Starting phenix.real_space_refine on Tue Feb 13 22:44:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/02_2024/7y48_33603_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/02_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/02_2024/7y48_33603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/02_2024/7y48_33603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/02_2024/7y48_33603_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/02_2024/7y48_33603_neut_trim_updated.pdb" } 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 Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 4324 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 4324 Number of conformers: 1 Conformer: "" Number of residues, atoms: 569, 4324 Unusual residues: {'CLR': 1, 'IE5': 1} Classifications: {'peptide': 567, 'undetermined': 2} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PTRANS': 20, 'TRANS': 546, None: 2} Not linked: pdbres="GLY B 724 " pdbres="CLR B 801 " Not linked: pdbres="CLR B 801 " pdbres="IE5 B 802 " 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 Time building chain proxies: 3.11, per 1000 atoms: 0.72 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 - 3.50 Amino acid : False - 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: 1.61 Conformation dependent library (CDL) restraints added in 852.3 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... running ksdssp... Secondary structure from input PDB file: 23 helices and 2 sheets defined 63.7% alpha, 5.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.01 Creating SS restraints... Processing helix chain 'B' and resid 156 through 200 Proline residue: B 166 - end of helix removed outlier: 5.446A pdb=" N ARG B 169 " --> pdb=" O TYR B 165 " (cutoff:3.500A) removed outlier: 6.233A pdb=" N ARG B 170 " --> pdb=" O PRO B 166 " (cutoff:3.500A) 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 208 through 257 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) removed outlier: 3.852A pdb=" N ARG B 257 " --> pdb=" O SER B 253 " (cutoff:3.500A) Processing helix chain 'B' and resid 260 through 265 Processing helix chain 'B' and resid 268 through 276 Processing helix chain 'B' and resid 278 through 287 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 290 through 310 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 312 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 322 through 359 Processing helix chain 'B' and resid 362 through 366 Processing helix chain 'B' and resid 371 through 418 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) Processing helix chain 'B' and resid 422 through 424 No H-bonds generated for 'chain 'B' and resid 422 through 424' Processing helix chain 'B' and resid 428 through 467 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) removed outlier: 4.322A pdb=" N GLU B 467 " --> pdb=" O GLY B 463 " (cutoff:3.500A) Processing helix chain 'B' and resid 533 through 540 removed outlier: 3.517A pdb=" N LEU B 540 " --> pdb=" O LEU B 537 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 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 587 No H-bonds generated for 'chain 'B' and resid 585 through 587' Processing helix chain 'B' and resid 589 through 591 No H-bonds generated for 'chain 'B' and resid 589 through 591' Processing helix chain 'B' and resid 595 through 597 No H-bonds generated for 'chain 'B' and resid 595 through 597' Processing helix chain 'B' and resid 600 through 609 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 613 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) No H-bonds generated for 'chain 'B' and resid 613 through 618' Processing helix chain 'B' and resid 622 through 624 No H-bonds generated for 'chain 'B' and resid 622 through 624' Processing helix chain 'B' and resid 636 through 650 removed outlier: 3.501A pdb=" N ARG B 641 " --> pdb=" O GLY B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 666 through 679 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 715 through 719 removed outlier: 3.650A pdb=" N LEU B 719 " --> pdb=" O HIS B 715 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 715 through 719' Processing sheet with id= A, first strand: chain 'B' and resid 515 through 517 Processing sheet with id= B, first strand: chain 'B' and resid 709 through 713 removed outlier: 7.204A pdb=" N VAL B 703 " --> pdb=" O THR B 710 " (cutoff:3.500A) removed outlier: 5.037A pdb=" N TYR B 712 " --> pdb=" O VAL B 701 " (cutoff:3.500A) removed outlier: 7.302A pdb=" N VAL B 701 " --> pdb=" O TYR B 712 " (cutoff:3.500A) removed outlier: 3.597A pdb=" N MET B 700 " --> pdb=" O VAL B 522 " (cutoff:3.500A) removed outlier: 3.711A pdb=" N LEU B 704 " --> pdb=" O VAL B 526 " (cutoff:3.500A) removed outlier: 6.613A pdb=" N VAL B 685 " --> pdb=" O THR B 523 " (cutoff:3.500A) removed outlier: 7.934A pdb=" N LEU B 525 " --> pdb=" O VAL B 685 " (cutoff:3.500A) removed outlier: 7.490A pdb=" N VAL B 687 " --> pdb=" O LEU B 525 " (cutoff:3.500A) removed outlier: 7.836A pdb=" N GLY B 527 " --> pdb=" O VAL B 687 " (cutoff:3.500A) 250 hydrogen bonds defined for protein. 729 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: 1.19 Time building geometry restraints manager: 1.76 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: 99.91 - 106.72: 127 106.72 - 113.52: 2453 113.52 - 120.33: 1629 120.33 - 127.14: 1725 127.14 - 133.94: 44 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: 1050 2.80 - 3.32: 4316 3.32 - 3.85: 6660 3.85 - 4.37: 7495 4.37 - 4.90: 13073 Nonbonded interactions: 32594 Sorted by model distance: nonbonded pdb=" O GLN B 489 " pdb=" OG SER B 519 " model vdw 2.271 2.440 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 2.520 nonbonded pdb=" OE1 GLU B 356 " pdb=" NH1 ARG B 357 " model vdw 2.403 2.520 nonbonded pdb=" OE1 GLU B 259 " pdb=" N LYS B 474 " model vdw 2.409 2.520 ... (remaining 32589 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: 2.980 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.060 Construct map_model_manager: 0.000 Extract box with map and model: 11.540 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 17.150 Find NCS groups from input model: 0.110 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:14.380 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.340 ------------------------------------------------------------------------------- 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= 0.718 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 fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.457 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: 1.2993 time to fit residues: 117.0356 Evaluate side-chains 85 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 83 time to evaluate : 0.474 ------------------------------------------------------------------------------- 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: 0.9990 chunk 23 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 0.5980 chunk 43 optimal weight: 0.0020 chunk 16 optimal weight: 0.8980 chunk 26 optimal weight: 0.0170 chunk 32 optimal weight: 0.9990 chunk 50 optimal weight: 0.0270 overall best weight: 0.2684 ------------------------------------------------------------------------------- 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: 0.6961 moved from start: 0.1163 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= 0.178 Angle : 0.495 5.496 5978 Z= 0.256 Chirality : 0.037 0.134 701 Planarity : 0.004 0.047 756 Dihedral : 6.748 59.700 719 Min Nonbonded Distance : 2.316 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.03 % Allowed : 8.78 % Favored : 89.19 % 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: 1.76 (0.35), residues: 563 helix: 2.47 (0.28), residues: 350 sheet: -1.25 (0.74), residues: 41 loop : -1.02 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 440 HIS 0.004 0.001 HIS B 425 PHE 0.013 0.001 PHE B 190 TYR 0.006 0.001 TYR B 335 ARG 0.006 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 99 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 90 time to evaluate : 0.495 Fit side-chains REVERT: B 537 LEU cc_start: 0.7326 (mp) cc_final: 0.7118 (mp) REVERT: B 687 VAL cc_start: 0.7166 (OUTLIER) cc_final: 0.6890 (m) outliers start: 9 outliers final: 3 residues processed: 94 average time/residue: 1.2734 time to fit residues: 123.8739 Evaluate side-chains 90 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 86 time to evaluate : 0.461 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 391 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: 0.4980 chunk 15 optimal weight: 0.0870 chunk 42 optimal weight: 0.0030 chunk 34 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.0980 chunk 17 optimal weight: 0.4980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.0050 overall best weight: 0.1382 ------------------------------------------------------------------------------- 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: 0.6916 moved from start: 0.1560 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= 0.137 Angle : 0.431 5.468 5978 Z= 0.224 Chirality : 0.036 0.126 701 Planarity : 0.004 0.042 756 Dihedral : 5.575 57.875 715 Min Nonbonded Distance : 2.399 Molprobity Statistics. All-atom Clashscore : 2.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.03 % Allowed : 12.61 % Favored : 85.36 % 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: 1.99 (0.36), residues: 563 helix: 2.68 (0.28), residues: 350 sheet: -1.10 (0.72), residues: 41 loop : -1.01 (0.41), residues: 172 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 466 HIS 0.003 0.001 HIS B 425 PHE 0.009 0.001 PHE B 439 TYR 0.005 0.001 TYR B 335 ARG 0.003 0.000 ARG B 242 *********************** 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 95 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.721 Fit side-chains REVERT: B 265 LYS cc_start: 0.7404 (ptpp) cc_final: 0.7085 (ptpp) REVERT: B 687 VAL cc_start: 0.7044 (OUTLIER) cc_final: 0.6775 (m) outliers start: 9 outliers final: 2 residues processed: 91 average time/residue: 1.3266 time to fit residues: 125.4196 Evaluate side-chains 86 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 83 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 281 LEU Chi-restraints excluded: chain B residue 459 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: 0.0970 chunk 5 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 34 optimal weight: 0.9990 chunk 51 optimal weight: 0.9980 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 14 optimal weight: 0.9980 chunk 45 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.5178 ------------------------------------------------------------------------------- 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: 0.7026 moved from start: 0.1665 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 4403 Z= 0.241 Angle : 0.506 6.929 5978 Z= 0.258 Chirality : 0.038 0.134 701 Planarity : 0.004 0.043 756 Dihedral : 5.442 56.156 715 Min Nonbonded Distance : 2.312 Molprobity Statistics. All-atom Clashscore : 3.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.25 % Allowed : 12.84 % 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: 1.74 (0.35), residues: 563 helix: 2.39 (0.28), residues: 351 sheet: -0.97 (0.74), residues: 41 loop : -0.98 (0.43), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 440 HIS 0.006 0.001 HIS B 498 PHE 0.014 0.002 PHE B 190 TYR 0.008 0.001 TYR B 200 ARG 0.005 0.000 ARG B 242 *********************** 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 99 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.484 Fit side-chains REVERT: B 265 LYS cc_start: 0.7395 (ptpp) cc_final: 0.7112 (ptpp) REVERT: B 287 THR cc_start: 0.8055 (m) cc_final: 0.7844 (p) REVERT: B 416 LYS cc_start: 0.8394 (mmmt) cc_final: 0.8155 (mmtt) REVERT: B 653 LYS cc_start: 0.7604 (mtpm) cc_final: 0.7386 (mttm) REVERT: B 687 VAL cc_start: 0.7104 (OUTLIER) cc_final: 0.6864 (m) outliers start: 10 outliers final: 5 residues processed: 95 average time/residue: 1.2746 time to fit residues: 125.0820 Evaluate side-chains 96 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 90 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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 566 LEU 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: 0.7980 chunk 22 optimal weight: 0.3980 chunk 46 optimal weight: 0.0980 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 48 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.7980 chunk 10 optimal weight: 0.9990 chunk 31 optimal weight: 0.7980 overall best weight: 0.5380 ------------------------------------------------------------------------------- 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: 0.7040 moved from start: 0.1791 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= 0.245 Angle : 0.499 5.308 5978 Z= 0.257 Chirality : 0.039 0.134 701 Planarity : 0.004 0.042 756 Dihedral : 5.234 54.998 715 Min Nonbonded Distance : 2.336 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % 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: 1.59 (0.35), residues: 563 helix: 2.25 (0.27), residues: 351 sheet: -0.97 (0.75), residues: 41 loop : -1.01 (0.43), residues: 171 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 0.005 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 99 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 89 time to evaluate : 0.466 Fit side-chains REVERT: B 265 LYS cc_start: 0.7347 (ptpp) cc_final: 0.6904 (ptpp) REVERT: B 416 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8191 (mmtt) REVERT: B 472 GLU cc_start: 0.7502 (OUTLIER) cc_final: 0.7255 (tp30) REVERT: B 653 LYS cc_start: 0.7572 (mtpm) cc_final: 0.7367 (mttm) REVERT: B 687 VAL cc_start: 0.7072 (OUTLIER) cc_final: 0.6845 (m) outliers start: 10 outliers final: 5 residues processed: 93 average time/residue: 1.3412 time to fit residues: 128.7126 Evaluate side-chains 94 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 87 time to evaluate : 0.463 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ASP 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 515 LEU Chi-restraints excluded: chain B residue 560 GLN 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: 2.9990 chunk 54 optimal weight: 2.9990 chunk 44 optimal weight: 0.2980 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 0.0030 chunk 17 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.8980 overall best weight: 0.4990 ------------------------------------------------------------------------------- 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: 0.7041 moved from start: 0.1869 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= 0.235 Angle : 0.501 7.144 5978 Z= 0.257 Chirality : 0.038 0.133 701 Planarity : 0.004 0.043 756 Dihedral : 5.167 55.331 715 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 3.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.60 % Favored : 98.40 % Rotamer: Outliers : 2.48 % Allowed : 15.32 % Favored : 82.21 % 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: 1.54 (0.35), residues: 563 helix: 2.23 (0.27), residues: 350 sheet: -1.10 (0.74), residues: 42 loop : -1.01 (0.43), residues: 171 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 0.007 0.001 TYR B 200 ARG 0.007 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 98 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.480 Fit side-chains REVERT: B 265 LYS cc_start: 0.7301 (ptpp) cc_final: 0.6864 (ptpp) REVERT: B 416 LYS cc_start: 0.8406 (mmmt) cc_final: 0.8196 (mmtt) REVERT: B 472 GLU cc_start: 0.7499 (OUTLIER) cc_final: 0.7256 (tp30) REVERT: B 653 LYS cc_start: 0.7551 (mtpm) cc_final: 0.7347 (mttm) REVERT: B 687 VAL cc_start: 0.7058 (OUTLIER) cc_final: 0.6831 (m) outliers start: 11 outliers final: 6 residues processed: 94 average time/residue: 1.3864 time to fit residues: 134.3103 Evaluate side-chains 98 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.451 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ASP 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 687 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.6980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 32 optimal weight: 0.9990 chunk 24 optimal weight: 0.5980 chunk 21 optimal weight: 0.9990 chunk 16 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.0170 chunk 36 optimal weight: 0.9980 overall best weight: 0.4818 ------------------------------------------------------------------------------- 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: 0.7042 moved from start: 0.1942 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= 0.229 Angle : 0.493 5.947 5978 Z= 0.254 Chirality : 0.038 0.133 701 Planarity : 0.004 0.037 756 Dihedral : 5.089 55.931 715 Min Nonbonded Distance : 2.347 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.03 % Allowed : 16.22 % Favored : 81.76 % 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: 1.53 (0.35), residues: 563 helix: 2.20 (0.27), residues: 350 sheet: -1.14 (0.73), residues: 42 loop : -0.95 (0.44), residues: 171 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 0.007 0.001 TYR B 200 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 95 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 86 time to evaluate : 0.479 Fit side-chains REVERT: B 265 LYS cc_start: 0.7252 (ptpp) cc_final: 0.6785 (ptpp) REVERT: B 416 LYS cc_start: 0.8408 (mmmt) cc_final: 0.8171 (mmtt) REVERT: B 653 LYS cc_start: 0.7549 (mtpm) cc_final: 0.7339 (mttm) REVERT: B 687 VAL cc_start: 0.7051 (OUTLIER) cc_final: 0.6831 (m) outliers start: 9 outliers final: 6 residues processed: 92 average time/residue: 1.2929 time to fit residues: 122.8494 Evaluate side-chains 95 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.418 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ASP Chi-restraints excluded: chain B residue 314 LEU 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: 0.9980 chunk 5 optimal weight: 0.9980 chunk 42 optimal weight: 0.0970 chunk 49 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 47 optimal weight: 0.0980 chunk 50 optimal weight: 0.1980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.8980 chunk 39 optimal weight: 0.3980 chunk 15 optimal weight: 0.0050 overall best weight: 0.1592 ------------------------------------------------------------------------------- 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: 0.6961 moved from start: 0.1945 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= 0.147 Angle : 0.438 5.413 5978 Z= 0.228 Chirality : 0.036 0.131 701 Planarity : 0.003 0.034 756 Dihedral : 4.600 57.665 715 Min Nonbonded Distance : 2.371 Molprobity Statistics. All-atom Clashscore : 3.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.35 % Allowed : 17.34 % Favored : 81.31 % 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: 1.89 (0.36), residues: 563 helix: 2.50 (0.27), residues: 350 sheet: -1.13 (0.73), residues: 42 loop : -0.80 (0.45), residues: 171 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 466 HIS 0.004 0.001 HIS B 425 PHE 0.007 0.001 PHE B 488 TYR 0.005 0.001 TYR B 335 ARG 0.005 0.000 ARG B 395 *********************** 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 91 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 85 time to evaluate : 0.470 Fit side-chains REVERT: B 265 LYS cc_start: 0.7115 (ptpp) cc_final: 0.6714 (ptpp) REVERT: B 416 LYS cc_start: 0.8317 (mmmt) cc_final: 0.8076 (mmtt) REVERT: B 653 LYS cc_start: 0.7522 (mtpm) cc_final: 0.7314 (mttm) REVERT: B 687 VAL cc_start: 0.6972 (OUTLIER) cc_final: 0.6727 (m) outliers start: 6 outliers final: 4 residues processed: 88 average time/residue: 1.2558 time to fit residues: 114.2071 Evaluate side-chains 92 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.456 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ASP 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.3980 chunk 47 optimal weight: 0.0770 chunk 50 optimal weight: 0.8980 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 0.0770 chunk 32 optimal weight: 1.9990 chunk 25 optimal weight: 0.6980 chunk 36 optimal weight: 0.4980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 0.9990 chunk 44 optimal weight: 0.0010 overall best weight: 0.2102 ------------------------------------------------------------------------------- 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: 0.6963 moved from start: 0.2042 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 4403 Z= 0.159 Angle : 0.454 6.140 5978 Z= 0.235 Chirality : 0.036 0.144 701 Planarity : 0.004 0.033 756 Dihedral : 4.564 59.351 715 Min Nonbonded Distance : 2.384 Molprobity Statistics. All-atom Clashscore : 3.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.03 % Allowed : 16.44 % 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: 2.08 (0.36), residues: 563 helix: 2.68 (0.27), residues: 348 sheet: -1.11 (0.73), residues: 42 loop : -0.73 (0.44), residues: 173 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP B 440 HIS 0.004 0.001 HIS B 425 PHE 0.009 0.001 PHE B 439 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 93 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 84 time to evaluate : 0.548 Fit side-chains REVERT: B 265 LYS cc_start: 0.7060 (ptpp) cc_final: 0.6853 (ptpp) REVERT: B 416 LYS cc_start: 0.8313 (mmmt) cc_final: 0.8112 (mmtt) REVERT: B 653 LYS cc_start: 0.7525 (mtpm) cc_final: 0.7323 (mttm) REVERT: B 687 VAL cc_start: 0.6945 (OUTLIER) cc_final: 0.6716 (m) outliers start: 9 outliers final: 4 residues processed: 90 average time/residue: 1.3695 time to fit residues: 127.6448 Evaluate side-chains 93 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 88 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.5980 chunk 34 optimal weight: 0.4980 chunk 27 optimal weight: 0.5980 chunk 35 optimal weight: 0.0370 chunk 47 optimal weight: 0.5980 chunk 13 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 6 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 44 optimal weight: 2.9990 chunk 18 optimal weight: 0.6980 overall best weight: 0.4458 ------------------------------------------------------------------------------- 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: 0.7016 moved from start: 0.2089 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= 0.222 Angle : 0.507 5.385 5978 Z= 0.260 Chirality : 0.038 0.136 701 Planarity : 0.004 0.038 756 Dihedral : 4.780 59.882 715 Min Nonbonded Distance : 2.390 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.13 % Allowed : 17.79 % Favored : 81.08 % 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: 1.91 (0.36), residues: 563 helix: 2.52 (0.27), residues: 348 sheet: -1.10 (0.73), residues: 42 loop : -0.77 (0.45), residues: 173 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 0.012 0.001 PHE B 190 TYR 0.009 0.001 TYR B 200 ARG 0.008 0.001 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 89 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 84 time to evaluate : 0.472 Fit side-chains REVERT: B 265 LYS cc_start: 0.7105 (ptpp) cc_final: 0.6790 (ptpp) REVERT: B 653 LYS cc_start: 0.7542 (mtpm) cc_final: 0.7337 (mttm) REVERT: B 687 VAL cc_start: 0.6991 (OUTLIER) cc_final: 0.6773 (m) outliers start: 5 outliers final: 4 residues processed: 86 average time/residue: 1.3224 time to fit residues: 117.5092 Evaluate side-chains 92 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 209 ASP 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=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.9980 chunk 5 optimal weight: 0.9980 chunk 8 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 38 optimal weight: 0.2980 chunk 1 optimal weight: 0.5980 chunk 35 optimal weight: 0.0970 overall best weight: 0.4578 ------------------------------------------------------------------------------- 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 = 0.152987 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3617 r_free = 0.3617 target = 0.126345 restraints weight = 5582.921| |-----------------------------------------------------------------------------| r_work (start): 0.3607 rms_B_bonded: 1.93 r_work: 0.3509 rms_B_bonded: 2.21 restraints_weight: 0.5000 r_work: 0.3366 rms_B_bonded: 3.86 restraints_weight: 0.2500 r_work (final): 0.3366 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7496 moved from start: 0.2135 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= 0.226 Angle : 0.513 7.944 5978 Z= 0.262 Chirality : 0.038 0.137 701 Planarity : 0.004 0.036 756 Dihedral : 4.816 59.797 715 Min Nonbonded Distance : 2.356 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.80 % Allowed : 17.12 % Favored : 81.08 % 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: 1.78 (0.35), residues: 563 helix: 2.41 (0.27), residues: 349 sheet: -1.13 (0.72), residues: 42 loop : -0.83 (0.45), residues: 172 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 439 TYR 0.007 0.001 TYR B 200 ARG 0.009 0.001 ARG B 257 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2727.65 seconds wall clock time: 48 minutes 51.44 seconds (2931.44 seconds total)