Starting phenix.real_space_refine on Tue Nov 14 06:55:01 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/11_2023/7y48_33603_neut_trim_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/11_2023/7y48_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_33603/11_2023/7y48_33603.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/11_2023/7y48_33603.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/11_2023/7y48_33603_neut_trim_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7y48_33603/11_2023/7y48_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: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5144/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: 1.70 Conformation dependent library (CDL) restraints added in 903.0 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: 1.07 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: 1.29 Time building geometry restraints manager: 1.86 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: 2390 17.83 - 35.66: 210 35.66 - 53.48: 30 53.48 - 71.31: 9 71.31 - 89.14: 3 Dihedral angle restraints: 2642 sinusoidal: 1022 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 2639 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: 2.660 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: 11.270 Check model and map are aligned: 0.070 Set scattering table: 0.060 Process input model: 17.650 Find NCS groups from input model: 0.120 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:12.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 44.790 ------------------------------------------------------------------------------- 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 : 13.701 89.138 1602 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 *********************** 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 : 0.438 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 87 average time/residue: 1.3899 time to fit residues: 124.8983 Evaluate side-chains 84 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 83 time to evaluate : 0.541 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 1.7248 time to fit residues: 2.7858 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 overall best weight: 0.4026 ------------------------------------------------------------------------------- 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: 0.6993 moved from start: 0.1266 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4403 Z= 0.215 Angle : 0.523 5.426 5978 Z= 0.268 Chirality : 0.038 0.138 701 Planarity : 0.004 0.049 756 Dihedral : 6.594 59.559 658 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.80 % Allowed : 8.56 % Favored : 89.64 % 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: 1.60 (0.35), residues: 563 helix: 2.32 (0.28), residues: 350 sheet: -1.29 (0.75), residues: 41 loop : -1.04 (0.41), residues: 172 *********************** 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 fitting. rotamer outliers: 8 poor density : 90 time to evaluate : 0.500 Fit side-chains outliers start: 8 outliers final: 2 residues processed: 93 average time/residue: 1.3090 time to fit residues: 125.7647 Evaluate side-chains 88 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 86 time to evaluate : 0.471 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 2.0170 time to fit residues: 2.7522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 28 optimal weight: 0.2980 chunk 15 optimal weight: 0.0570 chunk 42 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 14 optimal weight: 0.5980 chunk 50 optimal weight: 1.9990 chunk 55 optimal weight: 4.9990 chunk 45 optimal weight: 0.0570 chunk 17 optimal weight: 0.6980 chunk 40 optimal weight: 0.9980 chunk 38 optimal weight: 0.6980 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 699 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6994 moved from start: 0.1499 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= 0.186 Angle : 0.477 5.320 5978 Z= 0.245 Chirality : 0.037 0.132 701 Planarity : 0.004 0.042 756 Dihedral : 5.737 59.704 658 Min Nonbonded Distance : 2.343 Molprobity Statistics. All-atom Clashscore : 3.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.70 % Allowed : 10.81 % 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: 1.66 (0.35), residues: 563 helix: 2.37 (0.28), residues: 350 sheet: -1.28 (0.73), residues: 41 loop : -1.01 (0.41), residues: 172 *********************** 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 101 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 89 time to evaluate : 0.526 Fit side-chains outliers start: 12 outliers final: 5 residues processed: 94 average time/residue: 1.3085 time to fit residues: 127.2030 Evaluate side-chains 92 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.517 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 2 residues processed: 3 average time/residue: 1.0634 time to fit residues: 4.0128 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.8980 chunk 5 optimal weight: 0.9980 chunk 24 optimal weight: 0.2980 chunk 34 optimal weight: 0.9980 chunk 51 optimal weight: 0.4980 chunk 54 optimal weight: 3.9990 chunk 48 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 45 optimal weight: 0.8980 chunk 30 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7057 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 4403 Z= 0.286 Angle : 0.543 7.298 5978 Z= 0.276 Chirality : 0.040 0.135 701 Planarity : 0.004 0.042 756 Dihedral : 5.504 49.775 658 Min Nonbonded Distance : 2.320 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.13 % Favored : 97.87 % Rotamer: Outliers : 2.03 % Allowed : 12.84 % Favored : 85.14 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.35), residues: 563 helix: 2.10 (0.28), residues: 350 sheet: -1.28 (0.72), residues: 41 loop : -1.06 (0.42), residues: 172 *********************** 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 102 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.492 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 98 average time/residue: 1.3365 time to fit residues: 135.2537 Evaluate side-chains 95 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 90 time to evaluate : 0.478 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 1.0321 time to fit residues: 2.8032 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 40 optimal weight: 0.6980 chunk 22 optimal weight: 0.6980 chunk 46 optimal weight: 0.4980 chunk 37 optimal weight: 7.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.0970 chunk 48 optimal weight: 0.8980 chunk 13 optimal weight: 2.9990 chunk 18 optimal weight: 0.5980 chunk 10 optimal weight: 0.9980 chunk 31 optimal weight: 0.6980 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: 0.7049 moved from start: 0.1871 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= 0.242 Angle : 0.508 6.142 5978 Z= 0.261 Chirality : 0.039 0.132 701 Planarity : 0.004 0.043 756 Dihedral : 5.186 46.896 658 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.48 % Allowed : 14.64 % Favored : 82.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.33 (0.35), residues: 563 helix: 2.08 (0.28), residues: 350 sheet: -1.33 (0.71), residues: 42 loop : -1.09 (0.43), residues: 171 *********************** 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: 11 poor density : 88 time to evaluate : 0.512 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 95 average time/residue: 1.3360 time to fit residues: 131.0132 Evaluate side-chains 96 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 89 time to evaluate : 0.487 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.0906 time to fit residues: 0.9293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.9980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.5980 chunk 28 optimal weight: 0.8980 chunk 52 optimal weight: 1.9990 chunk 6 optimal weight: 0.5980 chunk 30 optimal weight: 0.6980 chunk 39 optimal weight: 0.6980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7072 moved from start: 0.2037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 4403 Z= 0.293 Angle : 0.542 7.460 5978 Z= 0.276 Chirality : 0.040 0.140 701 Planarity : 0.004 0.038 756 Dihedral : 5.206 43.335 658 Min Nonbonded Distance : 2.350 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.78 % Favored : 98.22 % Rotamer: Outliers : 2.25 % Allowed : 15.09 % Favored : 82.66 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.17 (0.35), residues: 563 helix: 1.94 (0.28), residues: 350 sheet: -1.32 (0.71), residues: 42 loop : -1.13 (0.43), residues: 171 *********************** 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 101 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 91 time to evaluate : 0.456 Fit side-chains outliers start: 10 outliers final: 9 residues processed: 98 average time/residue: 1.2938 time to fit residues: 130.9027 Evaluate side-chains 101 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 6 residues processed: 3 average time/residue: 1.2039 time to fit residues: 4.3941 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 30 optimal weight: 0.5980 chunk 45 optimal weight: 1.9990 chunk 53 optimal weight: 0.1980 chunk 33 optimal weight: 7.9990 chunk 32 optimal weight: 0.7980 chunk 24 optimal weight: 0.7980 chunk 21 optimal weight: 0.0870 chunk 16 optimal weight: 0.0470 chunk 10 optimal weight: 0.6980 chunk 34 optimal weight: 0.8980 chunk 36 optimal weight: 0.7980 overall best weight: 0.3256 ------------------------------------------------------------------------------- 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: 0.7022 moved from start: 0.1987 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= 0.182 Angle : 0.470 5.992 5978 Z= 0.242 Chirality : 0.037 0.143 701 Planarity : 0.004 0.035 756 Dihedral : 4.778 42.098 658 Min Nonbonded Distance : 2.348 Molprobity Statistics. All-atom Clashscore : 3.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 2.70 % Allowed : 15.32 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.35), residues: 563 helix: 2.19 (0.28), residues: 350 sheet: -1.34 (0.69), residues: 42 loop : -1.04 (0.44), residues: 171 *********************** 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 98 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 86 time to evaluate : 0.488 Fit side-chains outliers start: 12 outliers final: 8 residues processed: 94 average time/residue: 1.3270 time to fit residues: 128.7072 Evaluate side-chains 96 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 88 time to evaluate : 0.445 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 5 residues processed: 3 average time/residue: 0.5643 time to fit residues: 2.4795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 26 optimal weight: 0.0060 chunk 5 optimal weight: 0.0870 chunk 42 optimal weight: 1.9990 chunk 49 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 21 optimal weight: 0.9990 chunk 39 optimal weight: 0.9980 chunk 15 optimal weight: 0.2980 overall best weight: 0.3374 ------------------------------------------------------------------------------- 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: 0.7019 moved from start: 0.2023 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= 0.187 Angle : 0.476 5.894 5978 Z= 0.246 Chirality : 0.038 0.141 701 Planarity : 0.004 0.035 756 Dihedral : 4.714 41.924 658 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 3.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 2.48 % Allowed : 15.54 % Favored : 81.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.35), residues: 563 helix: 2.24 (0.28), residues: 350 sheet: -1.37 (0.68), residues: 42 loop : -0.99 (0.44), residues: 171 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 87 time to evaluate : 0.406 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 96 average time/residue: 1.2058 time to fit residues: 119.6892 Evaluate side-chains 95 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.425 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.0860 time to fit residues: 0.8567 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.2980 chunk 47 optimal weight: 0.0060 chunk 50 optimal weight: 1.9990 chunk 33 optimal weight: 7.9990 chunk 53 optimal weight: 1.9990 chunk 32 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 36 optimal weight: 0.5980 chunk 55 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 44 optimal weight: 0.0570 overall best weight: 0.2914 ------------------------------------------------------------------------------- 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: 0.7003 moved from start: 0.2051 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= 0.179 Angle : 0.479 5.903 5978 Z= 0.246 Chirality : 0.038 0.146 701 Planarity : 0.004 0.035 756 Dihedral : 4.580 41.173 658 Min Nonbonded Distance : 2.355 Molprobity Statistics. All-atom Clashscore : 4.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.42 % Favored : 98.58 % Rotamer: Outliers : 1.80 % Allowed : 16.67 % Favored : 81.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.36), residues: 563 helix: 2.30 (0.28), residues: 350 sheet: -1.30 (0.69), residues: 42 loop : -0.96 (0.44), residues: 171 *********************** 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 91 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 83 time to evaluate : 0.470 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 90 average time/residue: 1.3154 time to fit residues: 122.7806 Evaluate side-chains 91 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 86 time to evaluate : 0.479 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 5 residues processed: 0 time to fit residues: 0.6797 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 4 optimal weight: 0.0270 chunk 34 optimal weight: 0.5980 chunk 27 optimal weight: 0.0570 chunk 35 optimal weight: 0.4980 chunk 47 optimal weight: 0.0570 chunk 13 optimal weight: 0.9980 chunk 40 optimal weight: 0.8980 chunk 6 optimal weight: 0.4980 chunk 12 optimal weight: 0.7980 chunk 44 optimal weight: 4.9990 chunk 18 optimal weight: 0.5980 overall best weight: 0.2274 ------------------------------------------------------------------------------- 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: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 4403 Z= 0.167 Angle : 0.479 5.874 5978 Z= 0.247 Chirality : 0.037 0.140 701 Planarity : 0.004 0.034 756 Dihedral : 4.435 41.121 658 Min Nonbonded Distance : 2.391 Molprobity Statistics. All-atom Clashscore : 3.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % 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: 1.76 (0.36), residues: 563 helix: 2.40 (0.28), residues: 350 sheet: -1.21 (0.67), residues: 43 loop : -0.86 (0.45), residues: 170 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1126 Ramachandran restraints generated. 563 Oldfield, 0 Emsley, 563 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 84 time to evaluate : 0.483 Fit side-chains outliers start: 6 outliers final: 6 residues processed: 89 average time/residue: 1.2421 time to fit residues: 114.4273 Evaluate side-chains 92 residues out of total 466 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.442 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 5 residues processed: 1 average time/residue: 0.0890 time to fit residues: 0.7494 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 56 random chunks: chunk 45 optimal weight: 0.7980 chunk 5 optimal weight: 0.2980 chunk 8 optimal weight: 0.4980 chunk 39 optimal weight: 1.9990 chunk 2 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 50 optimal weight: 0.0970 chunk 29 optimal weight: 1.9990 chunk 38 optimal weight: 0.5980 chunk 1 optimal weight: 0.0050 chunk 35 optimal weight: 0.9980 overall best weight: 0.2792 ------------------------------------------------------------------------------- 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 = 0.3970 r_free = 0.3970 target = 0.155300 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 60)----------------| | r_work = 0.3644 r_free = 0.3644 target = 0.128690 restraints weight = 5582.404| |-----------------------------------------------------------------------------| r_work (start): 0.3634 rms_B_bonded: 1.98 r_work: 0.3536 rms_B_bonded: 2.29 restraints_weight: 0.5000 r_work: 0.3391 rms_B_bonded: 4.01 restraints_weight: 0.2500 r_work (final): 0.3391 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7465 moved from start: 0.2150 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= 0.176 Angle : 0.482 5.881 5978 Z= 0.249 Chirality : 0.038 0.139 701 Planarity : 0.004 0.036 756 Dihedral : 4.423 40.966 658 Min Nonbonded Distance : 2.363 Molprobity Statistics. All-atom Clashscore : 4.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 1.35 % Allowed : 16.89 % 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: 1.79 (0.36), residues: 563 helix: 2.42 (0.27), residues: 350 sheet: -1.18 (0.67), residues: 43 loop : -0.85 (0.45), residues: 170 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2774.22 seconds wall clock time: 49 minutes 51.50 seconds (2991.50 seconds total)