Starting phenix.real_space_refine on Wed Sep 25 07:33:53 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/09_2024/7psn_13615.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/09_2024/7psn_13615.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.9 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/09_2024/7psn_13615.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/09_2024/7psn_13615.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/09_2024/7psn_13615.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7psn_13615/09_2024/7psn_13615.cif" } resolution = 2.9 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.089 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 P 10 5.49 5 Mg 2 5.21 5 S 34 5.16 5 C 6088 2.51 5 N 1604 2.21 5 O 1726 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 12 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 9464 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 4622 Number of conformers: 1 Conformer: "" Number of residues, atoms: 585, 4622 Classifications: {'peptide': 585} Link IDs: {'PTRANS': 17, 'TRANS': 567} Chain: "A" Number of atoms: 110 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 110 Unusual residues: {' MG': 1, 'ANP': 1, 'LOP': 2} Classifications: {'undetermined': 4} Link IDs: {None: 3} Unresolved non-hydrogen bonds: 12 Unresolved non-hydrogen angles: 12 Unresolved non-hydrogen dihedrals: 12 Planarities with less than four sites: {'LOP:plan-2': 1} Unresolved non-hydrogen planarities: 4 Restraints were copied for chains: B Time building chain proxies: 8.94, per 1000 atoms: 0.94 Number of scatterers: 9464 At special positions: 0 Unit cell: (83.628, 75.348, 141.588, 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) S 34 16.00 P 10 15.00 Mg 2 11.99 O 1726 8.00 N 1604 7.00 C 6088 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.51 Conformation dependent library (CDL) restraints added in 1.0 seconds 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2184 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 68.7% alpha, 7.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.93 Creating SS restraints... Processing helix chain 'A' and resid 93 through 100 Processing helix chain 'A' and resid 104 through 140 removed outlier: 3.747A pdb=" N ARG A 108 " --> pdb=" O ASN A 104 " (cutoff:3.500A) Proline residue: A 129 - end of helix Processing helix chain 'A' and resid 151 through 201 removed outlier: 3.796A pdb=" N ASN A 185 " --> pdb=" O LYS A 181 " (cutoff:3.500A) Processing helix chain 'A' and resid 203 through 208 Processing helix chain 'A' and resid 210 through 233 Processing helix chain 'A' and resid 236 through 253 Processing helix chain 'A' and resid 256 through 304 removed outlier: 3.964A pdb=" N TRP A 279 " --> pdb=" O LYS A 275 " (cutoff:3.500A) removed outlier: 5.134A pdb=" N HIS A 282 " --> pdb=" O ALA A 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE A 283 " --> pdb=" O TRP A 279 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N ASN A 304 " --> pdb=" O ASP A 300 " (cutoff:3.500A) Processing helix chain 'A' and resid 304 through 310 Processing helix chain 'A' and resid 313 through 367 removed outlier: 3.583A pdb=" N LEU A 317 " --> pdb=" O ASN A 313 " (cutoff:3.500A) Processing helix chain 'A' and resid 371 through 396 Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 399 through 414 Processing helix chain 'A' and resid 475 through 483 removed outlier: 3.697A pdb=" N PHE A 483 " --> pdb=" O LEU A 479 " (cutoff:3.500A) Processing helix chain 'A' and resid 501 through 503 No H-bonds generated for 'chain 'A' and resid 501 through 503' Processing helix chain 'A' and resid 504 through 509 Processing helix chain 'A' and resid 525 through 531 Processing helix chain 'A' and resid 538 through 549 removed outlier: 3.545A pdb=" N VAL A 542 " --> pdb=" O THR A 538 " (cutoff:3.500A) Processing helix chain 'A' and resid 551 through 558 Processing helix chain 'A' and resid 567 through 571 removed outlier: 3.514A pdb=" N GLY A 570 " --> pdb=" O GLY A 567 " (cutoff:3.500A) Processing helix chain 'A' and resid 574 through 590 removed outlier: 3.738A pdb=" N LYS A 578 " --> pdb=" O SER A 574 " (cutoff:3.500A) Processing helix chain 'A' and resid 604 through 617 Processing helix chain 'A' and resid 632 through 636 removed outlier: 3.593A pdb=" N ILE A 636 " --> pdb=" O LEU A 633 " (cutoff:3.500A) Processing helix chain 'A' and resid 655 through 661 Processing helix chain 'A' and resid 665 through 676 Processing helix chain 'B' and resid 93 through 100 Processing helix chain 'B' and resid 104 through 140 removed outlier: 3.748A pdb=" N ARG B 108 " --> pdb=" O ASN B 104 " (cutoff:3.500A) Proline residue: B 129 - end of helix Processing helix chain 'B' and resid 151 through 201 removed outlier: 3.796A pdb=" N ASN B 185 " --> pdb=" O LYS B 181 " (cutoff:3.500A) Processing helix chain 'B' and resid 203 through 208 Processing helix chain 'B' and resid 210 through 233 Processing helix chain 'B' and resid 236 through 253 Processing helix chain 'B' and resid 256 through 304 removed outlier: 3.964A pdb=" N TRP B 279 " --> pdb=" O LYS B 275 " (cutoff:3.500A) removed outlier: 5.133A pdb=" N HIS B 282 " --> pdb=" O ALA B 278 " (cutoff:3.500A) removed outlier: 4.696A pdb=" N PHE B 283 " --> pdb=" O TRP B 279 " (cutoff:3.500A) removed outlier: 3.866A pdb=" N ASN B 304 " --> pdb=" O ASP B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 304 through 310 Processing helix chain 'B' and resid 313 through 367 removed outlier: 3.584A pdb=" N LEU B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 371 through 396 Proline residue: B 388 - end of helix Processing helix chain 'B' and resid 399 through 414 Processing helix chain 'B' and resid 475 through 483 removed outlier: 3.696A pdb=" N PHE B 483 " --> pdb=" O LEU B 479 " (cutoff:3.500A) Processing helix chain 'B' and resid 501 through 503 No H-bonds generated for 'chain 'B' and resid 501 through 503' Processing helix chain 'B' and resid 504 through 509 Processing helix chain 'B' and resid 525 through 531 Processing helix chain 'B' and resid 538 through 549 removed outlier: 3.545A pdb=" N VAL B 542 " --> pdb=" O THR B 538 " (cutoff:3.500A) Processing helix chain 'B' and resid 551 through 558 Processing helix chain 'B' and resid 567 through 571 removed outlier: 3.514A pdb=" N GLY B 570 " --> pdb=" O GLY B 567 " (cutoff:3.500A) Processing helix chain 'B' and resid 574 through 590 removed outlier: 3.738A pdb=" N LYS B 578 " --> pdb=" O SER B 574 " (cutoff:3.500A) Processing helix chain 'B' and resid 604 through 617 Processing helix chain 'B' and resid 632 through 636 removed outlier: 3.594A pdb=" N ILE B 636 " --> pdb=" O LEU B 633 " (cutoff:3.500A) Processing helix chain 'B' and resid 655 through 661 Processing helix chain 'B' and resid 665 through 676 Processing sheet with id=AA1, first strand: chain 'A' and resid 452 through 459 removed outlier: 5.687A pdb=" N LYS A 453 " --> pdb=" O PHE A 443 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE A 443 " --> pdb=" O LYS A 453 " (cutoff:3.500A) removed outlier: 7.454A pdb=" N PHE A 457 " --> pdb=" O GLU A 439 " (cutoff:3.500A) removed outlier: 5.123A pdb=" N GLU A 439 " --> pdb=" O PHE A 457 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE A 459 " --> pdb=" O THR A 437 " (cutoff:3.500A) removed outlier: 5.153A pdb=" N THR A 437 " --> pdb=" O ILE A 459 " (cutoff:3.500A) removed outlier: 4.013A pdb=" N VAL A 441 " --> pdb=" O SER A 490 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N SER A 490 " --> pdb=" O VAL A 441 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 512 through 515 removed outlier: 6.528A pdb=" N MET A 594 " --> pdb=" O VAL A 627 " (cutoff:3.500A) removed outlier: 7.442A pdb=" N ILE A 629 " --> pdb=" O MET A 594 " (cutoff:3.500A) removed outlier: 6.565A pdb=" N PHE A 596 " --> pdb=" O ILE A 629 " (cutoff:3.500A) removed outlier: 3.801A pdb=" N LYS A 641 " --> pdb=" O LYS A 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE A 642 " --> pdb=" O GLU A 653 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU A 653 " --> pdb=" O ILE A 642 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL A 644 " --> pdb=" O ARG A 651 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 452 through 459 removed outlier: 5.687A pdb=" N LYS B 453 " --> pdb=" O PHE B 443 " (cutoff:3.500A) removed outlier: 7.792A pdb=" N PHE B 443 " --> pdb=" O LYS B 453 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N PHE B 457 " --> pdb=" O GLU B 439 " (cutoff:3.500A) removed outlier: 5.124A pdb=" N GLU B 439 " --> pdb=" O PHE B 457 " (cutoff:3.500A) removed outlier: 6.999A pdb=" N ILE B 459 " --> pdb=" O THR B 437 " (cutoff:3.500A) removed outlier: 5.154A pdb=" N THR B 437 " --> pdb=" O ILE B 459 " (cutoff:3.500A) removed outlier: 4.012A pdb=" N VAL B 441 " --> pdb=" O SER B 490 " (cutoff:3.500A) removed outlier: 6.683A pdb=" N SER B 490 " --> pdb=" O VAL B 441 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 512 through 515 removed outlier: 6.529A pdb=" N MET B 594 " --> pdb=" O VAL B 627 " (cutoff:3.500A) removed outlier: 7.441A pdb=" N ILE B 629 " --> pdb=" O MET B 594 " (cutoff:3.500A) removed outlier: 6.566A pdb=" N PHE B 596 " --> pdb=" O ILE B 629 " (cutoff:3.500A) removed outlier: 3.803A pdb=" N LYS B 641 " --> pdb=" O LYS B 464 " (cutoff:3.500A) removed outlier: 6.430A pdb=" N ILE B 642 " --> pdb=" O GLU B 653 " (cutoff:3.500A) removed outlier: 4.133A pdb=" N GLU B 653 " --> pdb=" O ILE B 642 " (cutoff:3.500A) removed outlier: 6.924A pdb=" N VAL B 644 " --> pdb=" O ARG B 651 " (cutoff:3.500A) 634 hydrogen bonds defined for protein. 1878 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: 2.70 Time building geometry restraints manager: 2.90 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 1508 1.31 - 1.43: 2478 1.43 - 1.56: 5568 1.56 - 1.68: 14 1.68 - 1.80: 68 Bond restraints: 9636 Sorted by residual: bond pdb=" C3' ANP A 701 " pdb=" C4' ANP A 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C3' ANP B 701 " pdb=" C4' ANP B 701 " ideal model delta sigma weight residual 1.532 1.308 0.224 2.00e-02 2.50e+03 1.26e+02 bond pdb=" C4' ANP B 701 " pdb=" O4' ANP B 701 " ideal model delta sigma weight residual 1.431 1.626 -0.195 2.00e-02 2.50e+03 9.47e+01 bond pdb=" C4' ANP A 701 " pdb=" O4' ANP A 701 " ideal model delta sigma weight residual 1.431 1.625 -0.194 2.00e-02 2.50e+03 9.45e+01 bond pdb=" C6 ANP A 701 " pdb=" N6 ANP A 701 " ideal model delta sigma weight residual 1.340 1.471 -0.131 2.00e-02 2.50e+03 4.32e+01 ... (remaining 9631 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.77: 12846 2.77 - 5.54: 126 5.54 - 8.30: 28 8.30 - 11.07: 12 11.07 - 13.84: 8 Bond angle restraints: 13020 Sorted by residual: angle pdb=" C1' ANP B 701 " pdb=" N9 ANP B 701 " pdb=" C4 ANP B 701 " ideal model delta sigma weight residual 125.38 111.54 13.84 3.00e+00 1.11e-01 2.13e+01 angle pdb=" C1' ANP A 701 " pdb=" N9 ANP A 701 " pdb=" C4 ANP A 701 " ideal model delta sigma weight residual 125.38 111.59 13.79 3.00e+00 1.11e-01 2.11e+01 angle pdb=" O3 LOP A 704 " pdb=" P1 LOP A 704 " pdb=" O4 LOP A 704 " ideal model delta sigma weight residual 120.67 109.29 11.38 3.00e+00 1.11e-01 1.44e+01 angle pdb=" O3 LOP B 704 " pdb=" P1 LOP B 704 " pdb=" O4 LOP B 704 " ideal model delta sigma weight residual 120.67 109.32 11.35 3.00e+00 1.11e-01 1.43e+01 angle pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" O5' ANP A 701 " ideal model delta sigma weight residual 98.09 109.28 -11.19 3.00e+00 1.11e-01 1.39e+01 ... (remaining 13015 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 25.69: 5505 25.69 - 51.38: 293 51.38 - 77.07: 44 77.07 - 102.76: 8 102.76 - 128.44: 2 Dihedral angle restraints: 5852 sinusoidal: 2468 harmonic: 3384 Sorted by residual: dihedral pdb=" O1A ANP B 701 " pdb=" O3A ANP B 701 " pdb=" PA ANP B 701 " pdb=" PB ANP B 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.33 128.44 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O1A ANP A 701 " pdb=" O3A ANP A 701 " pdb=" PA ANP A 701 " pdb=" PB ANP A 701 " ideal model delta sinusoidal sigma weight residual 83.11 -45.31 128.42 1 3.00e+01 1.11e-03 1.73e+01 dihedral pdb=" O2' ANP B 701 " pdb=" C2' ANP B 701 " pdb=" C3' ANP B 701 " pdb=" O3' ANP B 701 " ideal model delta sinusoidal sigma weight residual 47.90 -36.39 84.29 1 3.00e+01 1.11e-03 9.61e+00 ... (remaining 5849 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 954 0.036 - 0.072: 408 0.072 - 0.108: 114 0.108 - 0.144: 14 0.144 - 0.180: 6 Chirality restraints: 1496 Sorted by residual: chirality pdb=" C2' ANP A 701 " pdb=" C1' ANP A 701 " pdb=" C3' ANP A 701 " pdb=" O2' ANP A 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.54 -0.18 2.00e-01 2.50e+01 8.10e-01 chirality pdb=" C2' ANP B 701 " pdb=" C1' ANP B 701 " pdb=" C3' ANP B 701 " pdb=" O2' ANP B 701 " both_signs ideal model delta sigma weight residual False -2.72 -2.55 -0.18 2.00e-01 2.50e+01 7.91e-01 chirality pdb=" C4 LOP A 704 " pdb=" C3 LOP A 704 " pdb=" C5 LOP A 704 " pdb=" O5 LOP A 704 " both_signs ideal model delta sigma weight residual False -2.34 -2.50 0.16 2.00e-01 2.50e+01 6.10e-01 ... (remaining 1493 not shown) Planarity restraints: 1620 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C13 LOP B 703 " 0.204 2.00e-02 2.50e+03 2.05e-01 4.21e+02 pdb=" C14 LOP B 703 " -0.200 2.00e-02 2.50e+03 pdb=" C15 LOP B 703 " -0.210 2.00e-02 2.50e+03 pdb=" C16 LOP B 703 " 0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C13 LOP A 703 " -0.204 2.00e-02 2.50e+03 2.05e-01 4.20e+02 pdb=" C14 LOP A 703 " 0.200 2.00e-02 2.50e+03 pdb=" C15 LOP A 703 " 0.210 2.00e-02 2.50e+03 pdb=" C16 LOP A 703 " -0.206 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 387 " -0.005 2.00e-02 2.50e+03 8.91e-03 7.93e-01 pdb=" C VAL A 387 " 0.015 2.00e-02 2.50e+03 pdb=" O VAL A 387 " -0.006 2.00e-02 2.50e+03 pdb=" N PRO A 388 " -0.005 2.00e-02 2.50e+03 ... (remaining 1617 not shown) Histogram of nonbonded interaction distances: 1.92 - 2.52: 70 2.52 - 3.11: 7626 3.11 - 3.71: 14350 3.71 - 4.30: 20897 4.30 - 4.90: 35778 Nonbonded interactions: 78721 Sorted by model distance: nonbonded pdb=" OE1 GLN B 517 " pdb="MG MG B 702 " model vdw 1.923 2.170 nonbonded pdb=" OE1 GLN A 517 " pdb="MG MG A 702 " model vdw 1.923 2.170 nonbonded pdb=" O2G ANP A 701 " pdb="MG MG A 702 " model vdw 1.963 2.170 nonbonded pdb=" O2G ANP B 701 " pdb="MG MG B 702 " model vdw 1.963 2.170 nonbonded pdb=" O2B ANP B 701 " pdb="MG MG B 702 " model vdw 2.047 2.170 ... (remaining 78716 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' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=0.98 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.830 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: 0.350 Check model and map are aligned: 0.060 Set scattering table: 0.090 Process input model: 26.650 Find NCS groups from input model: 0.270 Set up NCS constraints: 0.020 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:11.710 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 40.980 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7294 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 : 0.009 0.224 9636 Z= 0.565 Angle : 0.823 13.840 13020 Z= 0.365 Chirality : 0.042 0.180 1496 Planarity : 0.008 0.205 1620 Dihedral : 15.989 128.445 3668 Min Nonbonded Distance : 1.923 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.66 % Favored : 97.34 % Rotamer: Outliers : 0.00 % Allowed : 4.19 % Favored : 95.81 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -3.01 (0.21), residues: 1166 helix: -1.13 (0.16), residues: 772 sheet: -3.80 (0.43), residues: 52 loop : -3.49 (0.26), residues: 342 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 631 PHE 0.009 0.001 PHE A 179 TYR 0.011 0.002 TYR B 161 ARG 0.002 0.000 ARG A 209 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 122 time to evaluate : 1.060 Fit side-chains REVERT: A 426 LEU cc_start: 0.8655 (mm) cc_final: 0.8451 (mp) outliers start: 0 outliers final: 0 residues processed: 122 average time/residue: 1.2422 time to fit residues: 162.3341 Evaluate side-chains 74 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 1.043 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 97 optimal weight: 0.5980 chunk 87 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 30 optimal weight: 0.6980 chunk 59 optimal weight: 0.8980 chunk 46 optimal weight: 0.4980 chunk 90 optimal weight: 1.9990 chunk 35 optimal weight: 2.9990 chunk 55 optimal weight: 0.7980 chunk 67 optimal weight: 0.9980 chunk 105 optimal weight: 1.9990 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN ** A 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 454 ASN B 304 ASN ** B 347 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 454 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7376 moved from start: 0.1687 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 9636 Z= 0.190 Angle : 0.547 7.487 13020 Z= 0.278 Chirality : 0.041 0.148 1496 Planarity : 0.003 0.028 1620 Dihedral : 11.709 124.533 1470 Min Nonbonded Distance : 2.057 Molprobity Statistics. All-atom Clashscore : 5.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 0.60 % Allowed : 10.88 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.63 (0.24), residues: 1166 helix: 0.68 (0.18), residues: 780 sheet: -2.66 (0.50), residues: 62 loop : -2.64 (0.30), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 279 HIS 0.002 0.001 HIS B 197 PHE 0.012 0.001 PHE A 391 TYR 0.013 0.001 TYR B 161 ARG 0.005 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 120 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 114 time to evaluate : 1.246 Fit side-chains REVERT: A 331 SER cc_start: 0.7991 (m) cc_final: 0.7768 (m) REVERT: A 572 MET cc_start: 0.8512 (OUTLIER) cc_final: 0.8273 (mmm) REVERT: B 331 SER cc_start: 0.7994 (m) cc_final: 0.7770 (m) REVERT: B 572 MET cc_start: 0.8514 (OUTLIER) cc_final: 0.8274 (mmm) outliers start: 6 outliers final: 0 residues processed: 116 average time/residue: 1.1297 time to fit residues: 141.6684 Evaluate side-chains 98 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 96 time to evaluate : 1.008 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 572 MET Chi-restraints excluded: chain B residue 572 MET Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 58 optimal weight: 4.9990 chunk 32 optimal weight: 0.9990 chunk 87 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 105 optimal weight: 3.9990 chunk 114 optimal weight: 5.9990 chunk 93 optimal weight: 3.9990 chunk 104 optimal weight: 2.9990 chunk 35 optimal weight: 3.9990 chunk 84 optimal weight: 0.6980 overall best weight: 1.2786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 618 ASN B 304 ASN B 618 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7472 moved from start: 0.2477 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 9636 Z= 0.278 Angle : 0.576 7.374 13020 Z= 0.292 Chirality : 0.043 0.168 1496 Planarity : 0.003 0.032 1620 Dihedral : 10.277 114.315 1470 Min Nonbonded Distance : 1.968 Molprobity Statistics. All-atom Clashscore : 5.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.50 % Allowed : 13.07 % Favored : 85.43 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.06 (0.24), residues: 1166 helix: 1.00 (0.18), residues: 782 sheet: -2.32 (0.55), residues: 62 loop : -2.11 (0.32), residues: 322 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 143 HIS 0.004 0.001 HIS A 197 PHE 0.014 0.001 PHE A 391 TYR 0.011 0.001 TYR B 269 ARG 0.003 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 151 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 136 time to evaluate : 1.026 Fit side-chains REVERT: A 666 LEU cc_start: 0.7305 (tm) cc_final: 0.7029 (tm) REVERT: B 666 LEU cc_start: 0.7294 (tm) cc_final: 0.7024 (tm) outliers start: 15 outliers final: 6 residues processed: 142 average time/residue: 1.0730 time to fit residues: 165.3212 Evaluate side-chains 113 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 107 time to evaluate : 1.102 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 387 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain B residue 128 VAL Chi-restraints excluded: chain B residue 387 VAL Chi-restraints excluded: chain B residue 470 SER Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 104 optimal weight: 0.9980 chunk 79 optimal weight: 0.7980 chunk 54 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 50 optimal weight: 2.9990 chunk 70 optimal weight: 2.9990 chunk 105 optimal weight: 0.0270 chunk 112 optimal weight: 0.0070 chunk 55 optimal weight: 0.6980 chunk 100 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5056 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN B 134 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7421 moved from start: 0.2771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 9636 Z= 0.159 Angle : 0.499 6.917 13020 Z= 0.255 Chirality : 0.040 0.148 1496 Planarity : 0.003 0.026 1620 Dihedral : 9.674 109.600 1470 Min Nonbonded Distance : 2.016 Molprobity Statistics. All-atom Clashscore : 4.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 2.40 % Allowed : 14.57 % Favored : 83.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.64 (0.25), residues: 1166 helix: 1.49 (0.18), residues: 784 sheet: -2.07 (0.57), residues: 62 loop : -1.74 (0.33), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 279 HIS 0.003 0.000 HIS A 197 PHE 0.024 0.001 PHE A 350 TYR 0.027 0.002 TYR B 161 ARG 0.003 0.000 ARG A 424 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 118 time to evaluate : 1.051 Fit side-chains REVERT: A 134 GLN cc_start: 0.7035 (OUTLIER) cc_final: 0.6747 (mt0) REVERT: A 556 LYS cc_start: 0.7976 (mtmm) cc_final: 0.7655 (mptt) REVERT: A 581 LEU cc_start: 0.6934 (OUTLIER) cc_final: 0.6714 (mp) REVERT: A 666 LEU cc_start: 0.7271 (OUTLIER) cc_final: 0.7021 (tm) REVERT: B 134 GLN cc_start: 0.7029 (OUTLIER) cc_final: 0.6743 (mt0) REVERT: B 556 LYS cc_start: 0.7979 (mtmm) cc_final: 0.7660 (mptt) REVERT: B 581 LEU cc_start: 0.6917 (OUTLIER) cc_final: 0.6696 (mp) REVERT: B 666 LEU cc_start: 0.7283 (OUTLIER) cc_final: 0.7031 (tm) outliers start: 24 outliers final: 4 residues processed: 132 average time/residue: 1.2253 time to fit residues: 175.0532 Evaluate side-chains 114 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 104 time to evaluate : 0.985 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 93 optimal weight: 3.9990 chunk 63 optimal weight: 1.9990 chunk 1 optimal weight: 0.9990 chunk 83 optimal weight: 0.9990 chunk 46 optimal weight: 0.9980 chunk 95 optimal weight: 2.9990 chunk 77 optimal weight: 2.9990 chunk 0 optimal weight: 3.9990 chunk 57 optimal weight: 2.9990 chunk 100 optimal weight: 2.9990 chunk 28 optimal weight: 4.9990 overall best weight: 1.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 304 ASN A 379 ASN B 304 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7497 moved from start: 0.3004 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 9636 Z= 0.330 Angle : 0.575 6.728 13020 Z= 0.289 Chirality : 0.043 0.160 1496 Planarity : 0.003 0.025 1620 Dihedral : 9.837 110.541 1470 Min Nonbonded Distance : 1.944 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.06 % Favored : 97.94 % Rotamer: Outliers : 3.49 % Allowed : 14.07 % Favored : 82.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.61 (0.25), residues: 1166 helix: 1.42 (0.18), residues: 784 sheet: -1.87 (0.58), residues: 62 loop : -1.65 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 463 HIS 0.004 0.001 HIS B 197 PHE 0.018 0.001 PHE B 350 TYR 0.023 0.002 TYR B 161 ARG 0.004 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 144 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 35 poor density : 109 time to evaluate : 1.124 Fit side-chains REVERT: A 134 GLN cc_start: 0.6964 (OUTLIER) cc_final: 0.6631 (mt0) REVERT: A 581 LEU cc_start: 0.7002 (OUTLIER) cc_final: 0.6785 (mp) REVERT: A 666 LEU cc_start: 0.7305 (OUTLIER) cc_final: 0.7072 (tm) REVERT: B 134 GLN cc_start: 0.6966 (OUTLIER) cc_final: 0.6632 (mt0) REVERT: B 556 LYS cc_start: 0.7959 (mtmm) cc_final: 0.7625 (mptt) REVERT: B 581 LEU cc_start: 0.6998 (OUTLIER) cc_final: 0.6783 (mp) REVERT: B 666 LEU cc_start: 0.7314 (OUTLIER) cc_final: 0.7084 (tm) outliers start: 35 outliers final: 9 residues processed: 133 average time/residue: 1.0755 time to fit residues: 154.9878 Evaluate side-chains 119 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 104 time to evaluate : 1.098 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 581 LEU Chi-restraints excluded: chain A residue 614 THR Chi-restraints excluded: chain A residue 666 LEU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 581 LEU Chi-restraints excluded: chain B residue 614 THR Chi-restraints excluded: chain B residue 666 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 37 optimal weight: 6.9990 chunk 100 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 65 optimal weight: 0.8980 chunk 27 optimal weight: 5.9990 chunk 112 optimal weight: 5.9990 chunk 93 optimal weight: 2.9990 chunk 51 optimal weight: 4.9990 chunk 9 optimal weight: 1.9990 chunk 58 optimal weight: 3.9990 chunk 108 optimal weight: 0.7980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 304 ASN B 134 GLN B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7470 moved from start: 0.3146 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 9636 Z= 0.234 Angle : 0.524 7.033 13020 Z= 0.265 Chirality : 0.041 0.157 1496 Planarity : 0.003 0.024 1620 Dihedral : 9.574 107.874 1470 Min Nonbonded Distance : 1.976 Molprobity Statistics. All-atom Clashscore : 5.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer: Outliers : 3.29 % Allowed : 15.67 % Favored : 81.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.89 (0.25), residues: 1166 helix: 1.62 (0.18), residues: 784 sheet: -1.76 (0.59), residues: 62 loop : -1.50 (0.34), residues: 320 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 279 HIS 0.004 0.001 HIS B 197 PHE 0.016 0.001 PHE A 350 TYR 0.026 0.002 TYR B 161 ARG 0.004 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 33 poor density : 114 time to evaluate : 0.985 Fit side-chains REVERT: A 134 GLN cc_start: 0.7008 (OUTLIER) cc_final: 0.6766 (mt0) REVERT: A 556 LYS cc_start: 0.7952 (mtmm) cc_final: 0.7622 (mptt) REVERT: A 662 MET cc_start: 0.7262 (tmm) cc_final: 0.6960 (ttt) REVERT: B 134 GLN cc_start: 0.6991 (OUTLIER) cc_final: 0.6752 (mt0) REVERT: B 556 LYS cc_start: 0.7954 (mtmm) cc_final: 0.7625 (mptt) REVERT: B 662 MET cc_start: 0.7267 (tmm) cc_final: 0.6968 (ttt) outliers start: 33 outliers final: 13 residues processed: 134 average time/residue: 0.9547 time to fit residues: 139.3114 Evaluate side-chains 121 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 106 time to evaluate : 1.081 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 134 GLN Chi-restraints excluded: chain A residue 233 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 134 GLN Chi-restraints excluded: chain B residue 233 VAL Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 12 optimal weight: 0.1980 chunk 63 optimal weight: 4.9990 chunk 81 optimal weight: 1.9990 chunk 94 optimal weight: 0.9990 chunk 62 optimal weight: 0.5980 chunk 111 optimal weight: 0.5980 chunk 69 optimal weight: 1.9990 chunk 68 optimal weight: 0.6980 chunk 51 optimal weight: 4.9990 chunk 44 optimal weight: 2.9990 chunk 66 optimal weight: 1.9990 overall best weight: 0.6182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 304 ASN B 134 GLN B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 9636 Z= 0.177 Angle : 0.508 7.896 13020 Z= 0.258 Chirality : 0.040 0.163 1496 Planarity : 0.003 0.025 1620 Dihedral : 9.361 105.894 1470 Min Nonbonded Distance : 1.996 Molprobity Statistics. All-atom Clashscore : 5.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.10 % Allowed : 16.77 % Favored : 81.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.14 (0.25), residues: 1166 helix: 1.78 (0.18), residues: 786 sheet: -2.19 (0.58), residues: 52 loop : -1.28 (0.35), residues: 328 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 279 HIS 0.004 0.001 HIS A 197 PHE 0.018 0.001 PHE B 254 TYR 0.032 0.001 TYR B 161 ARG 0.004 0.000 ARG A 97 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 116 time to evaluate : 1.032 Fit side-chains REVERT: A 350 PHE cc_start: 0.7217 (t80) cc_final: 0.6599 (t80) REVERT: A 556 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7633 (mptt) REVERT: A 572 MET cc_start: 0.8472 (mmm) cc_final: 0.8199 (tpt) REVERT: A 662 MET cc_start: 0.7194 (tmm) cc_final: 0.6973 (ttt) REVERT: B 350 PHE cc_start: 0.7094 (t80) cc_final: 0.6507 (t80) REVERT: B 556 LYS cc_start: 0.7963 (mtmm) cc_final: 0.7637 (mptt) REVERT: B 572 MET cc_start: 0.8544 (mmm) cc_final: 0.8186 (tpt) REVERT: B 662 MET cc_start: 0.7194 (tmm) cc_final: 0.6872 (ttt) outliers start: 21 outliers final: 8 residues processed: 129 average time/residue: 1.0769 time to fit residues: 150.4093 Evaluate side-chains 117 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.006 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 128 VAL Chi-restraints excluded: chain A residue 403 LEU Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 609 GLN Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 33 optimal weight: 0.0770 chunk 21 optimal weight: 1.9990 chunk 71 optimal weight: 2.9990 chunk 76 optimal weight: 0.5980 chunk 55 optimal weight: 0.9990 chunk 10 optimal weight: 2.9990 chunk 87 optimal weight: 0.8980 chunk 101 optimal weight: 0.3980 chunk 107 optimal weight: 1.9990 chunk 97 optimal weight: 0.5980 chunk 104 optimal weight: 1.9990 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 304 ASN B 134 GLN B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3319 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.048 9636 Z= 0.162 Angle : 0.501 7.629 13020 Z= 0.254 Chirality : 0.039 0.157 1496 Planarity : 0.003 0.026 1620 Dihedral : 9.216 104.078 1470 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 2.50 % Allowed : 17.27 % Favored : 80.24 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.25), residues: 1166 helix: 1.95 (0.18), residues: 782 sheet: -2.16 (0.58), residues: 52 loop : -1.20 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 279 HIS 0.004 0.001 HIS A 197 PHE 0.021 0.001 PHE A 254 TYR 0.032 0.001 TYR B 161 ARG 0.006 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 109 time to evaluate : 1.161 Fit side-chains REVERT: A 350 PHE cc_start: 0.7231 (t80) cc_final: 0.6606 (t80) REVERT: A 556 LYS cc_start: 0.7962 (mtmm) cc_final: 0.7637 (mptt) REVERT: A 572 MET cc_start: 0.8398 (mmm) cc_final: 0.8151 (tpt) REVERT: A 662 MET cc_start: 0.7138 (tmm) cc_final: 0.6886 (ttt) REVERT: B 350 PHE cc_start: 0.7008 (t80) cc_final: 0.6538 (t80) REVERT: B 556 LYS cc_start: 0.7965 (mtmm) cc_final: 0.7640 (mptt) REVERT: B 572 MET cc_start: 0.8450 (mmm) cc_final: 0.8107 (tpt) REVERT: B 662 MET cc_start: 0.7136 (tmm) cc_final: 0.6883 (ttt) outliers start: 25 outliers final: 8 residues processed: 125 average time/residue: 0.9784 time to fit residues: 133.4153 Evaluate side-chains 117 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 109 time to evaluate : 1.013 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 107 optimal weight: 0.9990 chunk 62 optimal weight: 0.6980 chunk 45 optimal weight: 0.6980 chunk 81 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 94 optimal weight: 0.9980 chunk 98 optimal weight: 0.9990 chunk 103 optimal weight: 0.9980 chunk 68 optimal weight: 2.9990 chunk 110 optimal weight: 4.9990 chunk 67 optimal weight: 0.6980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 304 ASN B 134 GLN B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7444 moved from start: 0.3358 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9636 Z= 0.202 Angle : 0.521 7.886 13020 Z= 0.264 Chirality : 0.041 0.174 1496 Planarity : 0.003 0.027 1620 Dihedral : 9.233 105.074 1470 Min Nonbonded Distance : 1.982 Molprobity Statistics. All-atom Clashscore : 5.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.90 % Allowed : 18.16 % Favored : 79.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.31 (0.25), residues: 1166 helix: 1.94 (0.18), residues: 780 sheet: -1.74 (0.59), residues: 62 loop : -1.27 (0.35), residues: 324 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.004 0.001 HIS B 197 PHE 0.021 0.001 PHE A 254 TYR 0.031 0.001 TYR B 161 ARG 0.007 0.000 ARG B 424 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 128 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 109 time to evaluate : 0.964 Fit side-chains REVERT: A 350 PHE cc_start: 0.7257 (t80) cc_final: 0.6622 (t80) REVERT: A 556 LYS cc_start: 0.7971 (mtmm) cc_final: 0.7648 (mptt) REVERT: B 350 PHE cc_start: 0.7066 (t80) cc_final: 0.6563 (t80) REVERT: B 556 LYS cc_start: 0.7969 (mtmm) cc_final: 0.7648 (mptt) REVERT: B 572 MET cc_start: 0.8470 (mmm) cc_final: 0.8141 (tpt) outliers start: 19 outliers final: 8 residues processed: 121 average time/residue: 1.0627 time to fit residues: 139.8223 Evaluate side-chains 115 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 107 time to evaluate : 0.983 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 52 optimal weight: 0.2980 chunk 76 optimal weight: 0.5980 chunk 115 optimal weight: 0.3980 chunk 106 optimal weight: 2.9990 chunk 92 optimal weight: 0.9980 chunk 9 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 56 optimal weight: 8.9990 chunk 73 optimal weight: 2.9990 chunk 98 optimal weight: 0.9980 chunk 28 optimal weight: 0.6980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 134 GLN A 304 ASN B 134 GLN B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7423 moved from start: 0.3429 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 9636 Z= 0.172 Angle : 0.513 8.084 13020 Z= 0.260 Chirality : 0.040 0.175 1496 Planarity : 0.003 0.030 1620 Dihedral : 9.123 103.555 1470 Min Nonbonded Distance : 2.010 Molprobity Statistics. All-atom Clashscore : 6.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.97 % Favored : 98.03 % Rotamer: Outliers : 1.80 % Allowed : 18.76 % Favored : 79.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.50 (0.25), residues: 1166 helix: 2.05 (0.18), residues: 782 sheet: -2.11 (0.58), residues: 52 loop : -1.06 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP B 279 HIS 0.004 0.001 HIS B 197 PHE 0.020 0.001 PHE A 254 TYR 0.030 0.001 TYR B 161 ARG 0.007 0.000 ARG B 424 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2332 Ramachandran restraints generated. 1166 Oldfield, 0 Emsley, 1166 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 112 time to evaluate : 1.001 Fit side-chains REVERT: A 350 PHE cc_start: 0.7331 (t80) cc_final: 0.6632 (t80) REVERT: A 556 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7651 (mptt) REVERT: B 350 PHE cc_start: 0.6980 (t80) cc_final: 0.6559 (t80) REVERT: B 556 LYS cc_start: 0.7970 (mtmm) cc_final: 0.7651 (mptt) REVERT: B 572 MET cc_start: 0.8405 (mmm) cc_final: 0.8071 (tpt) outliers start: 18 outliers final: 11 residues processed: 122 average time/residue: 1.0210 time to fit residues: 135.3256 Evaluate side-chains 120 residues out of total 1002 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 109 time to evaluate : 0.926 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 358 MET Chi-restraints excluded: chain A residue 441 VAL Chi-restraints excluded: chain A residue 470 SER Chi-restraints excluded: chain A residue 609 GLN Chi-restraints excluded: chain A residue 652 GLU Chi-restraints excluded: chain B residue 403 LEU Chi-restraints excluded: chain B residue 441 VAL Chi-restraints excluded: chain B residue 470 SER Chi-restraints excluded: chain B residue 574 SER Chi-restraints excluded: chain B residue 609 GLN Chi-restraints excluded: chain B residue 652 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 116 random chunks: chunk 84 optimal weight: 0.5980 chunk 13 optimal weight: 0.6980 chunk 25 optimal weight: 2.9990 chunk 92 optimal weight: 0.6980 chunk 38 optimal weight: 1.9990 chunk 94 optimal weight: 0.8980 chunk 11 optimal weight: 0.6980 chunk 16 optimal weight: 2.9990 chunk 80 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 chunk 66 optimal weight: 0.8980 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 134 GLN A 304 ASN B 134 GLN B 304 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3661 r_free = 0.3661 target = 0.139327 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3358 r_free = 0.3358 target = 0.112003 restraints weight = 10827.976| |-----------------------------------------------------------------------------| r_work (start): 0.3352 rms_B_bonded: 2.15 r_work: 0.3237 rms_B_bonded: 2.71 restraints_weight: 0.5000 r_work: 0.3101 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7506 moved from start: 0.3459 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 9636 Z= 0.188 Angle : 0.525 8.117 13020 Z= 0.266 Chirality : 0.040 0.170 1496 Planarity : 0.003 0.029 1620 Dihedral : 9.105 104.084 1470 Min Nonbonded Distance : 1.994 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.14 % Favored : 97.86 % Rotamer: Outliers : 1.80 % Allowed : 19.26 % Favored : 78.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.49 (0.25), residues: 1166 helix: 2.03 (0.18), residues: 782 sheet: -2.04 (0.58), residues: 52 loop : -1.06 (0.35), residues: 332 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 463 HIS 0.004 0.001 HIS A 197 PHE 0.020 0.001 PHE A 254 TYR 0.031 0.001 TYR B 161 ARG 0.007 0.000 ARG B 424 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3209.57 seconds wall clock time: 57 minutes 3.25 seconds (3423.25 seconds total)