Starting phenix.real_space_refine on Sat Dec 28 02:55:59 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/7y48_33603/12_2024/7y48_33603_neut_trim.cif Found real_map, /net/cci-nas-00/data/ceres_data/7y48_33603/12_2024/7y48_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_33603/12_2024/7y48_33603.map" default_real_map = "/net/cci-nas-00/data/ceres_data/7y48_33603/12_2024/7y48_33603.map" model { file = "/net/cci-nas-00/data/ceres_data/7y48_33603/12_2024/7y48_33603_neut_trim.cif" } default_model = "/net/cci-nas-00/data/ceres_data/7y48_33603/12_2024/7y48_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-5532/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: 4.33, per 1000 atoms: 1.00 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: 1.28 Conformation dependent library (CDL) restraints added in 563.7 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: 0.45 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: 1.20 Time building geometry restraints manager: 1.35 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: 2.620 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: 0.000 Extract box with map and model: 0.180 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 15.780 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:13.590 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.360 ------------------------------------------------------------------------------- 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= 0.736 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 *********************** 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 : 0.433 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: 113.9338 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 : 0.458 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6977 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= 0.199 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 *********************** 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 : 0.416 Fit side-chains REVERT: B 265 LYS cc_start: 0.7451 (ptpp) cc_final: 0.7234 (ptpp) REVERT: B 472 GLU cc_start: 0.7495 (OUTLIER) cc_final: 0.7245 (tp30) REVERT: B 687 VAL cc_start: 0.7169 (OUTLIER) cc_final: 0.6892 (m) outliers start: 10 outliers final: 2 residues processed: 92 average time/residue: 1.2646 time to fit residues: 120.3765 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 : 0.470 ------------------------------------------------------------------------------- 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 28 optimal weight: 0.5980 chunk 15 optimal weight: 0.0980 chunk 42 optimal weight: 0.0980 chunk 34 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 0.5980 chunk 55 optimal weight: 2.9990 chunk 45 optimal weight: 2.9990 chunk 17 optimal weight: 0.5980 chunk 40 optimal weight: 0.9990 chunk 38 optimal weight: 0.1980 overall best weight: 0.3180 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6983 moved from start: 0.1634 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4403 Z= 0.180 Angle : 0.472 5.895 5978 Z= 0.246 Chirality : 0.038 0.129 701 Planarity : 0.004 0.041 756 Dihedral : 5.691 59.616 715 Min Nonbonded Distance : 2.505 Molprobity Statistics. All-atom Clashscore : 2.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 2.48 % Allowed : 11.04 % Favored : 86.49 % 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: 1.61 (0.35), residues: 563 helix: 2.28 (0.28), residues: 361 sheet: -1.22 (0.80), residues: 35 loop : -1.20 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 440 HIS 0.004 0.001 HIS B 425 PHE 0.011 0.001 PHE B 190 TYR 0.006 0.001 TYR B 335 ARG 0.005 0.000 ARG B 395 *********************** 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 99 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 88 time to evaluate : 0.398 Fit side-chains REVERT: B 265 LYS cc_start: 0.7330 (ptpp) cc_final: 0.7125 (ptpp) REVERT: B 687 VAL cc_start: 0.7119 (OUTLIER) cc_final: 0.6866 (m) outliers start: 11 outliers final: 4 residues processed: 91 average time/residue: 1.3640 time to fit residues: 128.1615 Evaluate side-chains 90 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 85 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 391 GLU Chi-restraints excluded: chain B residue 515 LEU Chi-restraints excluded: chain B residue 560 GLN Chi-restraints excluded: chain B residue 657 LEU 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 26 optimal weight: 0.6980 chunk 5 optimal weight: 0.8980 chunk 24 optimal weight: 0.3980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.7980 chunk 54 optimal weight: 2.9990 chunk 48 optimal weight: 0.8980 chunk 14 optimal weight: 0.8980 chunk 45 optimal weight: 0.9980 chunk 30 optimal weight: 0.7980 chunk 0 optimal weight: 2.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 313 ASN B 699 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7056 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 : 0.005 0.040 4403 Z= 0.310 Angle : 0.544 6.216 5978 Z= 0.281 Chirality : 0.041 0.137 701 Planarity : 0.004 0.045 756 Dihedral : 5.691 55.014 715 Min Nonbonded Distance : 2.449 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.03 % Allowed : 13.06 % 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: 1.26 (0.35), residues: 563 helix: 1.98 (0.28), residues: 359 sheet: -1.18 (0.81), residues: 35 loop : -1.26 (0.40), residues: 169 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 440 HIS 0.007 0.002 HIS B 498 PHE 0.014 0.002 PHE B 190 TYR 0.009 0.002 TYR B 200 ARG 0.005 0.001 ARG B 395 *********************** 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 100 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 91 time to evaluate : 0.506 Fit side-chains REVERT: B 265 LYS cc_start: 0.7370 (ptpp) cc_final: 0.7116 (ptpp) REVERT: B 687 VAL cc_start: 0.7082 (OUTLIER) cc_final: 0.6839 (m) outliers start: 9 outliers final: 5 residues processed: 95 average time/residue: 1.3987 time to fit residues: 137.1138 Evaluate side-chains 95 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 89 time to evaluate : 0.416 ------------------------------------------------------------------------------- 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 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.9980 chunk 22 optimal weight: 0.5980 chunk 46 optimal weight: 0.0670 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 48 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.0980 chunk 31 optimal weight: 0.9990 overall best weight: 0.2916 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6995 moved from start: 0.1911 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4403 Z= 0.167 Angle : 0.455 5.376 5978 Z= 0.240 Chirality : 0.037 0.130 701 Planarity : 0.004 0.041 756 Dihedral : 5.100 56.568 715 Min Nonbonded Distance : 2.508 Molprobity Statistics. All-atom Clashscore : 2.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.03 % Allowed : 14.41 % 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: 1.58 (0.35), residues: 563 helix: 2.24 (0.28), residues: 361 sheet: -1.11 (0.82), residues: 35 loop : -1.18 (0.40), residues: 167 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 466 HIS 0.004 0.001 HIS B 425 PHE 0.010 0.001 PHE B 190 TYR 0.005 0.001 TYR B 335 ARG 0.005 0.000 ARG B 257 *********************** 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 94 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 85 time to evaluate : 0.449 Fit side-chains REVERT: B 265 LYS cc_start: 0.7211 (ptpp) cc_final: 0.6927 (ptpp) REVERT: B 416 LYS cc_start: 0.8388 (mmmt) cc_final: 0.8064 (mmtt) REVERT: B 687 VAL cc_start: 0.7027 (OUTLIER) cc_final: 0.6786 (m) outliers start: 9 outliers final: 5 residues processed: 90 average time/residue: 1.3565 time to fit residues: 125.9818 Evaluate side-chains 92 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 86 time to evaluate : 0.442 ------------------------------------------------------------------------------- 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 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 13 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.7980 chunk 25 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.2980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.4980 chunk 30 optimal weight: 0.9990 chunk 39 optimal weight: 0.1980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7027 moved from start: 0.2003 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= 0.225 Angle : 0.484 5.326 5978 Z= 0.253 Chirality : 0.038 0.133 701 Planarity : 0.004 0.043 756 Dihedral : 5.174 56.634 715 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.25 % Allowed : 13.96 % Favored : 83.78 % 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: 2.18 (0.27), residues: 361 sheet: -1.19 (0.80), residues: 35 loop : -1.18 (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 0.012 0.002 PHE B 190 TYR 0.007 0.001 TYR B 200 ARG 0.006 0.000 ARG B 395 *********************** 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 97 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 87 time to evaluate : 0.462 Fit side-chains REVERT: B 265 LYS cc_start: 0.7195 (ptpp) cc_final: 0.6874 (ptpp) REVERT: B 416 LYS cc_start: 0.8411 (mmmt) cc_final: 0.7975 (mmtp) REVERT: B 687 VAL cc_start: 0.7032 (OUTLIER) cc_final: 0.6805 (m) outliers start: 10 outliers final: 7 residues processed: 92 average time/residue: 1.4428 time to fit residues: 136.7591 Evaluate side-chains 98 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 90 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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 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 30 optimal weight: 1.9990 chunk 45 optimal weight: 0.0570 chunk 53 optimal weight: 0.0670 chunk 33 optimal weight: 6.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.3980 chunk 21 optimal weight: 0.6980 chunk 16 optimal weight: 0.0770 chunk 10 optimal weight: 0.3980 chunk 34 optimal weight: 0.6980 chunk 36 optimal weight: 0.8980 overall best weight: 0.1994 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6965 moved from start: 0.2058 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 4403 Z= 0.154 Angle : 0.451 7.847 5978 Z= 0.235 Chirality : 0.037 0.127 701 Planarity : 0.004 0.035 756 Dihedral : 4.767 58.708 715 Min Nonbonded Distance : 2.458 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.80 % Allowed : 14.41 % Favored : 83.78 % 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: 1.79 (0.35), residues: 563 helix: 2.42 (0.27), residues: 361 sheet: -0.95 (0.84), residues: 32 loop : -1.18 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 440 HIS 0.003 0.001 HIS B 498 PHE 0.008 0.001 PHE B 190 TYR 0.005 0.001 TYR B 335 ARG 0.006 0.000 ARG B 395 *********************** 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 89 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 81 time to evaluate : 0.415 Fit side-chains REVERT: B 265 LYS cc_start: 0.7077 (ptpp) cc_final: 0.6747 (ptpp) REVERT: B 416 LYS cc_start: 0.8349 (mmmt) cc_final: 0.7896 (mmtt) REVERT: B 687 VAL cc_start: 0.6983 (OUTLIER) cc_final: 0.6744 (m) outliers start: 8 outliers final: 4 residues processed: 84 average time/residue: 1.3936 time to fit residues: 120.7735 Evaluate side-chains 89 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 84 time to evaluate : 0.460 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.1980 chunk 5 optimal weight: 0.3980 chunk 42 optimal weight: 0.0370 chunk 49 optimal weight: 0.7980 chunk 51 optimal weight: 0.5980 chunk 47 optimal weight: 0.8980 chunk 50 optimal weight: 0.5980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 overall best weight: 0.2858 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6981 moved from start: 0.2088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4403 Z= 0.170 Angle : 0.470 6.180 5978 Z= 0.244 Chirality : 0.037 0.135 701 Planarity : 0.004 0.035 756 Dihedral : 4.781 59.920 715 Min Nonbonded Distance : 2.451 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.58 % Allowed : 15.32 % Favored : 83.11 % 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: 1.85 (0.35), residues: 563 helix: 2.44 (0.27), residues: 361 sheet: -0.94 (0.84), residues: 32 loop : -1.09 (0.41), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 440 HIS 0.004 0.001 HIS B 498 PHE 0.010 0.001 PHE B 439 TYR 0.007 0.001 TYR B 335 ARG 0.008 0.001 ARG B 257 *********************** 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 88 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 81 time to evaluate : 0.537 Fit side-chains REVERT: B 265 LYS cc_start: 0.7073 (ptpp) cc_final: 0.6735 (ptpp) REVERT: B 416 LYS cc_start: 0.8354 (mmmt) cc_final: 0.7919 (mmtt) REVERT: B 687 VAL cc_start: 0.6967 (OUTLIER) cc_final: 0.6741 (m) outliers start: 7 outliers final: 5 residues processed: 85 average time/residue: 1.4380 time to fit residues: 126.3447 Evaluate side-chains 90 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.420 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 45 optimal weight: 0.1980 chunk 47 optimal weight: 0.0060 chunk 50 optimal weight: 0.5980 chunk 33 optimal weight: 8.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 36 optimal weight: 0.4980 chunk 55 optimal weight: 3.9990 chunk 51 optimal weight: 1.9990 chunk 44 optimal weight: 0.8980 overall best weight: 0.3796 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7000 moved from start: 0.2126 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= 0.196 Angle : 0.483 6.009 5978 Z= 0.250 Chirality : 0.038 0.134 701 Planarity : 0.004 0.035 756 Dihedral : 4.817 59.415 715 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.58 % Allowed : 15.09 % Favored : 83.33 % 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: 1.86 (0.35), residues: 563 helix: 2.42 (0.27), residues: 361 sheet: -0.90 (0.84), residues: 32 loop : -1.02 (0.42), residues: 170 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 440 HIS 0.004 0.001 HIS B 498 PHE 0.011 0.001 PHE B 190 TYR 0.007 0.001 TYR B 335 ARG 0.008 0.001 ARG B 257 *********************** 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 90 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 83 time to evaluate : 0.436 Fit side-chains REVERT: B 265 LYS cc_start: 0.7072 (ptpp) cc_final: 0.6632 (ptpp) REVERT: B 416 LYS cc_start: 0.8380 (mmmt) cc_final: 0.7964 (mmtp) REVERT: B 687 VAL cc_start: 0.6966 (OUTLIER) cc_final: 0.6756 (m) outliers start: 7 outliers final: 5 residues processed: 87 average time/residue: 1.4130 time to fit residues: 127.0568 Evaluate side-chains 90 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 84 time to evaluate : 0.471 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 4 optimal weight: 0.3980 chunk 34 optimal weight: 0.7980 chunk 27 optimal weight: 0.1980 chunk 35 optimal weight: 0.1980 chunk 47 optimal weight: 0.9990 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 1.9990 chunk 6 optimal weight: 0.2980 chunk 12 optimal weight: 0.5980 chunk 44 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.3380 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6997 moved from start: 0.2144 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 4403 Z= 0.186 Angle : 0.477 5.802 5978 Z= 0.248 Chirality : 0.038 0.132 701 Planarity : 0.004 0.035 756 Dihedral : 4.744 58.601 715 Min Nonbonded Distance : 2.501 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.07 % Favored : 98.93 % Rotamer: Outliers : 1.35 % Allowed : 15.54 % Favored : 83.11 % 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: 1.83 (0.35), residues: 563 helix: 2.38 (0.27), residues: 367 sheet: -0.96 (0.83), residues: 32 loop : -1.10 (0.43), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 440 HIS 0.004 0.001 HIS B 498 PHE 0.010 0.001 PHE B 190 TYR 0.006 0.001 TYR B 335 ARG 0.008 0.000 ARG B 257 ********************** 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 87 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 81 time to evaluate : 0.528 Fit side-chains REVERT: B 237 GLN cc_start: 0.8427 (tp40) cc_final: 0.8226 (mm-40) REVERT: B 265 LYS cc_start: 0.7046 (ptpp) cc_final: 0.6610 (ptpp) REVERT: B 416 LYS cc_start: 0.8382 (mmmt) cc_final: 0.7974 (mmtp) REVERT: B 687 VAL cc_start: 0.6956 (OUTLIER) cc_final: 0.6740 (m) outliers start: 6 outliers final: 5 residues processed: 84 average time/residue: 1.3815 time to fit residues: 119.7649 Evaluate side-chains 88 residues out of total 466 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 82 time to evaluate : 0.487 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 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 45 optimal weight: 0.0000 chunk 5 optimal weight: 0.8980 chunk 8 optimal weight: 0.7980 chunk 39 optimal weight: 0.0870 chunk 2 optimal weight: 0.9980 chunk 32 optimal weight: 0.7980 chunk 50 optimal weight: 0.4980 chunk 29 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 1 optimal weight: 0.3980 chunk 35 optimal weight: 0.1980 overall best weight: 0.2362 ------------------------------------------------------------------------------- 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 = 0.3985 r_free = 0.3985 target = 0.156096 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3659 r_free = 0.3659 target = 0.129480 restraints weight = 5580.728| |-----------------------------------------------------------------------------| r_work (start): 0.3649 rms_B_bonded: 1.95 r_work: 0.3552 rms_B_bonded: 2.25 restraints_weight: 0.5000 r_work: 0.3409 rms_B_bonded: 3.94 restraints_weight: 0.2500 r_work (final): 0.3409 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.2202 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= 0.163 Angle : 0.475 5.703 5978 Z= 0.247 Chirality : 0.037 0.134 701 Planarity : 0.004 0.036 756 Dihedral : 4.571 57.426 715 Min Nonbonded Distance : 2.497 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.35 % Allowed : 15.99 % 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: 1.94 (0.35), residues: 563 helix: 2.47 (0.27), residues: 367 sheet: -1.01 (0.82), residues: 32 loop : -1.04 (0.44), residues: 164 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP B 440 HIS 0.004 0.001 HIS B 498 PHE 0.009 0.001 PHE B 190 TYR 0.006 0.001 TYR B 335 ARG 0.008 0.001 ARG B 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2591.04 seconds wall clock time: 46 minutes 59.65 seconds (2819.65 seconds total)