Starting phenix.real_space_refine on Thu Jun 4 09:47:22 2026 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/28pn_56718/06_2026/28pn_56718.cif Found real_map, /net/cci-nas-00/data/ceres_data/28pn_56718/06_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_56718/06_2026/28pn_56718.cif" } default_model = "/net/cci-nas-00/data/ceres_data/28pn_56718/06_2026/28pn_56718.cif" real_map_files = "/net/cci-nas-00/data/ceres_data/28pn_56718/06_2026/28pn_56718.map" default_real_map = "/net/cci-nas-00/data/ceres_data/28pn_56718/06_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-6079/lib/python3.9/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, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "B" Number of atoms: 88 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 88 Unusual residues: {' CA': 1, ' FE': 1, 'HEM': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} 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: 5.35, per 1000 atoms: 0.45 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: 1.27 Conformation dependent library (CDL) restraints added in 832.9 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: 0.46 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: 1.82 Time building geometry restraints manager: 1.62 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 2.260 nonbonded pdb="FE FE B 803 " pdb=" O HOH B1000 " model vdw 1.936 2.260 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: 3.230 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.230 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 15.650 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:7.440 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8722 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 : 0.442 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: 0.7154 time to fit residues: 115.8708 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 : 0.437 ------------------------------------------------------------------------------- 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: 0.9980 chunk 122 optimal weight: 5.9990 chunk 91 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.6390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: 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 = 0.3334 r_free = 0.3334 target = 0.101630 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.072108 restraints weight = 29530.776| |-----------------------------------------------------------------------------| r_work (start): 0.2831 rms_B_bonded: 3.23 r_work: 0.2693 rms_B_bonded: 3.75 restraints_weight: 0.5000 r_work (final): 0.2693 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2665 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2665 r_free = 0.2665 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 = 0.2665 r_free = 0.2665 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.47 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2665 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8114 moved from start: 0.1298 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.121 11679 Z= 0.131 Angle : 0.651 13.742 15991 Z= 0.299 Chirality : 0.039 0.185 1676 Planarity : 0.004 0.040 1991 Dihedral : 6.605 87.735 1559 Min Nonbonded Distance : 2.108 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.09 % Favored : 96.77 % 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: 2.15 (0.24), residues: 1394 helix: 2.30 (0.17), residues: 970 sheet: -2.24 (1.52), residues: 10 loop : -0.62 (0.32), residues: 414 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.011 0.001 ARG B 514 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 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.13 (11675) covalent geometry : angle 0.65133 / 0.30 (15991) hydrogen bonds : bond 0.04629 / 3.12 ( 764) hydrogen bonds : angle 4.43428 / 3.31 ( 2215) Misc. bond : bond 0.08005 / 3.98 ( 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 146 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 35 poor density : 111 time to evaluate : 0.489 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.9226 (OUTLIER) cc_final: 0.8978 (p) REVERT: A 314 TYR cc_start: 0.7739 (m-80) cc_final: 0.7115 (m-80) REVERT: A 515 MET cc_start: 0.8086 (tmm) cc_final: 0.7854 (tmm) REVERT: A 579 ARG cc_start: 0.7826 (pmt-80) cc_final: 0.7418 (pmt-80) REVERT: B 314 TYR cc_start: 0.7596 (m-80) cc_final: 0.7031 (m-80) REVERT: B 549 MET cc_start: 0.8493 (ttp) cc_final: 0.8293 (ttm) REVERT: B 584 GLU cc_start: 0.8839 (OUTLIER) cc_final: 0.8511 (mm-30) outliers start: 35 outliers final: 11 residues processed: 132 average time/residue: 0.6730 time to fit residues: 96.1286 Evaluate side-chains 118 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.462 ------------------------------------------------------------------------------- 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 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 537 HIS 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: 4.9990 chunk 19 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 chunk 66 optimal weight: 5.9990 chunk 58 optimal weight: 0.9980 chunk 80 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS A 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3334 r_free = 0.3334 target = 0.101393 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.2854 r_free = 0.2854 target = 0.071847 restraints weight = 31537.115| |-----------------------------------------------------------------------------| r_work (start): 0.2825 rms_B_bonded: 3.33 r_work: 0.2685 rms_B_bonded: 3.82 restraints_weight: 0.5000 r_work (final): 0.2685 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2666 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2666 r_free = 0.2666 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 = 0.2666 r_free = 0.2666 target_work(ls_wunit_k1) = 0.063 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2666 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8127 moved from start: 0.1482 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.138 11679 Z= 0.134 Angle : 0.624 12.275 15991 Z= 0.287 Chirality : 0.039 0.197 1676 Planarity : 0.004 0.043 1991 Dihedral : 6.540 88.161 1555 Min Nonbonded Distance : 2.066 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.45 % Favored : 96.41 % Rotamer: Outliers : 2.17 % Allowed : 20.90 % Favored : 76.92 % 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 (0.23), residues: 1394 helix: 2.44 (0.17), residues: 966 sheet: -2.48 (1.51), residues: 10 loop : -0.58 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.000 ARG B 267 TYR 0.011 0.001 TYR A 156 PHE 0.024 0.001 PHE A 19 TRP 0.020 0.001 TRP B 338 HIS 0.010 0.001 HIS B 538 Details of bonding type rmsd/Z covalent geometry : bond 0.00319 / 0.13 (11675) covalent geometry : angle 0.62420 / 0.29 (15991) hydrogen bonds : bond 0.04371 / 2.95 ( 764) hydrogen bonds : angle 4.28920 / 3.18 ( 2215) Misc. bond : bond 0.09196 / 4.57 ( 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 131 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 24 poor density : 107 time to evaluate : 0.445 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 63 SER cc_start: 0.9249 (OUTLIER) cc_final: 0.8933 (p) REVERT: A 182 ASP cc_start: 0.7321 (OUTLIER) cc_final: 0.7093 (t70) REVERT: A 314 TYR cc_start: 0.7715 (m-80) cc_final: 0.7111 (m-80) REVERT: A 515 MET cc_start: 0.8152 (tmm) cc_final: 0.7923 (tmm) REVERT: A 579 ARG cc_start: 0.7909 (pmt-80) cc_final: 0.7501 (pmt-80) REVERT: B 38 GLU cc_start: 0.8775 (tp30) cc_final: 0.8443 (mm-30) REVERT: B 314 TYR cc_start: 0.7603 (m-80) cc_final: 0.7035 (m-80) REVERT: B 584 GLU cc_start: 0.8800 (OUTLIER) cc_final: 0.8511 (mm-30) REVERT: B 708 MET cc_start: 0.9275 (mmp) cc_final: 0.9068 (mmm) outliers start: 24 outliers final: 10 residues processed: 127 average time/residue: 0.6486 time to fit residues: 89.0856 Evaluate side-chains 120 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 107 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 182 ASP 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 435 VAL 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: 0.5980 chunk 12 optimal weight: 4.9990 chunk 41 optimal weight: 2.9990 chunk 90 optimal weight: 2.9990 chunk 50 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 chunk 98 optimal weight: 0.9990 chunk 82 optimal weight: 4.9990 chunk 66 optimal weight: 4.9990 chunk 106 optimal weight: 2.9990 overall best weight: 1.2584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 217 HIS A 568 HIS A 737 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.099643 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.2824 r_free = 0.2824 target = 0.070012 restraints weight = 38317.421| |-----------------------------------------------------------------------------| r_work (start): 0.2802 rms_B_bonded: 3.55 r_work: 0.2657 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2657 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2645 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2645 r_free = 0.2645 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2645 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8133 moved from start: 0.1694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.194 11679 Z= 0.155 Angle : 0.630 13.323 15991 Z= 0.288 Chirality : 0.040 0.163 1676 Planarity : 0.004 0.067 1991 Dihedral : 6.505 88.709 1555 Min Nonbonded Distance : 2.039 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.19 % Rotamer: Outliers : 2.35 % Allowed : 20.09 % Favored : 77.56 % 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: 2.43 (0.17), residues: 971 sheet: -2.66 (1.51), residues: 10 loop : -0.59 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.008 0.001 ARG B 267 TYR 0.014 0.001 TYR A 30 PHE 0.015 0.001 PHE B 635 TRP 0.019 0.001 TRP B 338 HIS 0.009 0.001 HIS B 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00379 / 0.15 (11675) covalent geometry : angle 0.63038 / 0.29 (15991) hydrogen bonds : bond 0.04594 / 3.11 ( 764) hydrogen bonds : angle 4.20473 / 3.11 ( 2215) Misc. bond : bond 0.13371 / 6.66 ( 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 134 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 26 poor density : 108 time to evaluate : 0.432 Fit side-chains REVERT: A 19 PHE cc_start: 0.7512 (t80) cc_final: 0.6980 (m-80) REVERT: A 63 SER cc_start: 0.9228 (OUTLIER) cc_final: 0.8908 (p) REVERT: A 182 ASP cc_start: 0.7467 (OUTLIER) cc_final: 0.7247 (t70) REVERT: A 314 TYR cc_start: 0.7731 (m-80) cc_final: 0.7163 (m-80) REVERT: A 515 MET cc_start: 0.8163 (tmm) cc_final: 0.7722 (tmm) REVERT: A 579 ARG cc_start: 0.8113 (pmt-80) cc_final: 0.7834 (pmt-80) REVERT: B 38 GLU cc_start: 0.8814 (tp30) cc_final: 0.8259 (tp30) REVERT: B 314 TYR cc_start: 0.7593 (m-80) cc_final: 0.7036 (m-80) REVERT: B 584 GLU cc_start: 0.8827 (OUTLIER) cc_final: 0.8512 (mm-30) outliers start: 26 outliers final: 13 residues processed: 125 average time/residue: 0.6495 time to fit residues: 87.7177 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 : 0.422 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 187 ARG 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 435 VAL 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 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: 1.9990 chunk 6 optimal weight: 4.9990 chunk 43 optimal weight: 3.9990 chunk 53 optimal weight: 8.9990 chunk 83 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 82 optimal weight: 0.4980 chunk 22 optimal weight: 0.8980 chunk 0 optimal weight: 9.9990 chunk 69 optimal weight: 2.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS A 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3305 r_free = 0.3305 target = 0.099468 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.2827 r_free = 0.2827 target = 0.070379 restraints weight = 31913.565| |-----------------------------------------------------------------------------| r_work (start): 0.2799 rms_B_bonded: 3.29 r_work: 0.2659 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2659 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2655 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| |-occupancy refinement: end---------------------------------------------------| | r_work = 0.2655 r_free = 0.2655 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2655 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8140 moved from start: 0.1800 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.178 11679 Z= 0.153 Angle : 0.631 12.683 15991 Z= 0.287 Chirality : 0.040 0.162 1676 Planarity : 0.004 0.041 1991 Dihedral : 6.512 88.735 1555 Min Nonbonded Distance : 2.052 Molprobity Statistics. All-atom Clashscore : 5.24 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.81 % Favored : 96.05 % Rotamer: Outliers : 2.53 % Allowed : 19.91 % Favored : 77.56 % 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: 2.29 (0.24), residues: 1394 helix: 2.39 (0.17), residues: 976 sheet: -2.77 (1.51), residues: 10 loop : -0.58 (0.33), residues: 408 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.009 0.000 ARG B 267 TYR 0.015 0.001 TYR B 30 PHE 0.014 0.001 PHE B 635 TRP 0.025 0.001 TRP B 582 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00378 / 0.15 (11675) covalent geometry : angle 0.63083 / 0.29 (15991) hydrogen bonds : bond 0.04523 / 3.07 ( 764) hydrogen bonds : angle 4.16107 / 3.08 ( 2215) Misc. bond : bond 0.12130 / 6.04 ( 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 134 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 27 poor density : 107 time to evaluate : 0.308 Fit side-chains REVERT: A 19 PHE cc_start: 0.7565 (t80) cc_final: 0.7033 (m-80) REVERT: A 63 SER cc_start: 0.9233 (OUTLIER) cc_final: 0.8898 (p) REVERT: A 182 ASP cc_start: 0.7513 (OUTLIER) cc_final: 0.7259 (t70) REVERT: A 208 SER cc_start: 0.9058 (m) cc_final: 0.8424 (t) REVERT: A 314 TYR cc_start: 0.7705 (m-80) cc_final: 0.7117 (m-80) REVERT: A 515 MET cc_start: 0.8125 (tmm) cc_final: 0.7649 (tmm) REVERT: A 579 ARG cc_start: 0.8133 (pmt-80) cc_final: 0.7899 (pmt-80) REVERT: B 38 GLU cc_start: 0.8842 (tp30) cc_final: 0.8303 (tp30) REVERT: B 267 ARG cc_start: 0.8249 (ttt-90) cc_final: 0.7900 (tmt90) REVERT: B 314 TYR cc_start: 0.7601 (m-80) cc_final: 0.7046 (m-80) outliers start: 27 outliers final: 15 residues processed: 128 average time/residue: 0.6333 time to fit residues: 87.6175 Evaluate side-chains 121 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 104 time to evaluate : 0.363 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 486 HIS 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 435 VAL Chi-restraints excluded: chain B residue 467 PHE Chi-restraints excluded: chain B residue 486 HIS 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: 5.9990 chunk 128 optimal weight: 0.9990 chunk 30 optimal weight: 0.2980 chunk 90 optimal weight: 0.8980 chunk 53 optimal weight: 0.9990 chunk 70 optimal weight: 3.9990 chunk 55 optimal weight: 2.9990 chunk 58 optimal weight: 0.8980 chunk 59 optimal weight: 0.6980 chunk 2 optimal weight: 0.7980 chunk 31 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS A 737 GLN B 217 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 = 0.101157 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 68)----------------| | r_work = 0.2886 r_free = 0.2886 target = 0.072438 restraints weight = 25634.087| |-----------------------------------------------------------------------------| r_work (start): 0.2853 rms_B_bonded: 2.99 r_work: 0.2725 rms_B_bonded: 3.58 restraints_weight: 0.5000 r_work (final): 0.2725 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2707 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2707 r_free = 0.2707 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 = 0.2707 r_free = 0.2707 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.50 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2707 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8087 moved from start: 0.1986 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.108 11679 Z= 0.118 Angle : 0.599 11.855 15991 Z= 0.273 Chirality : 0.038 0.159 1676 Planarity : 0.004 0.043 1991 Dihedral : 6.425 87.483 1555 Min Nonbonded Distance : 2.092 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.14 % Allowed : 3.66 % Favored : 96.19 % Rotamer: Outliers : 2.17 % Allowed : 20.27 % Favored : 77.56 % 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: 2.40 (0.24), residues: 1394 helix: 2.49 (0.17), residues: 970 sheet: None (None), residues: 0 loop : -0.59 (0.32), residues: 424 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 0.025 0.001 TRP B 582 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00281 / 0.12 (11675) covalent geometry : angle 0.59868 / 0.27 (15991) hydrogen bonds : bond 0.04027 / 2.74 ( 764) hydrogen bonds : angle 4.06752 / 3.01 ( 2215) Misc. bond : bond 0.07086 / 3.52 ( 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 131 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 23 poor density : 108 time to evaluate : 0.429 Fit side-chains REVERT: A 19 PHE cc_start: 0.7532 (t80) cc_final: 0.7043 (m-80) REVERT: A 63 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8924 (p) REVERT: A 182 ASP cc_start: 0.7446 (OUTLIER) cc_final: 0.7227 (t70) REVERT: A 208 SER cc_start: 0.9032 (m) cc_final: 0.8423 (t) REVERT: A 314 TYR cc_start: 0.7669 (m-80) cc_final: 0.7102 (m-80) REVERT: A 515 MET cc_start: 0.8132 (tmm) cc_final: 0.7620 (tmm) REVERT: A 579 ARG cc_start: 0.8205 (pmt-80) cc_final: 0.7846 (pmt-80) REVERT: B 38 GLU cc_start: 0.8826 (tp30) cc_final: 0.8277 (tp30) REVERT: B 314 TYR cc_start: 0.7561 (m-80) cc_final: 0.7015 (m-80) REVERT: B 477 MET cc_start: 0.8002 (tmm) cc_final: 0.7759 (tmm) outliers start: 23 outliers final: 14 residues processed: 123 average time/residue: 0.6625 time to fit residues: 87.9636 Evaluate side-chains 122 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 106 time to evaluate : 0.332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 63 SER Chi-restraints excluded: chain A residue 182 ASP Chi-restraints excluded: chain A residue 187 ARG Chi-restraints excluded: chain A residue 247 LEU Chi-restraints excluded: chain A residue 486 HIS 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: 9.9990 chunk 77 optimal weight: 0.8980 chunk 78 optimal weight: 4.9990 chunk 110 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 62 optimal weight: 2.9990 chunk 108 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 94 optimal weight: 0.0980 chunk 100 optimal weight: 1.9990 chunk 97 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 568 HIS A 737 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3340 r_free = 0.3340 target = 0.101023 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.2870 r_free = 0.2870 target = 0.072278 restraints weight = 31553.320| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.28 r_work: 0.2712 rms_B_bonded: 3.81 restraints_weight: 0.5000 r_work (final): 0.2712 ------------------------------------------------------------------------------- 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 = 0.50 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 | |-----------------------------------------------------------------------------| r_final: 0.2676 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8088 moved from start: 0.2013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.154 11679 Z= 0.134 Angle : 0.611 12.843 15991 Z= 0.278 Chirality : 0.039 0.161 1676 Planarity : 0.004 0.043 1991 Dihedral : 6.436 88.794 1555 Min Nonbonded Distance : 2.048 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 2.81 % Allowed : 20.18 % 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: 2.38 (0.24), residues: 1394 helix: 2.49 (0.17), residues: 970 sheet: None (None), residues: 0 loop : -0.64 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG B 514 TYR 0.015 0.001 TYR B 30 PHE 0.014 0.001 PHE B 635 TRP 0.022 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 0.61079 / 0.28 (15991) hydrogen bonds : bond 0.04221 / 2.87 ( 764) hydrogen bonds : angle 4.05109 / 2.99 ( 2215) Misc. bond : bond 0.10497 / 5.22 ( 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 139 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 30 poor density : 109 time to evaluate : 0.437 Fit side-chains REVERT: A 19 PHE cc_start: 0.7564 (t80) cc_final: 0.6808 (m-80) REVERT: A 63 SER cc_start: 0.9208 (OUTLIER) cc_final: 0.8882 (p) REVERT: A 208 SER cc_start: 0.9040 (m) cc_final: 0.8444 (t) REVERT: A 314 TYR cc_start: 0.7706 (m-80) cc_final: 0.7141 (m-80) REVERT: A 467 PHE cc_start: 0.6530 (OUTLIER) cc_final: 0.6022 (m-80) REVERT: A 515 MET cc_start: 0.8129 (tmm) cc_final: 0.7619 (tmm) REVERT: A 579 ARG cc_start: 0.8245 (pmt-80) cc_final: 0.7939 (pmt-80) REVERT: B 38 GLU cc_start: 0.8879 (tp30) cc_final: 0.8337 (tp30) REVERT: B 314 TYR cc_start: 0.7557 (m-80) cc_final: 0.7003 (m-80) REVERT: B 708 MET cc_start: 0.9267 (mmm) cc_final: 0.9037 (mmp) outliers start: 30 outliers final: 14 residues processed: 129 average time/residue: 0.6390 time to fit residues: 89.1689 Evaluate side-chains 121 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 105 time to evaluate : 0.360 ------------------------------------------------------------------------------- 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 467 PHE Chi-restraints excluded: chain A residue 486 HIS 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 486 HIS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 139 random chunks: chunk 59 optimal weight: 3.9990 chunk 95 optimal weight: 6.9990 chunk 30 optimal weight: 1.9990 chunk 113 optimal weight: 2.9990 chunk 2 optimal weight: 2.9990 chunk 79 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 105 optimal weight: 2.9990 chunk 73 optimal weight: 0.9980 chunk 125 optimal weight: 4.9990 chunk 43 optimal weight: 4.9990 overall best weight: 1.5784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS A 737 GLN B 568 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3304 r_free = 0.3304 target = 0.098749 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.2839 r_free = 0.2839 target = 0.070597 restraints weight = 28159.374| |-----------------------------------------------------------------------------| r_work (start): 0.2800 rms_B_bonded: 3.06 r_work: 0.2667 rms_B_bonded: 3.60 restraints_weight: 0.5000 r_work (final): 0.2667 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2648 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2648 r_free = 0.2648 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 = 0.2648 r_free = 0.2648 target_work(ls_wunit_k1) = 0.062 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2648 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2039 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.225 11679 Z= 0.176 Angle : 0.651 13.895 15991 Z= 0.296 Chirality : 0.041 0.163 1676 Planarity : 0.004 0.043 1991 Dihedral : 6.531 87.417 1555 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 5.11 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.02 % Favored : 95.91 % Rotamer: Outliers : 1.81 % Allowed : 20.81 % Favored : 77.38 % 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: 2.26 (0.24), residues: 1394 helix: 2.41 (0.17), residues: 971 sheet: -2.97 (1.46), residues: 10 loop : -0.66 (0.32), residues: 413 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.006 0.000 ARG A 358 TYR 0.012 0.001 TYR A 30 PHE 0.016 0.001 PHE B 635 TRP 0.020 0.001 TRP B 582 HIS 0.009 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00436 / 0.18 (11675) covalent geometry : angle 0.65123 / 0.30 (15991) hydrogen bonds : bond 0.04854 / 3.30 ( 764) hydrogen bonds : angle 4.13262 / 3.06 ( 2215) Misc. bond : bond 0.15821 / 7.88 ( 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 125 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 19 poor density : 106 time to evaluate : 0.492 Fit side-chains REVERT: A 19 PHE cc_start: 0.7151 (t80) cc_final: 0.6817 (m-80) REVERT: A 63 SER cc_start: 0.9229 (OUTLIER) cc_final: 0.8876 (p) REVERT: A 208 SER cc_start: 0.9116 (m) cc_final: 0.8505 (t) REVERT: A 314 TYR cc_start: 0.7655 (m-80) cc_final: 0.7113 (m-80) REVERT: A 467 PHE cc_start: 0.6584 (OUTLIER) cc_final: 0.6063 (m-80) REVERT: A 515 MET cc_start: 0.8133 (tmm) cc_final: 0.7661 (tmm) REVERT: A 579 ARG cc_start: 0.8359 (pmt-80) cc_final: 0.8037 (pmt-80) REVERT: B 38 GLU cc_start: 0.8877 (tp30) cc_final: 0.8324 (tp30) REVERT: B 314 TYR cc_start: 0.7588 (m-80) cc_final: 0.7030 (m-80) REVERT: B 477 MET cc_start: 0.7997 (tmm) cc_final: 0.7743 (tmm) outliers start: 19 outliers final: 14 residues processed: 119 average time/residue: 0.6492 time to fit residues: 83.5518 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 : 0.459 ------------------------------------------------------------------------------- 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 467 PHE Chi-restraints excluded: chain A residue 486 HIS 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 486 HIS Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 624 ASN 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: 0.5980 chunk 16 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 74 optimal weight: 0.9990 chunk 4 optimal weight: 0.8980 chunk 15 optimal weight: 0.7980 chunk 103 optimal weight: 0.0010 chunk 19 optimal weight: 0.4980 chunk 127 optimal weight: 1.9990 chunk 81 optimal weight: 6.9990 chunk 7 optimal weight: 0.7980 overall best weight: 0.5186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS A 737 GLN B 568 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 = 0.3348 r_free = 0.3348 target = 0.101129 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.071956 restraints weight = 31372.142| |-----------------------------------------------------------------------------| r_work (start): 0.2846 rms_B_bonded: 3.27 r_work: 0.2711 rms_B_bonded: 3.80 restraints_weight: 0.5000 r_work (final): 0.2711 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2702 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2702 r_free = 0.2702 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 = 0.2702 r_free = 0.2702 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2702 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8077 moved from start: 0.2236 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.084 11679 Z= 0.112 Angle : 0.603 11.554 15991 Z= 0.274 Chirality : 0.038 0.156 1676 Planarity : 0.004 0.044 1991 Dihedral : 6.369 88.010 1555 Min Nonbonded Distance : 2.112 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.81 % Favored : 96.12 % Rotamer: Outliers : 1.99 % Allowed : 20.81 % 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: 2.41 (0.24), residues: 1394 helix: 2.51 (0.17), residues: 970 sheet: None (None), residues: 0 loop : -0.62 (0.32), residues: 424 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.010 0.000 ARG B 267 TYR 0.015 0.001 TYR B 30 PHE 0.009 0.001 PHE B 635 TRP 0.026 0.001 TRP B 582 HIS 0.005 0.001 HIS A 537 Details of bonding type rmsd/Z covalent geometry : bond 0.00258 / 0.11 (11675) covalent geometry : angle 0.60310 / 0.27 (15991) hydrogen bonds : bond 0.03900 / 2.66 ( 764) hydrogen bonds : angle 3.99829 / 2.95 ( 2215) Misc. bond : bond 0.05432 / 2.69 ( 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 130 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 21 poor density : 109 time to evaluate : 0.531 Fit side-chains revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7102 (t80) cc_final: 0.6814 (m-80) REVERT: A 63 SER cc_start: 0.9231 (OUTLIER) cc_final: 0.8912 (p) REVERT: A 208 SER cc_start: 0.9069 (m) cc_final: 0.8482 (t) REVERT: A 314 TYR cc_start: 0.7604 (m-80) cc_final: 0.7035 (m-80) REVERT: A 515 MET cc_start: 0.8120 (tmm) cc_final: 0.7623 (tmm) REVERT: B 38 GLU cc_start: 0.8881 (tp30) cc_final: 0.8319 (tp30) REVERT: B 314 TYR cc_start: 0.7510 (m-80) cc_final: 0.6933 (m-80) REVERT: B 477 MET cc_start: 0.7934 (tmm) cc_final: 0.7706 (tmm) REVERT: B 720 ARG cc_start: 0.7788 (OUTLIER) cc_final: 0.7519 (ttt180) outliers start: 21 outliers final: 11 residues processed: 123 average time/residue: 0.6110 time to fit residues: 81.5528 Evaluate side-chains 118 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 105 time to evaluate : 0.478 ------------------------------------------------------------------------------- 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 486 HIS 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 486 HIS Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 624 ASN 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: 1.9990 chunk 0 optimal weight: 10.0000 chunk 51 optimal weight: 1.9990 chunk 62 optimal weight: 0.8980 chunk 137 optimal weight: 3.9990 chunk 37 optimal weight: 0.9990 chunk 66 optimal weight: 5.9990 chunk 133 optimal weight: 0.6980 chunk 81 optimal weight: 7.9990 chunk 113 optimal weight: 0.0270 overall best weight: 0.9242 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS A 737 GLN B 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3336 r_free = 0.3336 target = 0.100293 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.2885 r_free = 0.2885 target = 0.071972 restraints weight = 25359.787| |-----------------------------------------------------------------------------| r_work (start): 0.2850 rms_B_bonded: 2.96 r_work: 0.2722 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.2722 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2704 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2704 r_free = 0.2704 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 = 0.2704 r_free = 0.2704 target_work(ls_wunit_k1) = 0.065 | | occupancies: max = 1.00 min = 0.48 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2704 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8099 moved from start: 0.2257 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.131 11679 Z= 0.130 Angle : 0.618 12.306 15991 Z= 0.281 Chirality : 0.039 0.152 1676 Planarity : 0.004 0.044 1991 Dihedral : 6.411 89.616 1555 Min Nonbonded Distance : 2.056 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.07 % Allowed : 3.88 % Favored : 96.05 % Rotamer: Outliers : 1.63 % Allowed : 21.27 % 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: 2.36 (0.24), residues: 1394 helix: 2.47 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -0.69 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 358 TYR 0.014 0.001 TYR A 30 PHE 0.013 0.001 PHE B 635 TRP 0.034 0.001 TRP B 582 HIS 0.007 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00317 / 0.13 (11675) covalent geometry : angle 0.61843 / 0.28 (15991) hydrogen bonds : bond 0.04081 / 2.78 ( 764) hydrogen bonds : angle 3.99971 / 2.96 ( 2215) Misc. bond : bond 0.08896 / 4.42 ( 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 124 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 107 time to evaluate : 0.470 Fit side-chains revert: symmetry clash REVERT: A 19 PHE cc_start: 0.7184 (t80) cc_final: 0.6920 (m-80) REVERT: A 63 SER cc_start: 0.9216 (OUTLIER) cc_final: 0.8886 (p) REVERT: A 208 SER cc_start: 0.9087 (m) cc_final: 0.8503 (t) REVERT: A 314 TYR cc_start: 0.7611 (m-80) cc_final: 0.7056 (m-80) REVERT: A 515 MET cc_start: 0.8107 (tmm) cc_final: 0.7642 (tmm) REVERT: B 38 GLU cc_start: 0.8873 (tp30) cc_final: 0.8311 (tp30) REVERT: B 314 TYR cc_start: 0.7567 (m-80) cc_final: 0.7005 (m-80) REVERT: B 477 MET cc_start: 0.7944 (tmm) cc_final: 0.7708 (tmm) REVERT: B 720 ARG cc_start: 0.7803 (OUTLIER) cc_final: 0.7543 (ttt180) outliers start: 17 outliers final: 12 residues processed: 119 average time/residue: 0.6207 time to fit residues: 80.1806 Evaluate side-chains 118 residues out of total 1104 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 104 time to evaluate : 0.427 ------------------------------------------------------------------------------- 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 486 HIS 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 486 HIS Chi-restraints excluded: chain B residue 493 PHE Chi-restraints excluded: chain B residue 624 ASN 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: 0.8980 chunk 122 optimal weight: 4.9990 chunk 96 optimal weight: 0.7980 chunk 81 optimal weight: 5.9990 chunk 64 optimal weight: 0.5980 chunk 91 optimal weight: 0.9990 chunk 113 optimal weight: 0.9990 chunk 65 optimal weight: 1.9990 chunk 78 optimal weight: 0.7980 chunk 11 optimal weight: 0.8980 chunk 55 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 568 HIS A 737 GLN B 320 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3346 r_free = 0.3346 target = 0.100958 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.2876 r_free = 0.2876 target = 0.071284 restraints weight = 37125.325| |-----------------------------------------------------------------------------| r_work (start): 0.2837 rms_B_bonded: 3.54 r_work: 0.2695 rms_B_bonded: 4.01 restraints_weight: 0.5000 r_work (final): 0.2695 ------------------------------------------------------------------------------- Occupancy refinement ******************** r_start: 0.2685 |-occupancy refinement: start-------------------------------------------------| | r_work = 0.2685 r_free = 0.2685 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 = 0.2685 r_free = 0.2685 target_work(ls_wunit_k1) = 0.064 | | occupancies: max = 1.00 min = 0.49 number of occupancies < 0.1: 0 | |-----------------------------------------------------------------------------| r_final: 0.2685 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8086 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.106 11679 Z= 0.122 Angle : 0.611 11.974 15991 Z= 0.279 Chirality : 0.039 0.152 1676 Planarity : 0.004 0.044 1991 Dihedral : 6.375 89.239 1555 Min Nonbonded Distance : 2.081 Molprobity Statistics. All-atom Clashscore : 5.47 Ramachandran Plot: Outliers : 0.07 % Allowed : 4.17 % Favored : 95.76 % Rotamer: Outliers : 1.54 % Allowed : 21.45 % 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: 2.35 (0.24), residues: 1394 helix: 2.47 (0.17), residues: 976 sheet: None (None), residues: 0 loop : -0.71 (0.32), residues: 418 Max deviation from planes: Type MaxDev MeanDev LineInFile ARG 0.007 0.000 ARG B 358 TYR 0.018 0.001 TYR B 30 PHE 0.011 0.001 PHE B 635 TRP 0.035 0.001 TRP A 582 HIS 0.005 0.001 HIS A 331 Details of bonding type rmsd/Z covalent geometry : bond 0.00296 / 0.12 (11675) covalent geometry : angle 0.61140 / 0.28 (15991) hydrogen bonds : bond 0.03938 / 2.68 ( 764) hydrogen bonds : angle 3.97048 / 2.93 ( 2215) Misc. bond : bond 0.07036 / 3.49 ( 4) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4256.74 seconds wall clock time: 73 minutes 9.88 seconds (4389.88 seconds total)