihedral : 6.549 88.136 1559 Min Nonbonded Distance : 2.504 Molprobity Statistics. All-atom Clashscore : 5.33 Ramachandran Plot: Outliers : 0.14 % Allowed : 2.95 % Favored : 96.91 % Rotamer: Outliers : 3.17 % Allowed : 20.63 % Favored : 76.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.17 (0.24), residues: 1394 helix: 2.31 (0.17), residues: 970 sheet: -2.25 (1.51), residues: 10 loop : -0.61 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.013 0.001 ARG B 187 TYR 0.013 0.001 TYR A 156 PHE 0.011 0.001 PHE B 635 TRP 0.022 0.001 TRP B 338 HIS 0.004 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00294 / 0.13 (11675) covalent geometry : angle 0.66780 / 0.30 (15991) hydrogen bonds : bond 0.04575 / 3.08 ( 764) hydrogen bonds : angle 4.42952 / 3.30 ( 2215) Misc. bond : bond 0.08814 / 4.29 ( 4) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 110 time to evaluate : 0.435 Fit side-chains revert: symmetry clash REVERT: A 31 ARG cc_start: 0.9088 (ttm110) cc_final: 0.8749 (ttp-110) REVERT: A 63 SER cc_start: 0.9223 (OUTLIER) cc_final: 0.8988 (p) REVERT: A 314 TYR cc_start: 0.7745 (m-80) cc_final: 0.7187 (m-80) REVERT: A 515 MET cc_start: 0.8079 (tmm) cc_final: 0.7847 (tmm) REVERT: A 579 ARG cc_start: 0.7830 (pmt-80) cc_final: 0.7426 (pmt-80) REVERT: A 583 MET cc_start: 0.8321 (mpp) cc_final: 0.8060 (mpt) REVERT: B 267 ARG cc_start: 0.8633 (ttp80) cc_final: 0.8316 (ttt-90) REVERT: B 314 TYR cc_start: 0.7608 (m-80) cc_final: 0.7031 (m-80) REVERT: B 549 MET cc_start: 0.8495 (ttp) cc_final: 0.8288 (ttm) REVERT: B 584 GLU cc_start: 0.8834 (OUTLIER) cc_final: 0.8536 (mm-30) outliers start: 35 outliers final: 9 residues processed: 132 average time/residue: 0.6223 time to fit residues: 89.1246 Evaluate side-chains 114 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 103 time to evaluate : 0.469 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 97 optimal weight: 0.6980 chunk 48 optimal weight: 3.9990 chunk 35 optimal weight: 4.9990 chunk 89 optimal weight: 5.9990 chunk 19 optimal weight: 0.0050 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 3.9990 chunk 58 optimal weight: 0.9990 chunk 80 optimal weight: 0.1980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 1.9990 overall best weight: 0.5396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 217 HIS A 568 HIS A 737 GLN B 537 HIS B 612 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.102751 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2877 r_free = 0.2877 target = 0.073198 restraints weight = 31699.701| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.34 r_work: 0.2711 rms_B_bonded: 3.85 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2687 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2687 r_free = 0.2687 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2687 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8256 moved from start: 0.1628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.101 11679 Z= 0.119 Angle : 0.615 13.265 15991 Z= 0.281 Chirality : 0.039 0.175 1676 Planarity : 0.004 0.052 1991 Dihedral : 6.475 89.617 1555 Min Nonbonded Distance : 2.510 Molprobity Statistics. All-atom Clashscore : 5.73 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.26 % Rotamer: Outliers : 1.99 % Allowed : 21.36 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.38 (0.23), residues: 1394 helix: 2.46 (0.17), residues: 972 sheet: None (None), residues: 0 loop : -0.57 (0.32), residues: 422 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.005 0.000 ARG B 106 TYR 0.011 0.001 TYR A 156 PHE 0.027 0.001 PHE A 19 TRP 0.021 0.001 TRP B 338 HIS 0.005 0.001 HIS B 568 Details of bonding type rmsd/Z covalent geometry : bond 0.00273 / 0.12 (11675) covalent geometry : angle 0.61504 / 0.28 (15991) hydrogen bonds : bond 0.04034 / 2.72 ( 764) hydrogen bonds : angle 4.23128 / 3.12 ( 2215) Misc. bond : bond 0.06340 / 3.13 ( 4) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 22 poor density : 106 time to evaluate : 0.498 Fit side-chains revert: symmetry clash REVERT: A 63 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.8948 (p) REVERT: A 314 TYR cc_start: 0.7709 (m-80) cc_final: 0.7108 (m-80) REVERT: A 515 MET cc_start: 0.8120 (tmm) cc_final: 0.7799 (tmm) REVERT: A 579 ARG cc_start: 0.7964 (pmt-80) cc_final: 0.7595 (pmt-80) REVERT: A 583 MET cc_start: 0.8301 (tpp) cc_final: 0.8090 (mpt) REVERT: B 38 GLU cc_start: 0.8748 (tp30) cc_final: 0.8407 (mm-30) REVERT: B 314 TYR cc_start: 0.7558 (m-80) cc_final: 0.7012 (m-80) REVERT: B 515 MET cc_start: 0.8045 (tmm) cc_final: 0.7841 (tmm) REVERT: B 584 GLU cc_start: 0.8777 (OUTLIER) cc_final: 0.8548 (mm-30) outliers start: 22 outliers final: 9 residues processed: 124 average time/residue: 0.6254 time to fit residues: 84.2982 Evaluate side-chains 116 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.430 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 434 ILE Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 46 optimal weight: 5.9990 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 41 optimal weight: 0.9980 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.0020 chunk 4 optimal weight: 0.8980 chunk 98 optimal weight: 2.9990 chunk 82 optimal weight: 0.1980 chunk 66 optimal weight: 1.9990 chunk 106 optimal weight: 2.9990 overall best weight: 0.8190 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN B 217 HIS B 537 HIS Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3343 r_free = 0.3343 target = 0.102006 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2868 r_free = 0.2868 target = 0.072464 restraints weight = 38323.736| |-----------------------------------------------------------------------------| r_work (start): 0.2835 rms_B_bonded: 3.59 r_work: 0.2688 rms_B_bonded: 4.07 restraints_weight: 0.5000 r_work (final): 0.2688 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2676 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2676 r_free = 0.2676 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8294 moved from start: 0.1801 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.141 11679 Z= 0.127 Angle : 0.608 13.107 15991 Z= 0.276 Chirality : 0.039 0.162 1676 Planarity : 0.004 0.042 1991 Dihedral : 6.406 89.759 1555 Min Nonbonded Distance : 2.523 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.59 % Favored : 96.26 % Rotamer: Outliers : 2.08 % Allowed : 20.81 % Favored : 77.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.46 (0.24), residues: 1394 helix: 2.54 (0.17), residues: 966 sheet: None (None), residues: 0 loop : -0.55 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 514 TYR 0.013 0.001 TYR A 30 PHE 0.014 0.001 PHE B 635 TRP 0.018 0.001 TRP B 338 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00303 / 0.13 (11675) covalent geometry : angle 0.60778 / 0.28 (15991) hydrogen bonds : bond 0.04069 / 2.76 ( 764) hydrogen bonds : angle 4.12690 / 3.05 ( 2215) Misc. bond : bond 0.09321 / 4.64 ( 4) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 133 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 110 time to evaluate : 0.434 Fit side-chains revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7525 (t80) cc_final: 0.6978 (m-80) REVERT: A 314 TYR cc_start: 0.7739 (m-80) cc_final: 0.7124 (m-80) REVERT: A 515 MET cc_start: 0.8151 (tmm) cc_final: 0.7696 (tmm) REVERT: A 579 ARG cc_start: 0.8230 (pmt-80) cc_final: 0.7918 (pmt-80) REVERT: A 583 MET cc_start: 0.8306 (OUTLIER) cc_final: 0.8018 (mpt) REVERT: B 38 GLU cc_start: 0.8785 (tp30) cc_final: 0.8215 (tp30) REVERT: B 314 TYR cc_start: 0.7543 (m-80) cc_final: 0.7006 (m-80) REVERT: B 584 GLU cc_start: 0.8779 (OUTLIER) cc_final: 0.8462 (mm-30) outliers start: 23 outliers final: 9 residues processed: 124 average time/residue: 0.6191 time to fit residues: 83.4809 Evaluate side-chains 116 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 583 MET Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 584 GLU Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 79 optimal weight: 2.9990 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 chunk 53 optimal weight: 3.9990 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 2.9990 chunk 50 optimal weight: 0.5980 chunk 82 optimal weight: 0.8980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 3.9990 overall best weight: 1.4784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN B 537 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3306 r_free = 0.3306 target = 0.099181 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.2820 r_free = 0.2820 target = 0.070006 restraints weight = 32117.226| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.34 r_work: 0.2655 rms_B_bonded: 3.84 restraints_weight: 0.5000 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2643 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2643 r_free = 0.2643 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2643 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8359 moved from start: 0.1818 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.215 11679 Z= 0.168 Angle : 0.646 14.117 15991 Z= 0.291 Chirality : 0.040 0.163 1676 Planarity : 0.005 0.120 1991 Dihedral : 6.445 88.557 1555 Min Nonbonded Distance : 2.524 Molprobity Statistics. All-atom Clashscore : 5.60 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.19 % Rotamer: Outliers : 2.53 % Allowed : 20.45 % Favored : 77.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.31 (0.24), residues: 1394 helix: 2.42 (0.17), residues: 972 sheet: -2.83 (1.44), residues: 10 loop : -0.59 (0.33), residues: 412 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.001 ARG B 267 TYR 0.015 0.001 TYR B 30 PHE 0.015 0.001 PHE B 635 TRP 0.022 0.001 TRP B 582 HIS 0.009 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00415 / 0.17 (11675) covalent geometry : angle 0.64582 / 0.29 (15991) hydrogen bonds : bond 0.04673 / 3.17 ( 764) hydrogen bonds : angle 4.16527 / 3.08 ( 2215) Misc. bond : bond 0.14975 / 7.43 ( 4) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 132 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 105 time to evaluate : 0.452 Fit side-chains revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7586 (t80) cc_final: 0.7052 (m-80) REVERT: A 63 SER cc_start: 0.9253 (OUTLIER) cc_final: 0.8922 (p) REVERT: A 208 SER cc_start: 0.9064 (m) cc_final: 0.8456 (t) REVERT: A 314 TYR cc_start: 0.7680 (m-80) cc_final: 0.7129 (m-80) REVERT: A 515 MET cc_start: 0.8152 (tmm) cc_final: 0.7670 (tmm) REVERT: A 579 ARG cc_start: 0.8238 (pmt-80) cc_final: 0.7817 (pmt-80) REVERT: B 38 GLU cc_start: 0.8850 (tp30) cc_final: 0.8307 (tp30) REVERT: B 314 TYR cc_start: 0.7582 (m-80) cc_final: 0.7035 (m-80) outliers start: 27 outliers final: 13 residues processed: 124 average time/residue: 0.6247 time to fit residues: 84.3683 Evaluate side-chains 117 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.531 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 56 optimal weight: 4.9990 chunk 128 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 chunk 90 optimal weight: 0.7980 chunk 53 optimal weight: 4.9990 chunk 70 optimal weight: 1.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.9980 chunk 59 optimal weight: 0.9980 chunk 2 optimal weight: 0.5980 chunk 31 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN B 537 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.100902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2865 r_free = 0.2865 target = 0.072427 restraints weight = 25995.726| |-----------------------------------------------------------------------------| r_work (start): 0.2847 rms_B_bonded: 3.01 r_work: 0.2715 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2715 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2703 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2703 r_free = 0.2703 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 4 (7 function evaluations) r_final: 0.2703 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8295 moved from start: 0.2002 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.127 11679 Z= 0.125 Angle : 0.613 13.732 15991 Z= 0.275 Chirality : 0.039 0.160 1676 Planarity : 0.004 0.044 1991 Dihedral : 6.343 87.694 1555 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.19 % Rotamer: Outliers : 2.17 % Allowed : 21.18 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.42 (0.24), residues: 1394 helix: 2.52 (0.17), residues: 966 sheet: None (None), residues: 0 loop : -0.61 (0.32), residues: 428 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 514 TYR 0.011 0.001 TYR A 30 PHE 0.011 0.001 PHE B 635 TRP 0.020 0.001 TRP B 338 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00299 / 0.12 (11675) covalent geometry : angle 0.61320 / 0.28 (15991) hydrogen bonds : bond 0.04127 / 2.81 ( 764) hydrogen bonds : angle 4.07389 / 3.01 ( 2215) Misc. bond : bond 0.08414 / 4.19 ( 4) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 129 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 106 time to evaluate : 0.448 Fit side-chains revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7543 (t80) cc_final: 0.7050 (m-80) REVERT: A 63 SER cc_start: 0.9211 (OUTLIER) cc_final: 0.8893 (p) REVERT: A 208 SER cc_start: 0.9048 (m) cc_final: 0.8440 (t) REVERT: A 314 TYR cc_start: 0.7680 (m-80) cc_final: 0.7117 (m-80) REVERT: A 515 MET cc_start: 0.8113 (tmm) cc_final: 0.7610 (tmm) REVERT: A 579 ARG cc_start: 0.8249 (pmt-80) cc_final: 0.7915 (pmt-80) REVERT: B 38 GLU cc_start: 0.8797 (tp30) cc_final: 0.8237 (tp30) REVERT: B 314 TYR cc_start: 0.7565 (m-80) cc_final: 0.7041 (m-80) outliers start: 23 outliers final: 13 residues processed: 123 average time/residue: 0.6266 time to fit residues: 83.8348 Evaluate side-chains 117 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 103 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 52 optimal weight: 2.9990 chunk 77 optimal weight: 0.6980 chunk 78 optimal weight: 2.9990 chunk 110 optimal weight: 1.9990 chunk 65 optimal weight: 0.0370 chunk 62 optimal weight: 0.8980 chunk 108 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 94 optimal weight: 0.0470 chunk 100 optimal weight: 0.9980 chunk 97 optimal weight: 0.7980 overall best weight: 0.4956 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN B 537 HIS B 600 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3356 r_free = 0.3356 target = 0.102847 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.073892 restraints weight = 31505.600| |-----------------------------------------------------------------------------| r_work (start): 0.2868 rms_B_bonded: 3.31 r_work: 0.2729 rms_B_bonded: 3.86 restraints_weight: 0.5000 r_work (final): 0.2729 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2738 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2738 r_free = 0.2738 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2738 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8302 moved from start: 0.2193 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 11679 Z= 0.111 Angle : 0.589 11.559 15991 Z= 0.268 Chirality : 0.038 0.158 1676 Planarity : 0.004 0.044 1991 Dihedral : 6.320 89.802 1555 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 5.82 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 1.72 % Allowed : 21.63 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.46 (0.24), residues: 1394 helix: 2.55 (0.17), residues: 963 sheet: None (None), residues: 0 loop : -0.58 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 514 TYR 0.015 0.001 TYR B 30 PHE 0.011 0.001 PHE B 635 TRP 0.029 0.001 TRP B 582 HIS 0.004 0.001 HIS A 305 Details of bonding type rmsd/Z covalent geometry : bond 0.00259 / 0.11 (11675) covalent geometry : angle 0.58927 / 0.27 (15991) hydrogen bonds : bond 0.03649 / 2.48 ( 764) hydrogen bonds : angle 3.98485 / 2.94 ( 2215) Misc. bond : bond 0.03873 / 1.90 ( 4) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 126 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 108 time to evaluate : 0.437 Fit side-chains revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7553 (t80) cc_final: 0.7113 (m-80) REVERT: A 63 SER cc_start: 0.9255 (OUTLIER) cc_final: 0.8966 (p) REVERT: A 208 SER cc_start: 0.9040 (m) cc_final: 0.8446 (t) REVERT: A 314 TYR cc_start: 0.7692 (m-80) cc_final: 0.7140 (m-80) REVERT: A 515 MET cc_start: 0.8100 (tmm) cc_final: 0.7589 (tmm) REVERT: A 579 ARG cc_start: 0.8311 (pmt-80) cc_final: 0.8049 (pmt-80) REVERT: B 38 GLU cc_start: 0.8857 (tp30) cc_final: 0.8290 (tp30) REVERT: B 314 TYR cc_start: 0.7547 (m-80) cc_final: 0.7000 (m-80) outliers start: 18 outliers final: 10 residues processed: 122 average time/residue: 0.5938 time to fit residues: 79.0570 Evaluate side-chains 116 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 105 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 640 PHE Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 5.9990 chunk 30 optimal weight: 0.0980 chunk 113 optimal weight: 1.9990 chunk 2 optimal weight: 1.9990 chunk 79 optimal weight: 0.9990 chunk 13 optimal weight: 0.9990 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 0.7980 chunk 125 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN B 537 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3351 r_free = 0.3351 target = 0.101833 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2895 r_free = 0.2895 target = 0.073569 restraints weight = 27929.659| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.09 r_work: 0.2709 rms_B_bonded: 3.65 restraints_weight: 0.5000 r_work (final): 0.2709 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2700 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2700 r_free = 0.2700 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2700 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8296 moved from start: 0.2160 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 11679 Z= 0.134 Angle : 0.615 12.574 15991 Z= 0.277 Chirality : 0.039 0.162 1676 Planarity : 0.004 0.044 1991 Dihedral : 6.371 89.483 1555 Min Nonbonded Distance : 2.536 Molprobity Statistics. All-atom Clashscore : 5.78 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 2.26 % Allowed : 21.09 % Favored : 76.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.44 (0.24), residues: 1394 helix: 2.55 (0.17), residues: 963 sheet: None (None), residues: 0 loop : -0.59 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 267 TYR 0.011 0.001 TYR B 406 PHE 0.015 0.001 PHE B 527 TRP 0.033 0.001 TRP B 582 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00327 / 0.13 (11675) covalent geometry : angle 0.61527 / 0.28 (15991) hydrogen bonds : bond 0.04088 / 2.78 ( 764) hydrogen bonds : angle 4.01011 / 2.96 ( 2215) Misc. bond : bond 0.10427 / 5.16 ( 4) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 104 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7553 (t80) cc_final: 0.7167 (m-80) REVERT: A 63 SER cc_start: 0.9224 (OUTLIER) cc_final: 0.8898 (p) REVERT: A 208 SER cc_start: 0.9067 (m) cc_final: 0.8466 (t) REVERT: A 314 TYR cc_start: 0.7672 (m-80) cc_final: 0.7147 (m-80) REVERT: A 515 MET cc_start: 0.8084 (tmm) cc_final: 0.7571 (tmm) REVERT: A 579 ARG cc_start: 0.8391 (pmt-80) cc_final: 0.8108 (pmt-80) REVERT: B 38 GLU cc_start: 0.8867 (tp30) cc_final: 0.8317 (tp30) REVERT: B 67 MET cc_start: 0.8026 (mtt) cc_final: 0.7630 (mtt) REVERT: B 314 TYR cc_start: 0.7516 (m-80) cc_final: 0.6957 (m-80) outliers start: 24 outliers final: 15 residues processed: 122 average time/residue: 0.5825 time to fit residues: 77.6226 Evaluate side-chains 120 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 104 time to evaluate : 0.434 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 213 ASN Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain A residue 563 LEU Chi-restraints excluded: chain A residue 737 GLN Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 85 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 74 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 103 optimal weight: 0.0870 chunk 19 optimal weight: 4.9990 chunk 127 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 7 optimal weight: 0.8980 overall best weight: 0.5558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN B 537 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3344 r_free = 0.3344 target = 0.101902 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.073030 restraints weight = 31506.411| |-----------------------------------------------------------------------------| r_work (start): 0.2866 rms_B_bonded: 3.29 r_work: 0.2725 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2706 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2706 r_free = 0.2706 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2706 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8293 moved from start: 0.2230 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.116 11679 Z= 0.115 Angle : 0.607 12.647 15991 Z= 0.273 Chirality : 0.038 0.159 1676 Planarity : 0.004 0.045 1991 Dihedral : 6.355 89.586 1555 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 1.81 % Allowed : 21.36 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.47 (0.24), residues: 1394 helix: 2.57 (0.17), residues: 963 sheet: None (None), residues: 0 loop : -0.59 (0.32), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 358 TYR 0.015 0.001 TYR B 30 PHE 0.017 0.001 PHE B 527 TRP 0.037 0.001 TRP B 582 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00269 / 0.11 (11675) covalent geometry : angle 0.60721 / 0.27 (15991) hydrogen bonds : bond 0.03877 / 2.64 ( 764) hydrogen bonds : angle 3.98172 / 2.94 ( 2215) Misc. bond : bond 0.07550 / 3.75 ( 4) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 125 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.424 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7554 (t80) cc_final: 0.6916 (m-80) REVERT: A 63 SER cc_start: 0.9240 (OUTLIER) cc_final: 0.8920 (p) REVERT: A 208 SER cc_start: 0.9062 (m) cc_final: 0.8467 (t) REVERT: A 314 TYR cc_start: 0.7663 (m-80) cc_final: 0.7134 (m-80) REVERT: A 515 MET cc_start: 0.8097 (tmm) cc_final: 0.7618 (tmm) REVERT: B 38 GLU cc_start: 0.8878 (tp30) cc_final: 0.8329 (tp30) REVERT: B 314 TYR cc_start: 0.7478 (m-80) cc_final: 0.6925 (m-80) REVERT: B 720 ARG cc_start: 0.7767 (OUTLIER) cc_final: 0.7520 (ttt180) outliers start: 19 outliers final: 13 residues processed: 120 average time/residue: 0.6252 time to fit residues: 81.5347 Evaluate side-chains 119 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 104 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain A residue 561 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Chi-restraints excluded: chain B residue 720 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 60 optimal weight: 3.9990 chunk 121 optimal weight: 0.8980 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 62 optimal weight: 0.8980 chunk 137 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 66 optimal weight: 2.9990 chunk 133 optimal weight: 0.3980 chunk 81 optimal weight: 6.9990 chunk 113 optimal weight: 0.6980 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN B 537 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3364 r_free = 0.3364 target = 0.102722 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.074759 restraints weight = 25347.488| |-----------------------------------------------------------------------------| r_work (start): 0.2876 rms_B_bonded: 2.96 r_work: 0.2743 rms_B_bonded: 3.56 restraints_weight: 0.5000 r_work (final): 0.2743 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2723 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2723 r_free = 0.2723 target_work(ls_wunit_k1) = 0.066 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2723 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8289 moved from start: 0.2287 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.114 11679 Z= 0.122 Angle : 0.610 11.984 15991 Z= 0.275 Chirality : 0.039 0.162 1676 Planarity : 0.004 0.044 1991 Dihedral : 6.335 89.026 1555 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 5.91 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 1.63 % Allowed : 21.54 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.44 (0.24), residues: 1394 helix: 2.55 (0.17), residues: 963 sheet: None (None), residues: 0 loop : -0.61 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.014 0.001 TYR B 406 PHE 0.019 0.001 PHE B 527 TRP 0.031 0.001 TRP B 582 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00295 / 0.12 (11675) covalent geometry : angle 0.61044 / 0.28 (15991) hydrogen bonds : bond 0.03885 / 2.65 ( 764) hydrogen bonds : angle 3.96719 / 2.93 ( 2215) Misc. bond : bond 0.07640 / 3.77 ( 4) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2788 Ramachandran restraints generated. 1394 Oldfield, 0 Emsley, 1394 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 105 time to evaluate : 0.303 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7202 (t80) cc_final: 0.6892 (m-80) REVERT: A 31 ARG cc_start: 0.8969 (ttp80) cc_final: 0.8748 (ttp80) REVERT: A 63 SER cc_start: 0.9232 (OUTLIER) cc_final: 0.8927 (p) REVERT: A 208 SER cc_start: 0.9067 (m) cc_final: 0.8478 (t) REVERT: A 314 TYR cc_start: 0.7621 (m-80) cc_final: 0.6989 (m-80) REVERT: A 515 MET cc_start: 0.7982 (tmm) cc_final: 0.7549 (tmm) REVERT: B 38 GLU cc_start: 0.8876 (tp30) cc_final: 0.8327 (tp30) REVERT: B 314 TYR cc_start: 0.7502 (m-80) cc_final: 0.6986 (m-80) REVERT: B 720 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7557 (ttt180) outliers start: 17 outliers final: 12 residues processed: 117 average time/residue: 0.6285 time to fit residues: 79.4535 Evaluate side-chains 119 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 493 PHE Chi-restraints excluded: chain A residue 525 SER Chi-restraints excluded: chain A residue 548 VAL Chi-restraints excluded: chain B residue 247 LEU Chi-restraints excluded: chain B residue 435 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 624 ASN Chi-restraints excluded: chain B residue 640 PHE Chi-restraints excluded: chain B residue 651 ARG Chi-restraints excluded: chain B residue 720 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 7 optimal weight: 0.9990 chunk 122 optimal weight: 7.9990 chunk 96 optimal weight: 0.8980 chunk 81 optimal weight: 7.9990 chunk 64 optimal weight: 0.6980 chunk 91 optimal weight: 0.7980 chunk 113 optimal weight: 0.6980 chunk 65 optimal weight: 0.7980 chunk 78 optimal weight: 9.9990 chunk 11 optimal weight: 0.9990 chunk 55 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... A 568 HIS A 737 GLN B 537 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.102734 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 54)----------------| | r_work = 0.2890 r_free = 0.2890 target = 0.073259 restraints weight = 37305.238| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 3.58 r_work: 0.2708 rms_B_bonded: 4.04 restraints_weight: 0.5000 r_work (final): 0.2708 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2692 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2692 r_free = 0.2692 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| Number of minimizer iterations: 3 (3 function evaluations) r_final: 0.2692 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8284 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.112 11679 Z= 0.122 Angle : 0.614 12.052 15991 Z= 0.276 Chirality : 0.039 0.159 1676 Planarity : 0.004 0.044 1991 Dihedral : 6.322 88.564 1555 Min Nonbonded Distance : 2.462 Molprobity Statistics. All-atom Clashscore : 6.09 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 1.81 % Allowed : 21.36 % Favored : 76.83 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.03 % 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 are not related in a simple way. whole: 2.46 (0.24), residues: 1394 helix: 2.57 (0.17), residues: 963 sheet: None (None), residues: 0 loop : -0.62 (0.31), residues: 431 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 358 TYR 0.014 0.001 TYR B 30 PHE 0.019 0.001 PHE B 527 TRP 0.030 0.001 TRP B 582 HIS 0.006 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00297 / 0.12 (11675) covalent geometry : angle 0.61443 / 0.28 (15991) hydrogen bonds : bond 0.03857 / 2.63 ( 764) hydrogen bonds : angle 3.95549 / 2.92 ( 2215) Misc. bond : bond 0.07485 / 3.70 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4059.42 seconds wall clock time: 69 minutes 57.70 seconds (4197.70 seconds total)