Starting phenix.real_space_refine on Sun May 11 04:49:49 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y48_33603/05_2025/7y48_33603_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y48_33603/05_2025/7y48_33603.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.85 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/7y48_33603/05_2025/7y48_33603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y48_33603/05_2025/7y48_33603.map" model { file = "/net/cci-nas-00/data/ceres_data/7y48_33603/05_2025/7y48_33603_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y48_33603/05_2025/7y48_33603_neut_trim.cif" } resolution = 2.85 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= 0.016 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 3638 atoms to isotropic. 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: 4 Type Number sf(0) Gaussians S 16 5.16 5 C 2776 2.51 5 N 744 2.21 5 O 788 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5687/modules/chem_data/mon_lib" Total number of atoms: 4324 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4253 Number of conformers: 1 Conformer: "" Number of residues, atoms: 567, 4253 Classifications: {'peptide': 567} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 20, 'TRANS': 546} Chain breaks: 1 Unresolved non-hydrogen bonds: 77 Unresolved non-hydrogen angles: 94 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLU:plan': 7, 'ARG:plan': 1, 'ASN:plan1': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 42 Chain: "B" Number of atoms: 71 Number of conformers: 1 Conformer: "" Number of residues, atoms: 2, 71 Unusual residues: {'CLR': 1, 'IE5': 1} Classifications: {'undetermined': 2} Link IDs: {None: 1} Time building chain proxies: 4.18, per 1000 atoms: 0.97 Number of scatterers: 4324 At special positions: 0 Unit cell: (64.6, 89.25, 147.05, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 16 16.00 O 788 8.00 N 744 7.00 C 2776 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: 1.20 Conformation dependent library (CDL) restraints added in 620.7 milliseconds 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1040 Finding SS restraints... Secondary structure from input PDB file: 23 helices and 3 sheets defined 69.5% alpha, 7.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.50 Creating SS restraints... Processing helix chain 'B' and resid 155 through 165 Processing helix chain 'B' and resid 167 through 201 removed outlier: 4.042A pdb=" N ALA B 173 " --> pdb=" O ARG B 169 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N MET B 180 " --> pdb=" O GLY B 176 " (cutoff:3.500A) Proline residue: B 189 - end of helix Processing helix chain 'B' and resid 207 through 256 removed outlier: 3.546A pdb=" N LEU B 223 " --> pdb=" O SER B 219 " (cutoff:3.500A) removed outlier: 3.769A pdb=" N CYS B 224 " --> pdb=" O ALA B 220 " (cutoff:3.500A) removed outlier: 3.665A pdb=" N GLY B 240 " --> pdb=" O MET B 236 " (cutoff:3.500A) removed outlier: 3.754A pdb=" N GLN B 241 " --> pdb=" O GLN B 237 " (cutoff:3.500A) removed outlier: 3.620A pdb=" N ARG B 246 " --> pdb=" O ARG B 242 " (cutoff:3.500A) Processing helix chain 'B' and resid 259 through 266 removed outlier: 3.794A pdb=" N PHE B 263 " --> pdb=" O GLU B 259 " (cutoff:3.500A) Processing helix chain 'B' and resid 267 through 277 removed outlier: 3.675A pdb=" N LEU B 271 " --> pdb=" O ARG B 267 " (cutoff:3.500A) Processing helix chain 'B' and resid 277 through 288 removed outlier: 3.817A pdb=" N VAL B 286 " --> pdb=" O LEU B 282 " (cutoff:3.500A) removed outlier: 3.710A pdb=" N THR B 287 " --> pdb=" O GLY B 283 " (cutoff:3.500A) Processing helix chain 'B' and resid 289 through 311 removed outlier: 3.596A pdb=" N VAL B 302 " --> pdb=" O ALA B 298 " (cutoff:3.500A) removed outlier: 4.219A pdb=" N GLY B 303 " --> pdb=" O GLN B 299 " (cutoff:3.500A) removed outlier: 3.960A pdb=" N ILE B 304 " --> pdb=" O ALA B 300 " (cutoff:3.500A) Processing helix chain 'B' and resid 311 through 320 removed outlier: 3.515A pdb=" N THR B 316 " --> pdb=" O PRO B 312 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N PHE B 317 " --> pdb=" O ASN B 313 " (cutoff:3.500A) Processing helix chain 'B' and resid 321 through 360 removed outlier: 3.531A pdb=" N VAL B 325 " --> pdb=" O VAL B 321 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N ASN B 360 " --> pdb=" O GLU B 356 " (cutoff:3.500A) Processing helix chain 'B' and resid 361 through 367 Processing helix chain 'B' and resid 370 through 419 removed outlier: 4.083A pdb=" N ILE B 374 " --> pdb=" O GLU B 370 " (cutoff:3.500A) removed outlier: 4.120A pdb=" N LYS B 390 " --> pdb=" O GLN B 386 " (cutoff:3.500A) removed outlier: 3.929A pdb=" N GLU B 391 " --> pdb=" O LEU B 387 " (cutoff:3.500A) removed outlier: 3.962A pdb=" N GLY B 403 " --> pdb=" O PHE B 399 " (cutoff:3.500A) removed outlier: 4.100A pdb=" N LEU B 404 " --> pdb=" O GLY B 400 " (cutoff:3.500A) removed outlier: 3.739A pdb=" N VAL B 410 " --> pdb=" O GLY B 406 " (cutoff:3.500A) removed outlier: 3.593A pdb=" N LEU B 411 " --> pdb=" O ASN B 407 " (cutoff:3.500A) removed outlier: 3.539A pdb=" N LEU B 419 " --> pdb=" O TYR B 415 " (cutoff:3.500A) Processing helix chain 'B' and resid 421 through 425 removed outlier: 4.279A pdb=" N ALA B 424 " --> pdb=" O MET B 421 " (cutoff:3.500A) Processing helix chain 'B' and resid 427 through 466 removed outlier: 3.828A pdb=" N GLY B 446 " --> pdb=" O GLY B 442 " (cutoff:3.500A) removed outlier: 3.631A pdb=" N SER B 450 " --> pdb=" O GLY B 446 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N PHE B 451 " --> pdb=" O GLY B 447 " (cutoff:3.500A) Processing helix chain 'B' and resid 534 through 541 removed outlier: 3.980A pdb=" N SER B 538 " --> pdb=" O SER B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 562 through 569 removed outlier: 3.555A pdb=" N SER B 568 " --> pdb=" O VAL B 564 " (cutoff:3.500A) removed outlier: 3.729A pdb=" N LYS B 569 " --> pdb=" O TRP B 565 " (cutoff:3.500A) Processing helix chain 'B' and resid 585 through 592 removed outlier: 4.209A pdb=" N ALA B 589 " --> pdb=" O GLU B 586 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N TYR B 590 " --> pdb=" O ASN B 587 " (cutoff:3.500A) removed outlier: 3.922A pdb=" N GLY B 591 " --> pdb=" O ILE B 588 " (cutoff:3.500A) Processing helix chain 'B' and resid 594 through 598 Processing helix chain 'B' and resid 599 through 610 removed outlier: 3.643A pdb=" N ILE B 603 " --> pdb=" O THR B 599 " (cutoff:3.500A) removed outlier: 3.764A pdb=" N ALA B 607 " --> pdb=" O ILE B 603 " (cutoff:3.500A) removed outlier: 3.635A pdb=" N GLU B 608 " --> pdb=" O GLN B 604 " (cutoff:3.500A) Processing helix chain 'B' and resid 612 through 618 removed outlier: 3.892A pdb=" N ARG B 617 " --> pdb=" O VAL B 613 " (cutoff:3.500A) removed outlier: 4.109A pdb=" N ASN B 618 " --> pdb=" O ALA B 614 " (cutoff:3.500A) Processing helix chain 'B' and resid 621 through 624 Processing helix chain 'B' and resid 635 through 651 removed outlier: 3.501A pdb=" N ARG B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 665 through 680 removed outlier: 4.013A pdb=" N GLN B 673 " --> pdb=" O GLU B 669 " (cutoff:3.500A) removed outlier: 4.252A pdb=" N ARG B 678 " --> pdb=" O GLU B 674 " (cutoff:3.500A) removed outlier: 3.761A pdb=" N LEU B 679 " --> pdb=" O ALA B 675 " (cutoff:3.500A) Processing helix chain 'B' and resid 714 through 720 removed outlier: 3.589A pdb=" N LEU B 718 " --> pdb=" O LYS B 714 " (cutoff:3.500A) removed outlier: 3.650A pdb=" N LEU B 719 " --> pdb=" O HIS B 715 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'B' and resid 510 through 517 removed outlier: 7.066A pdb=" N GLN B 511 " --> pdb=" O HIS B 498 " (cutoff:3.500A) removed outlier: 6.991A pdb=" N HIS B 498 " --> pdb=" O GLN B 511 " (cutoff:3.500A) removed outlier: 5.487A pdb=" N PHE B 513 " --> pdb=" O ASN B 496 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 570 through 573 removed outlier: 6.685A pdb=" N THR B 523 " --> pdb=" O VAL B 687 " (cutoff:3.500A) removed outlier: 6.532A pdb=" N VAL B 522 " --> pdb=" O MET B 700 " (cutoff:3.500A) removed outlier: 8.119A pdb=" N ALA B 702 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 6.302A pdb=" N ALA B 524 " --> pdb=" O ALA B 702 " (cutoff:3.500A) removed outlier: 7.382A pdb=" N LEU B 704 " --> pdb=" O ALA B 524 " (cutoff:3.500A) removed outlier: 7.633A pdb=" N VAL B 526 " --> pdb=" O LEU B 704 " (cutoff:3.500A) removed outlier: 3.903A pdb=" N GLU B 711 " --> pdb=" O VAL B 703 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 582 through 583 278 hydrogen bonds defined for protein. 807 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: 1.28 Time building geometry restraints manager: 1.34 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 698 1.31 - 1.43: 1123 1.43 - 1.56: 2549 1.56 - 1.68: 4 1.68 - 1.81: 29 Bond restraints: 4403 Sorted by residual: bond pdb=" C13 IE5 B 802 " pdb=" C14 IE5 B 802 " ideal model delta sigma weight residual 1.357 1.612 -0.255 2.00e-02 2.50e+03 1.63e+02 bond pdb=" C1' IE5 B 802 " pdb=" CAC IE5 B 802 " ideal model delta sigma weight residual 1.353 1.594 -0.241 2.00e-02 2.50e+03 1.45e+02 bond pdb=" C2 IE5 B 802 " pdb=" N3 IE5 B 802 " ideal model delta sigma weight residual 1.321 1.499 -0.178 2.00e-02 2.50e+03 7.91e+01 bond pdb=" C15 IE5 B 802 " pdb=" C2 IE5 B 802 " ideal model delta sigma weight residual 1.450 1.610 -0.160 2.00e-02 2.50e+03 6.42e+01 bond pdb=" C15 IE5 B 802 " pdb=" C17 IE5 B 802 " ideal model delta sigma weight residual 1.363 1.521 -0.158 2.00e-02 2.50e+03 6.23e+01 ... (remaining 4398 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.44: 5847 2.44 - 4.89: 95 4.89 - 7.33: 27 7.33 - 9.78: 7 9.78 - 12.22: 2 Bond angle restraints: 5978 Sorted by residual: angle pdb=" N MET B 186 " pdb=" CA MET B 186 " pdb=" C MET B 186 " ideal model delta sigma weight residual 113.97 104.97 9.00 1.28e+00 6.10e-01 4.94e+01 angle pdb=" N GLY B 480 " pdb=" CA GLY B 480 " pdb=" C GLY B 480 " ideal model delta sigma weight residual 110.38 115.60 -5.22 1.28e+00 6.10e-01 1.66e+01 angle pdb=" C1' IE5 B 802 " pdb=" C27 IE5 B 802 " pdb=" N4 IE5 B 802 " ideal model delta sigma weight residual 106.14 118.36 -12.22 3.00e+00 1.11e-01 1.66e+01 angle pdb=" N VAL B 687 " pdb=" CA VAL B 687 " pdb=" C VAL B 687 " ideal model delta sigma weight residual 107.80 113.25 -5.45 1.45e+00 4.76e-01 1.41e+01 angle pdb=" C13 IE5 B 802 " pdb=" C12 IE5 B 802 " pdb=" NAA IE5 B 802 " ideal model delta sigma weight residual 105.60 116.36 -10.76 3.00e+00 1.11e-01 1.29e+01 ... (remaining 5973 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.83: 2446 17.83 - 35.66: 210 35.66 - 53.48: 30 53.48 - 71.31: 9 71.31 - 89.14: 3 Dihedral angle restraints: 2698 sinusoidal: 1078 harmonic: 1620 Sorted by residual: dihedral pdb=" CA ILE B 199 " pdb=" C ILE B 199 " pdb=" N TYR B 200 " pdb=" CA TYR B 200 " ideal model delta harmonic sigma weight residual -180.00 -162.18 -17.82 0 5.00e+00 4.00e-02 1.27e+01 dihedral pdb=" CA ASP B 681 " pdb=" CB ASP B 681 " pdb=" CG ASP B 681 " pdb=" OD1 ASP B 681 " ideal model delta sinusoidal sigma weight residual -30.00 -89.38 59.38 1 2.00e+01 2.50e-03 1.18e+01 dihedral pdb=" CA ASN B 478 " pdb=" CB ASN B 478 " pdb=" CG ASN B 478 " pdb=" OD1 ASN B 478 " ideal model delta sinusoidal sigma weight residual 120.00 -176.79 -63.21 2 2.00e+01 2.50e-03 9.56e+00 ... (remaining 2695 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.036: 496 0.036 - 0.072: 153 0.072 - 0.109: 38 0.109 - 0.145: 10 0.145 - 0.181: 4 Chirality restraints: 701 Sorted by residual: chirality pdb=" C9 CLR B 801 " pdb=" C10 CLR B 801 " pdb=" C11 CLR B 801 " pdb=" C8 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.45 -2.63 0.18 2.00e-01 2.50e+01 8.19e-01 chirality pdb=" C10 CLR B 801 " pdb=" C1 CLR B 801 " pdb=" C5 CLR B 801 " pdb=" C9 CLR B 801 " both_signs ideal model delta sigma weight residual False -2.85 -2.68 -0.17 2.00e-01 2.50e+01 6.93e-01 chirality pdb=" CA PHE B 499 " pdb=" N PHE B 499 " pdb=" C PHE B 499 " pdb=" CB PHE B 499 " both_signs ideal model delta sigma weight residual False 2.51 2.36 0.16 2.00e-01 2.50e+01 6.02e-01 ... (remaining 698 not shown) Planarity restraints: 756 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C1' IE5 B 802 " -0.046 2.00e-02 2.50e+03 1.70e-01 7.24e+02 pdb=" C27 IE5 B 802 " 0.025 2.00e-02 2.50e+03 pdb=" C31 IE5 B 802 " 0.025 2.00e-02 2.50e+03 pdb=" C33 IE5 B 802 " -0.175 2.00e-02 2.50e+03 pdb=" C8 IE5 B 802 " 0.130 2.00e-02 2.50e+03 pdb=" CAA IE5 B 802 " -0.387 2.00e-02 2.50e+03 pdb=" CAB IE5 B 802 " 0.263 2.00e-02 2.50e+03 pdb=" CAC IE5 B 802 " 0.040 2.00e-02 2.50e+03 pdb=" N4 IE5 B 802 " 0.135 2.00e-02 2.50e+03 pdb=" O2' IE5 B 802 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C10 IE5 B 802 " -0.209 2.00e-02 2.50e+03 1.49e-01 5.56e+02 pdb=" C11 IE5 B 802 " -0.126 2.00e-02 2.50e+03 pdb=" C12 IE5 B 802 " -0.034 2.00e-02 2.50e+03 pdb=" C13 IE5 B 802 " 0.031 2.00e-02 2.50e+03 pdb=" C14 IE5 B 802 " -0.034 2.00e-02 2.50e+03 pdb=" C2 IE5 B 802 " 0.342 2.00e-02 2.50e+03 pdb=" C28 IE5 B 802 " -0.002 2.00e-02 2.50e+03 pdb=" C29 IE5 B 802 " 0.164 2.00e-02 2.50e+03 pdb=" NAA IE5 B 802 " -0.126 2.00e-02 2.50e+03 pdb=" OP3 IE5 B 802 " -0.007 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C17 IE5 B 802 " -0.022 2.00e-02 2.50e+03 2.31e-02 6.65e+00 pdb=" C4 IE5 B 802 " 0.005 2.00e-02 2.50e+03 pdb=" C5 IE5 B 802 " 0.036 2.00e-02 2.50e+03 pdb=" C6 IE5 B 802 " -0.028 2.00e-02 2.50e+03 pdb=" N3 IE5 B 802 " 0.008 2.00e-02 2.50e+03 ... (remaining 753 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1049 2.80 - 3.32: 4296 3.32 - 3.85: 6634 3.85 - 4.37: 7439 4.37 - 4.90: 13064 Nonbonded interactions: 32482 Sorted by model distance: nonbonded pdb=" O GLN B 489 " pdb=" OG SER B 519 " model vdw 2.271 3.040 nonbonded pdb=" O ALA B 378 " pdb=" OD1 ASP B 382 " model vdw 2.277 3.040 nonbonded pdb=" N GLU B 373 " pdb=" OE1 GLU B 373 " model vdw 2.371 3.120 nonbonded pdb=" OE1 GLU B 356 " pdb=" NH1 ARG B 357 " model vdw 2.403 3.120 nonbonded pdb=" OE1 GLU B 259 " pdb=" N LYS B 474 " model vdw 2.409 3.120 ... (remaining 32477 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.360 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.050 Construct map_model_manager: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.150 Find NCS groups from input model: 0.040 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:13.750 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6938 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 : 0.010 0.255 4403 Z= 0.525 Angle : 0.839 12.224 5978 Z= 0.446 Chirality : 0.039 0.181 701 Planarity : 0.009 0.170 756 Dihedral : 13.515 89.138 1658 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.31 % Favored : 97.69 % Rotamer: Outliers : 0.90 % Allowed : 2.03 % Favored : 97.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.13 (0.36), residues: 563 helix: 1.91 (0.28), residues: 352 sheet: -1.68 (0.81), residues: 35 loop : -1.13 (0.41), residues: 176 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.003 0.001 HIS B 425 PHE 0.009 0.001 PHE B 190 TYR 0.005 0.001 TYR B 332 ARG 0.002 0.000 ARG B 248 Details of bonding type rmsd hydrogen bonds : bond 0.20111 ( 278) hydrogen bonds : angle 6.00166 ( 807) covalent geometry : bond 0.00958 ( 4403) covalent geometry : angle 0.83907 ( 5978) *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 85 time to evaluate : 0.448 Fit side-chains REVERT: B 185 SER cc_start: 0.7948 (t) cc_final: 0.7729 (m) REVERT: B 687 VAL cc_start: 0.6728 (OUTLIER) cc_final: 0.6507 (m) outliers start: 4 outliers final: 1 residues processed: 87 average time/residue: 1.2670 time to fit residues: 113.8656 Evaluate side-chains 85 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 2 poor density : 83 time to evaluate : 0.421 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 569 LYS Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 47 optimal weight: 2.9990 chunk 42 optimal weight: 0.0570 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 28 optimal weight: 0.5980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.6980 chunk 16 optimal weight: 0.3980 chunk 26 optimal weight: 0.0570 chunk 32 optimal weight: 0.9980 chunk 50 optimal weight: 1.9990 overall best weight: 0.3416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 237 GLN B 313 ASN B 478 ASN B 699 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3975 r_free = 0.3975 target = 0.155264 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3656 r_free = 0.3656 target = 0.129117 restraints weight = 5574.383| |-----------------------------------------------------------------------------| r_work (start): 0.3647 rms_B_bonded: 1.89 r_work: 0.3553 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.80 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7441 moved from start: 0.1306 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 4403 Z= 0.158 Angle : 0.516 5.466 5978 Z= 0.268 Chirality : 0.038 0.137 701 Planarity : 0.004 0.048 756 Dihedral : 6.765 60.267 719 Min Nonbonded Distance : 2.534 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.25 % Allowed : 8.33 % Favored : 89.41 % 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: 1.51 (0.35), residues: 563 helix: 2.21 (0.28), residues: 360 sheet: -1.40 (0.81), residues: 35 loop : -1.21 (0.40), residues: 168 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.005 0.001 HIS B 498 PHE 0.014 0.001 PHE B 190 TYR 0.007 0.001 TYR B 712 ARG 0.005 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.07665 ( 278) hydrogen bonds : angle 4.36944 ( 807) covalent geometry : bond 0.00304 ( 4403) covalent geometry : angle 0.51613 ( 5978) *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.461 Fit side-chains REVERT: B 265 LYS cc_start: 0.7582 (ptpp) cc_final: 0.7348 (ptpp) REVERT: B 472 GLU cc_start: 0.7729 (OUTLIER) cc_final: 0.7458 (tp30) REVERT: B 687 VAL cc_start: 0.7485 (OUTLIER) cc_final: 0.7098 (m) outliers start: 10 outliers final: 2 residues processed: 92 average time/residue: 1.2070 time to fit residues: 114.8961 Evaluate side-chains 91 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 87 time to evaluate : 0.473 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 15 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 40 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 16 optimal weight: 0.0060 chunk 29 optimal weight: 0.9980 chunk 21 optimal weight: 0.0370 chunk 45 optimal weight: 2.9990 chunk 54 optimal weight: 3.9990 overall best weight: 0.4674 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3950 r_free = 0.3950 target = 0.153294 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126752 restraints weight = 5597.141| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.91 r_work: 0.3518 rms_B_bonded: 2.17 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.81 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7493 moved from start: 0.1672 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4403 Z= 0.169 Angle : 0.506 5.831 5978 Z= 0.262 Chirality : 0.039 0.130 701 Planarity : 0.004 0.044 756 Dihedral : 5.834 59.215 715 Min Nonbonded Distance : 2.506 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.25 % Allowed : 11.04 % Favored : 86.71 % 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: 1.43 (0.35), residues: 563 helix: 2.12 (0.28), residues: 361 sheet: -1.26 (0.80), residues: 35 loop : -1.23 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 440 HIS 0.005 0.002 HIS B 425 PHE 0.014 0.002 PHE B 190 TYR 0.006 0.001 TYR B 544 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.08190 ( 278) hydrogen bonds : angle 4.18870 ( 807) covalent geometry : bond 0.00348 ( 4403) covalent geometry : angle 0.50579 ( 5978) *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 93 time to evaluate : 0.450 Fit side-chains REVERT: B 265 LYS cc_start: 0.7560 (ptpp) cc_final: 0.7317 (ptpp) REVERT: B 687 VAL cc_start: 0.7454 (OUTLIER) cc_final: 0.7053 (m) outliers start: 10 outliers final: 4 residues processed: 97 average time/residue: 1.3345 time to fit residues: 133.6087 Evaluate side-chains 94 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 89 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 5 optimal weight: 0.5980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.8980 chunk 31 optimal weight: 0.7980 chunk 44 optimal weight: 0.9990 chunk 34 optimal weight: 0.6980 chunk 18 optimal weight: 0.3980 chunk 22 optimal weight: 0.4980 chunk 4 optimal weight: 0.2980 chunk 29 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152688 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125576 restraints weight = 5623.044| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 2.00 r_work: 0.3498 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3348 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3348 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 moved from start: 0.1858 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4403 Z= 0.172 Angle : 0.506 6.320 5978 Z= 0.263 Chirality : 0.039 0.138 701 Planarity : 0.004 0.040 756 Dihedral : 5.511 55.171 715 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 1.58 % Allowed : 13.51 % Favored : 84.91 % 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: 1.34 (0.35), residues: 563 helix: 2.03 (0.27), residues: 361 sheet: -1.16 (0.81), residues: 35 loop : -1.24 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.006 0.001 HIS B 498 PHE 0.013 0.002 PHE B 190 TYR 0.007 0.001 TYR B 200 ARG 0.006 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.08316 ( 278) hydrogen bonds : angle 4.10995 ( 807) covalent geometry : bond 0.00360 ( 4403) covalent geometry : angle 0.50627 ( 5978) *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 94 time to evaluate : 0.493 Fit side-chains REVERT: B 185 SER cc_start: 0.8215 (p) cc_final: 0.7984 (m) REVERT: B 265 LYS cc_start: 0.7459 (ptpp) cc_final: 0.7166 (ptpp) REVERT: B 353 LEU cc_start: 0.7386 (tp) cc_final: 0.7054 (tt) REVERT: B 416 LYS cc_start: 0.8438 (mmmt) cc_final: 0.8031 (mmtp) REVERT: B 687 VAL cc_start: 0.7484 (OUTLIER) cc_final: 0.7060 (m) outliers start: 7 outliers final: 5 residues processed: 97 average time/residue: 1.3422 time to fit residues: 134.2653 Evaluate side-chains 98 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 92 time to evaluate : 0.467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 32 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 chunk 1 optimal weight: 0.0070 chunk 4 optimal weight: 0.0870 chunk 45 optimal weight: 0.9980 chunk 36 optimal weight: 2.9990 chunk 15 optimal weight: 0.7980 chunk 41 optimal weight: 0.6980 chunk 48 optimal weight: 0.8980 overall best weight: 0.4776 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 44)----------------| | r_work = 0.3611 r_free = 0.3611 target = 0.125663 restraints weight = 5624.147| |-----------------------------------------------------------------------------| r_work (start): 0.3601 rms_B_bonded: 1.99 r_work: 0.3496 rms_B_bonded: 2.32 restraints_weight: 0.5000 r_work: 0.3346 rms_B_bonded: 4.04 restraints_weight: 0.2500 r_work (final): 0.3346 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7523 moved from start: 0.1994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4403 Z= 0.168 Angle : 0.490 5.343 5978 Z= 0.256 Chirality : 0.039 0.134 701 Planarity : 0.004 0.041 756 Dihedral : 5.328 55.756 715 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.25 % Allowed : 14.19 % Favored : 83.56 % 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: 1.41 (0.35), residues: 563 helix: 2.09 (0.27), residues: 361 sheet: -1.11 (0.81), residues: 35 loop : -1.22 (0.41), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.005 0.001 HIS B 498 PHE 0.013 0.002 PHE B 190 TYR 0.009 0.001 TYR B 452 ARG 0.004 0.000 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.08279 ( 278) hydrogen bonds : angle 4.05578 ( 807) covalent geometry : bond 0.00346 ( 4403) covalent geometry : angle 0.48975 ( 5978) *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 91 time to evaluate : 0.441 Fit side-chains REVERT: B 265 LYS cc_start: 0.7370 (ptpp) cc_final: 0.6980 (ptpp) REVERT: B 416 LYS cc_start: 0.8449 (mmmt) cc_final: 0.8017 (mmtp) REVERT: B 687 VAL cc_start: 0.7455 (OUTLIER) cc_final: 0.7017 (m) outliers start: 10 outliers final: 7 residues processed: 96 average time/residue: 1.3474 time to fit residues: 133.3796 Evaluate side-chains 100 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 92 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 2 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 55 optimal weight: 3.9990 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 0.5980 chunk 36 optimal weight: 0.0170 chunk 29 optimal weight: 0.9980 chunk 7 optimal weight: 0.9980 chunk 31 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 38 optimal weight: 0.2980 overall best weight: 0.4618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3946 r_free = 0.3946 target = 0.152697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3615 r_free = 0.3615 target = 0.125973 restraints weight = 5628.784| |-----------------------------------------------------------------------------| r_work (start): 0.3606 rms_B_bonded: 1.93 r_work: 0.3507 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3361 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3361 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7507 moved from start: 0.2061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 4403 Z= 0.167 Angle : 0.491 5.311 5978 Z= 0.256 Chirality : 0.039 0.131 701 Planarity : 0.004 0.037 756 Dihedral : 5.218 56.240 715 Min Nonbonded Distance : 2.482 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.93 % Allowed : 13.51 % Favored : 83.56 % 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: 1.41 (0.35), residues: 563 helix: 2.10 (0.27), residues: 361 sheet: -0.92 (0.85), residues: 32 loop : -1.30 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.005 0.001 HIS B 498 PHE 0.012 0.001 PHE B 190 TYR 0.009 0.001 TYR B 452 ARG 0.008 0.000 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.08245 ( 278) hydrogen bonds : angle 4.01952 ( 807) covalent geometry : bond 0.00341 ( 4403) covalent geometry : angle 0.49059 ( 5978) *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 91 time to evaluate : 0.431 Fit side-chains REVERT: B 265 LYS cc_start: 0.7311 (ptpp) cc_final: 0.6915 (ptpp) REVERT: B 416 LYS cc_start: 0.8445 (mmmt) cc_final: 0.8040 (mmtp) REVERT: B 472 GLU cc_start: 0.7783 (OUTLIER) cc_final: 0.7515 (tp30) REVERT: B 687 VAL cc_start: 0.7410 (OUTLIER) cc_final: 0.6980 (m) outliers start: 13 outliers final: 7 residues processed: 97 average time/residue: 1.3611 time to fit residues: 136.0560 Evaluate side-chains 103 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 94 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 0 optimal weight: 2.9990 chunk 10 optimal weight: 0.9980 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 51 optimal weight: 0.9990 chunk 11 optimal weight: 0.8980 chunk 3 optimal weight: 0.7980 chunk 38 optimal weight: 0.1980 chunk 24 optimal weight: 0.5980 chunk 34 optimal weight: 0.9980 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3930 r_free = 0.3930 target = 0.151389 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3590 r_free = 0.3590 target = 0.124179 restraints weight = 5560.280| |-----------------------------------------------------------------------------| r_work (start): 0.3583 rms_B_bonded: 1.97 r_work: 0.3477 rms_B_bonded: 2.30 restraints_weight: 0.5000 r_work: 0.3328 rms_B_bonded: 3.99 restraints_weight: 0.2500 r_work (final): 0.3328 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7544 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.033 4403 Z= 0.191 Angle : 0.531 7.444 5978 Z= 0.275 Chirality : 0.040 0.131 701 Planarity : 0.004 0.036 756 Dihedral : 5.335 56.049 715 Min Nonbonded Distance : 2.454 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 3.15 % Allowed : 13.29 % Favored : 83.56 % 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 (0.35), residues: 563 helix: 2.02 (0.27), residues: 361 sheet: -0.99 (0.84), residues: 32 loop : -1.33 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.006 0.001 HIS B 498 PHE 0.013 0.002 PHE B 190 TYR 0.010 0.002 TYR B 452 ARG 0.005 0.000 ARG B 395 Details of bonding type rmsd hydrogen bonds : bond 0.08817 ( 278) hydrogen bonds : angle 4.09204 ( 807) covalent geometry : bond 0.00412 ( 4403) covalent geometry : angle 0.53111 ( 5978) *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 87 time to evaluate : 0.492 Fit side-chains REVERT: B 265 LYS cc_start: 0.7314 (ptpp) cc_final: 0.6831 (ptpp) REVERT: B 472 GLU cc_start: 0.7795 (OUTLIER) cc_final: 0.7521 (tp30) REVERT: B 687 VAL cc_start: 0.7445 (OUTLIER) cc_final: 0.7021 (m) outliers start: 14 outliers final: 9 residues processed: 96 average time/residue: 1.3084 time to fit residues: 129.5767 Evaluate side-chains 99 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 467 GLU Chi-restraints excluded: chain B residue 472 GLU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 22 optimal weight: 0.6980 chunk 1 optimal weight: 0.6980 chunk 16 optimal weight: 0.0570 chunk 27 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 37 optimal weight: 0.5980 chunk 2 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 42 optimal weight: 1.9990 chunk 4 optimal weight: 0.2980 overall best weight: 0.3698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.153281 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3623 r_free = 0.3623 target = 0.126701 restraints weight = 5565.554| |-----------------------------------------------------------------------------| r_work (start): 0.3613 rms_B_bonded: 1.91 r_work: 0.3516 rms_B_bonded: 2.19 restraints_weight: 0.5000 r_work: 0.3373 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3373 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7491 moved from start: 0.2173 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4403 Z= 0.155 Angle : 0.481 6.187 5978 Z= 0.252 Chirality : 0.038 0.126 701 Planarity : 0.004 0.036 756 Dihedral : 5.051 56.999 715 Min Nonbonded Distance : 2.438 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.25 % Allowed : 15.09 % Favored : 82.66 % 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 (0.35), residues: 563 helix: 2.20 (0.27), residues: 361 sheet: -1.14 (0.83), residues: 32 loop : -1.28 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.004 0.001 HIS B 498 PHE 0.011 0.001 PHE B 190 TYR 0.008 0.001 TYR B 452 ARG 0.006 0.000 ARG B 242 Details of bonding type rmsd hydrogen bonds : bond 0.07883 ( 278) hydrogen bonds : angle 3.94528 ( 807) covalent geometry : bond 0.00302 ( 4403) covalent geometry : angle 0.48111 ( 5978) *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 88 time to evaluate : 0.428 Fit side-chains REVERT: B 265 LYS cc_start: 0.7261 (ptpp) cc_final: 0.6776 (ptpp) REVERT: B 687 VAL cc_start: 0.7390 (OUTLIER) cc_final: 0.6949 (m) outliers start: 10 outliers final: 7 residues processed: 93 average time/residue: 1.2926 time to fit residues: 124.0410 Evaluate side-chains 97 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 89 time to evaluate : 0.475 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 13 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 0.4980 chunk 37 optimal weight: 0.0060 chunk 1 optimal weight: 0.4980 chunk 24 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 12 optimal weight: 1.9990 chunk 11 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 chunk 47 optimal weight: 0.0670 overall best weight: 0.3534 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3954 r_free = 0.3954 target = 0.153474 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 50)----------------| | r_work = 0.3625 r_free = 0.3625 target = 0.126830 restraints weight = 5629.262| |-----------------------------------------------------------------------------| r_work (start): 0.3615 rms_B_bonded: 1.93 r_work: 0.3517 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3372 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3372 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7490 moved from start: 0.2195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 4403 Z= 0.152 Angle : 0.493 6.765 5978 Z= 0.254 Chirality : 0.038 0.127 701 Planarity : 0.004 0.035 756 Dihedral : 5.009 58.146 715 Min Nonbonded Distance : 2.417 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.70 % Allowed : 15.32 % Favored : 81.98 % 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: 1.59 (0.35), residues: 563 helix: 2.30 (0.27), residues: 361 sheet: -1.17 (0.82), residues: 32 loop : -1.30 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.004 0.001 HIS B 498 PHE 0.011 0.001 PHE B 190 TYR 0.008 0.001 TYR B 452 ARG 0.008 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.07770 ( 278) hydrogen bonds : angle 3.91038 ( 807) covalent geometry : bond 0.00294 ( 4403) covalent geometry : angle 0.49275 ( 5978) *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.483 Fit side-chains REVERT: B 265 LYS cc_start: 0.7252 (ptpp) cc_final: 0.6764 (ptpp) REVERT: B 334 ARG cc_start: 0.7472 (mtp85) cc_final: 0.7259 (mtp85) REVERT: B 687 VAL cc_start: 0.7382 (OUTLIER) cc_final: 0.6920 (m) outliers start: 12 outliers final: 8 residues processed: 96 average time/residue: 1.2592 time to fit residues: 124.9356 Evaluate side-chains 100 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 428 VAL Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 21 optimal weight: 0.8980 chunk 24 optimal weight: 0.5980 chunk 18 optimal weight: 0.4980 chunk 43 optimal weight: 0.9990 chunk 7 optimal weight: 0.3980 chunk 19 optimal weight: 0.8980 chunk 23 optimal weight: 0.0970 chunk 47 optimal weight: 0.0010 chunk 9 optimal weight: 0.0970 chunk 50 optimal weight: 0.7980 chunk 40 optimal weight: 1.9990 overall best weight: 0.2182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3985 r_free = 0.3985 target = 0.155943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3664 r_free = 0.3664 target = 0.129795 restraints weight = 5582.519| |-----------------------------------------------------------------------------| r_work (start): 0.3655 rms_B_bonded: 1.91 r_work: 0.3560 rms_B_bonded: 2.18 restraints_weight: 0.5000 r_work: 0.3419 rms_B_bonded: 3.83 restraints_weight: 0.2500 r_work (final): 0.3419 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7435 moved from start: 0.2229 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 4403 Z= 0.132 Angle : 0.463 6.176 5978 Z= 0.240 Chirality : 0.037 0.126 701 Planarity : 0.004 0.036 756 Dihedral : 4.720 59.699 715 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.25 % Allowed : 15.77 % Favored : 81.98 % 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: 1.84 (0.35), residues: 563 helix: 2.47 (0.27), residues: 361 sheet: -1.23 (0.80), residues: 32 loop : -1.11 (0.44), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.004 0.001 HIS B 498 PHE 0.008 0.001 PHE B 190 TYR 0.008 0.001 TYR B 452 ARG 0.008 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.06893 ( 278) hydrogen bonds : angle 3.75587 ( 807) covalent geometry : bond 0.00240 ( 4403) covalent geometry : angle 0.46328 ( 5978) ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 80 time to evaluate : 0.443 Fit side-chains REVERT: B 265 LYS cc_start: 0.7187 (ptpp) cc_final: 0.6892 (ptpp) REVERT: B 334 ARG cc_start: 0.7396 (mtp85) cc_final: 0.7189 (mtp85) REVERT: B 687 VAL cc_start: 0.7277 (OUTLIER) cc_final: 0.6772 (m) outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 1.3434 time to fit residues: 117.9056 Evaluate side-chains 87 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 80 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 459 LEU Chi-restraints excluded: chain B residue 481 VAL Chi-restraints excluded: chain B residue 507 VAL Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 685 VAL Chi-restraints excluded: chain B residue 687 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 25 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 52 optimal weight: 1.9990 chunk 48 optimal weight: 0.6980 chunk 42 optimal weight: 0.3980 chunk 36 optimal weight: 0.8980 chunk 13 optimal weight: 0.8980 chunk 31 optimal weight: 0.5980 chunk 7 optimal weight: 0.4980 chunk 10 optimal weight: 0.2980 chunk 50 optimal weight: 0.9980 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3948 r_free = 0.3948 target = 0.152862 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3620 r_free = 0.3620 target = 0.126182 restraints weight = 5688.827| |-----------------------------------------------------------------------------| r_work (start): 0.3602 rms_B_bonded: 1.97 r_work: 0.3498 rms_B_bonded: 2.28 restraints_weight: 0.5000 r_work: 0.3351 rms_B_bonded: 3.97 restraints_weight: 0.2500 r_work (final): 0.3351 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.2285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4403 Z= 0.173 Angle : 0.519 6.186 5978 Z= 0.267 Chirality : 0.039 0.129 701 Planarity : 0.004 0.039 756 Dihedral : 5.041 59.854 715 Min Nonbonded Distance : 2.393 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.25 % Allowed : 16.22 % Favored : 81.53 % 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: 1.66 (0.35), residues: 563 helix: 2.33 (0.27), residues: 361 sheet: -1.24 (0.79), residues: 32 loop : -1.21 (0.43), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 440 HIS 0.005 0.001 HIS B 498 PHE 0.013 0.002 PHE B 190 TYR 0.011 0.001 TYR B 452 ARG 0.009 0.000 ARG B 257 Details of bonding type rmsd hydrogen bonds : bond 0.08181 ( 278) hydrogen bonds : angle 3.93981 ( 807) covalent geometry : bond 0.00364 ( 4403) covalent geometry : angle 0.51872 ( 5978) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 4528.13 seconds wall clock time: 78 minutes 20.95 seconds (4700.95 seconds total)