Starting phenix.real_space_refine (version: 1.21rc1) on Mon Jul 3 23:24:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/07_2023/8e27_27827.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/07_2023/8e27_27827.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/07_2023/8e27_27827.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/07_2023/8e27_27827.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/07_2023/8e27_27827.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8e27_27827/07_2023/8e27_27827.pdb" } resolution = 3.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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= -0.000 sd= 0.018 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 30 5.16 5 C 3430 2.51 5 N 927 2.21 5 O 984 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 53": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 74": "NH1" <-> "NH2" Residue "A GLU 82": "OE1" <-> "OE2" Residue "A PHE 84": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 92": "NH1" <-> "NH2" Residue "A ARG 102": "NH1" <-> "NH2" Residue "A ASP 109": "OD1" <-> "OD2" Residue "A TYR 237": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 250": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 265": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 272": "OD1" <-> "OD2" Residue "A ARG 277": "NH1" <-> "NH2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 296": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 334": "OE1" <-> "OE2" Residue "A GLU 339": "OE1" <-> "OE2" Residue "A TYR 340": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 346": "OD1" <-> "OD2" Residue "A GLU 350": "OE1" <-> "OE2" Residue "A GLU 367": "OE1" <-> "OE2" Residue "A PHE 368": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ASP 373": "OD1" <-> "OD2" Residue "A ARG 375": "NH1" <-> "NH2" Residue "A ASP 377": "OD1" <-> "OD2" Residue "A PHE 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 388": "NH1" <-> "NH2" Residue "A ASP 389": "OD1" <-> "OD2" Residue "A PHE 404": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 412": "OD1" <-> "OD2" Residue "A TYR 415": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 416": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 419": "OE1" <-> "OE2" Residue "A GLU 429": "OE1" <-> "OE2" Residue "A GLU 450": "OE1" <-> "OE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 483": "NH1" <-> "NH2" Residue "A TYR 494": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 524": "OE1" <-> "OE2" Residue "A ASP 546": "OD1" <-> "OD2" Residue "A PHE 558": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 561": "OD1" <-> "OD2" Residue "A GLU 574": "OE1" <-> "OE2" Residue "A TYR 575": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 584": "OE1" <-> "OE2" Residue "A GLU 603": "OE1" <-> "OE2" Residue "A ARG 608": "NH1" <-> "NH2" Residue "A GLU 623": "OE1" <-> "OE2" Residue "A PHE 634": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 650": "OD1" <-> "OD2" Residue "A TYR 653": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 674": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 687": "NH1" <-> "NH2" Residue "A TYR 689": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 721": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 782": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 796": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 828": "OE1" <-> "OE2" Residue "A GLU 841": "OE1" <-> "OE2" Residue "A GLU 847": "OE1" <-> "OE2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5013/modules/chem_data/mon_lib" Total number of atoms: 5371 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 5371 Number of conformers: 1 Conformer: "" Number of residues, atoms: 676, 5371 Classifications: {'peptide': 676} Link IDs: {'PTRANS': 39, 'TRANS': 636} Chain breaks: 3 Time building chain proxies: 3.25, per 1000 atoms: 0.61 Number of scatterers: 5371 At special positions: 0 Unit cell: (75.24, 83.16, 93.06, 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 30 16.00 O 984 8.00 N 927 7.00 C 3430 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: 1.82 Conformation dependent library (CDL) restraints added in 676.0 milliseconds 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1290 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 10 sheets defined 34.3% alpha, 21.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing helix chain 'A' and resid 55 through 66 Processing helix chain 'A' and resid 99 through 103 Processing helix chain 'A' and resid 286 through 292 removed outlier: 3.814A pdb=" N VAL A 290 " --> pdb=" O PRO A 286 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ALA A 291 " --> pdb=" O GLN A 287 " (cutoff:3.500A) Processing helix chain 'A' and resid 293 through 297 Processing helix chain 'A' and resid 329 through 341 Processing helix chain 'A' and resid 348 through 353 Processing helix chain 'A' and resid 364 through 369 removed outlier: 3.641A pdb=" N PHE A 368 " --> pdb=" O PRO A 365 " (cutoff:3.500A) removed outlier: 3.865A pdb=" N SER A 369 " --> pdb=" O GLU A 366 " (cutoff:3.500A) Processing helix chain 'A' and resid 421 through 430 Processing helix chain 'A' and resid 445 through 451 Processing helix chain 'A' and resid 495 through 503 removed outlier: 3.542A pdb=" N SER A 499 " --> pdb=" O GLU A 495 " (cutoff:3.500A) Processing helix chain 'A' and resid 509 through 513 removed outlier: 3.726A pdb=" N GLU A 512 " --> pdb=" O PRO A 509 " (cutoff:3.500A) removed outlier: 3.658A pdb=" N LEU A 513 " --> pdb=" O ALA A 510 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 509 through 513' Processing helix chain 'A' and resid 521 through 546 removed outlier: 3.673A pdb=" N VAL A 525 " --> pdb=" O SER A 521 " (cutoff:3.500A) removed outlier: 3.915A pdb=" N GLN A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 577 through 601 removed outlier: 3.752A pdb=" N VAL A 582 " --> pdb=" O SER A 578 " (cutoff:3.500A) removed outlier: 3.842A pdb=" N GLU A 583 " --> pdb=" O ASN A 579 " (cutoff:3.500A) removed outlier: 4.010A pdb=" N PHE A 585 " --> pdb=" O LEU A 581 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N PHE A 601 " --> pdb=" O ILE A 597 " (cutoff:3.500A) Processing helix chain 'A' and resid 614 through 626 removed outlier: 3.772A pdb=" N ASP A 620 " --> pdb=" O ARG A 616 " (cutoff:3.500A) removed outlier: 3.942A pdb=" N LEU A 621 " --> pdb=" O MET A 617 " (cutoff:3.500A) Processing helix chain 'A' and resid 636 through 647 removed outlier: 3.679A pdb=" N THR A 647 " --> pdb=" O SER A 643 " (cutoff:3.500A) Processing helix chain 'A' and resid 651 through 666 removed outlier: 4.329A pdb=" N ALA A 656 " --> pdb=" O LYS A 652 " (cutoff:3.500A) Processing helix chain 'A' and resid 706 through 719 Processing helix chain 'A' and resid 728 through 765 removed outlier: 3.620A pdb=" N GLN A 733 " --> pdb=" O PRO A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 798 through 800 No H-bonds generated for 'chain 'A' and resid 798 through 800' Processing sheet with id=AA1, first strand: chain 'A' and resid 70 through 72 removed outlier: 7.598A pdb=" N LEU A 110 " --> pdb=" O LEU A 239 " (cutoff:3.500A) removed outlier: 3.653A pdb=" N LEU A 239 " --> pdb=" O LEU A 110 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 74 through 75 Processing sheet with id=AA3, first strand: chain 'A' and resid 246 through 252 removed outlier: 7.316A pdb=" N LEU A 316 " --> pdb=" O VAL A 306 " (cutoff:3.500A) removed outlier: 6.926A pdb=" N ILE A 302 " --> pdb=" O ALA A 320 " (cutoff:3.500A) removed outlier: 5.098A pdb=" N SER A 322 " --> pdb=" O LEU A 300 " (cutoff:3.500A) removed outlier: 7.303A pdb=" N LEU A 300 " --> pdb=" O SER A 322 " (cutoff:3.500A) removed outlier: 7.102A pdb=" N THR A 299 " --> pdb=" O LEU A 251 " (cutoff:3.500A) removed outlier: 4.687A pdb=" N LEU A 251 " --> pdb=" O THR A 299 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 372 through 373 removed outlier: 3.862A pdb=" N ASP A 478 " --> pdb=" O THR A 469 " (cutoff:3.500A) removed outlier: 3.718A pdb=" N THR A 469 " --> pdb=" O ASP A 478 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 382 removed outlier: 6.325A pdb=" N THR A 381 " --> pdb=" O LEU A 492 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 434 through 435 Processing sheet with id=AA7, first strand: chain 'A' and resid 556 through 560 Processing sheet with id=AA8, first strand: chain 'A' and resid 606 through 609 Processing sheet with id=AA9, first strand: chain 'A' and resid 794 through 796 removed outlier: 6.974A pdb=" N ALA A 781 " --> pdb=" O ILE A 777 " (cutoff:3.500A) removed outlier: 5.101A pdb=" N ILE A 777 " --> pdb=" O ALA A 781 " (cutoff:3.500A) removed outlier: 6.616A pdb=" N ASP A 783 " --> pdb=" O MET A 775 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N MET A 773 " --> pdb=" O LEU A 785 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'A' and resid 804 through 810 231 hydrogen bonds defined for protein. 642 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: 1.67 Time building geometry restraints manager: 1.98 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 1458 1.33 - 1.45: 925 1.45 - 1.57: 3059 1.57 - 1.69: 0 1.69 - 1.81: 45 Bond restraints: 5487 Sorted by residual: bond pdb=" CB ASN A 391 " pdb=" CG ASN A 391 " ideal model delta sigma weight residual 1.516 1.469 0.047 2.50e-02 1.60e+03 3.46e+00 bond pdb=" CB TRP A 468 " pdb=" CG TRP A 468 " ideal model delta sigma weight residual 1.498 1.443 0.055 3.10e-02 1.04e+03 3.20e+00 bond pdb=" CG PRO A 702 " pdb=" CD PRO A 702 " ideal model delta sigma weight residual 1.503 1.443 0.060 3.40e-02 8.65e+02 3.16e+00 bond pdb=" CB PRO A 702 " pdb=" CG PRO A 702 " ideal model delta sigma weight residual 1.492 1.404 0.088 5.00e-02 4.00e+02 3.11e+00 bond pdb=" C ARG A 743 " pdb=" O ARG A 743 " ideal model delta sigma weight residual 1.237 1.216 0.020 1.17e-02 7.31e+03 3.06e+00 ... (remaining 5482 not shown) Histogram of bond angle deviations from ideal: 99.22 - 106.21: 181 106.21 - 113.19: 2926 113.19 - 120.18: 2097 120.18 - 127.16: 2160 127.16 - 134.15: 63 Bond angle restraints: 7427 Sorted by residual: angle pdb=" N PHE A 464 " pdb=" CA PHE A 464 " pdb=" C PHE A 464 " ideal model delta sigma weight residual 107.69 100.15 7.54 2.01e+00 2.48e-01 1.41e+01 angle pdb=" N THR A 700 " pdb=" CA THR A 700 " pdb=" C THR A 700 " ideal model delta sigma weight residual 112.92 117.25 -4.33 1.23e+00 6.61e-01 1.24e+01 angle pdb=" CA GLN A 538 " pdb=" CB GLN A 538 " pdb=" CG GLN A 538 " ideal model delta sigma weight residual 114.10 107.46 6.64 2.00e+00 2.50e-01 1.10e+01 angle pdb=" N ARG A 667 " pdb=" CA ARG A 667 " pdb=" C ARG A 667 " ideal model delta sigma weight residual 109.81 116.73 -6.92 2.21e+00 2.05e-01 9.80e+00 angle pdb=" C VAL A 236 " pdb=" N TYR A 237 " pdb=" CA TYR A 237 " ideal model delta sigma weight residual 121.85 116.34 5.51 1.77e+00 3.19e-01 9.69e+00 ... (remaining 7422 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.81: 3023 17.81 - 35.62: 259 35.62 - 53.43: 67 53.43 - 71.24: 8 71.24 - 89.06: 3 Dihedral angle restraints: 3360 sinusoidal: 1379 harmonic: 1981 Sorted by residual: dihedral pdb=" CA MET A 617 " pdb=" C MET A 617 " pdb=" N LEU A 618 " pdb=" CA LEU A 618 " ideal model delta harmonic sigma weight residual 180.00 157.28 22.72 0 5.00e+00 4.00e-02 2.07e+01 dihedral pdb=" CA ARG A 277 " pdb=" C ARG A 277 " pdb=" N ILE A 278 " pdb=" CA ILE A 278 " ideal model delta harmonic sigma weight residual -180.00 -160.56 -19.44 0 5.00e+00 4.00e-02 1.51e+01 dihedral pdb=" CA LEU A 673 " pdb=" C LEU A 673 " pdb=" N TYR A 674 " pdb=" CA TYR A 674 " ideal model delta harmonic sigma weight residual 180.00 163.41 16.59 0 5.00e+00 4.00e-02 1.10e+01 ... (remaining 3357 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.050: 476 0.050 - 0.099: 248 0.099 - 0.148: 85 0.148 - 0.197: 22 0.197 - 0.247: 6 Chirality restraints: 837 Sorted by residual: chirality pdb=" CB ILE A 508 " pdb=" CA ILE A 508 " pdb=" CG1 ILE A 508 " pdb=" CG2 ILE A 508 " both_signs ideal model delta sigma weight residual False 2.64 2.40 0.25 2.00e-01 2.50e+01 1.52e+00 chirality pdb=" CA ILE A 379 " pdb=" N ILE A 379 " pdb=" C ILE A 379 " pdb=" CB ILE A 379 " both_signs ideal model delta sigma weight residual False 2.43 2.68 -0.24 2.00e-01 2.50e+01 1.48e+00 chirality pdb=" CA GLU A 450 " pdb=" N GLU A 450 " pdb=" C GLU A 450 " pdb=" CB GLU A 450 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 834 not shown) Planarity restraints: 958 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA PHE A 464 " -0.018 2.00e-02 2.50e+03 3.56e-02 1.27e+01 pdb=" C PHE A 464 " 0.062 2.00e-02 2.50e+03 pdb=" O PHE A 464 " -0.023 2.00e-02 2.50e+03 pdb=" N SER A 465 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA PHE A 699 " 0.015 2.00e-02 2.50e+03 3.01e-02 9.06e+00 pdb=" C PHE A 699 " -0.052 2.00e-02 2.50e+03 pdb=" O PHE A 699 " 0.019 2.00e-02 2.50e+03 pdb=" N THR A 700 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE A 508 " -0.014 2.00e-02 2.50e+03 2.74e-02 7.53e+00 pdb=" C ILE A 508 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE A 508 " -0.017 2.00e-02 2.50e+03 pdb=" N PRO A 509 " -0.016 2.00e-02 2.50e+03 ... (remaining 955 not shown) Histogram of nonbonded interaction distances: 2.30 - 2.82: 1474 2.82 - 3.34: 4320 3.34 - 3.86: 7906 3.86 - 4.38: 8806 4.38 - 4.90: 15989 Nonbonded interactions: 38495 Sorted by model distance: nonbonded pdb=" O SER A 701 " pdb=" OD2 ASP A 708 " model vdw 2.297 3.040 nonbonded pdb=" OE2 GLU A 419 " pdb=" NH2 ARG A 722 " model vdw 2.339 2.520 nonbonded pdb=" OD1 ASP A 343 " pdb=" OG SER A 345 " model vdw 2.394 2.440 nonbonded pdb=" N ASP A 633 " pdb=" OD1 ASP A 633 " model vdw 2.402 2.520 nonbonded pdb=" OG SER A 701 " pdb=" OD2 ASP A 708 " model vdw 2.434 2.440 ... (remaining 38490 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: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.190 Check model and map are aligned: 0.080 Set scattering table: 0.040 Process input model: 18.080 Find NCS groups from input model: 0.140 Set up NCS constraints: 0.030 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:2.720 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 28.410 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8138 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 0.088 5487 Z= 0.660 Angle : 1.095 10.119 7427 Z= 0.598 Chirality : 0.067 0.247 837 Planarity : 0.008 0.067 958 Dihedral : 14.240 89.056 2070 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.20 % Favored : 98.80 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.92 (0.29), residues: 668 helix: -0.31 (0.32), residues: 213 sheet: 0.33 (0.50), residues: 103 loop : -1.05 (0.30), residues: 352 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 87 time to evaluate : 0.701 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 89 average time/residue: 0.2361 time to fit residues: 25.9818 Evaluate side-chains 55 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 54 time to evaluate : 0.571 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0595 time to fit residues: 0.9909 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 56 optimal weight: 0.8980 chunk 50 optimal weight: 0.0170 chunk 28 optimal weight: 0.9980 chunk 17 optimal weight: 0.4980 chunk 34 optimal weight: 8.9990 chunk 27 optimal weight: 0.8980 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 10.0000 chunk 31 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 60 optimal weight: 0.0470 overall best weight: 0.4716 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8011 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 5487 Z= 0.145 Angle : 0.511 5.344 7427 Z= 0.265 Chirality : 0.041 0.137 837 Planarity : 0.005 0.044 958 Dihedral : 4.224 17.214 732 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % Rotamer Outliers : 1.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.14 (0.31), residues: 668 helix: 0.78 (0.37), residues: 214 sheet: 0.65 (0.48), residues: 118 loop : -0.94 (0.30), residues: 336 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 72 time to evaluate : 0.563 Fit side-chains outliers start: 9 outliers final: 5 residues processed: 79 average time/residue: 0.2153 time to fit residues: 21.6000 Evaluate side-chains 63 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 58 time to evaluate : 0.633 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1099 time to fit residues: 1.6467 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 10.0000 chunk 50 optimal weight: 0.0040 chunk 41 optimal weight: 0.5980 chunk 16 optimal weight: 0.0020 chunk 60 optimal weight: 9.9990 chunk 65 optimal weight: 0.9990 chunk 54 optimal weight: 4.9990 chunk 20 optimal weight: 6.9990 chunk 48 optimal weight: 6.9990 chunk 45 optimal weight: 0.0030 overall best weight: 0.3212 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 526 HIS A 598 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7989 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 : 0.002 0.038 5487 Z= 0.132 Angle : 0.492 9.212 7427 Z= 0.246 Chirality : 0.040 0.137 837 Planarity : 0.004 0.040 958 Dihedral : 3.858 16.049 732 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 4.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.50 % Favored : 98.50 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.21 (0.32), residues: 668 helix: 1.14 (0.38), residues: 214 sheet: 0.53 (0.46), residues: 132 loop : -0.69 (0.31), residues: 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 72 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 68 time to evaluate : 0.630 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 71 average time/residue: 0.2018 time to fit residues: 18.5012 Evaluate side-chains 63 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 60 time to evaluate : 0.630 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0736 time to fit residues: 1.2332 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 10.0000 chunk 29 optimal weight: 0.9980 chunk 40 optimal weight: 0.0370 chunk 61 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 57 optimal weight: 3.9990 chunk 17 optimal weight: 0.1980 chunk 53 optimal weight: 2.9990 chunk 36 optimal weight: 3.9990 chunk 0 optimal weight: 10.0000 overall best weight: 1.0060 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8031 moved from start: 0.2210 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 5487 Z= 0.169 Angle : 0.484 6.156 7427 Z= 0.243 Chirality : 0.041 0.136 837 Planarity : 0.004 0.038 958 Dihedral : 3.800 19.456 732 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 4.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.34 (0.32), residues: 668 helix: 1.20 (0.38), residues: 214 sheet: 0.69 (0.45), residues: 138 loop : -0.63 (0.32), residues: 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 62 time to evaluate : 0.636 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 65 average time/residue: 0.2566 time to fit residues: 20.5884 Evaluate side-chains 61 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 59 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0587 time to fit residues: 1.1866 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 48 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 55 optimal weight: 0.9990 chunk 44 optimal weight: 2.9990 chunk 0 optimal weight: 10.0000 chunk 33 optimal weight: 6.9990 chunk 58 optimal weight: 0.8980 chunk 16 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 3.9990 chunk 38 optimal weight: 2.9990 overall best weight: 1.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 moved from start: 0.2269 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 5487 Z= 0.197 Angle : 0.497 6.440 7427 Z= 0.253 Chirality : 0.042 0.138 837 Planarity : 0.004 0.038 958 Dihedral : 3.831 19.634 732 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 4.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.65 % Favored : 98.35 % Rotamer Outliers : 0.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.38 (0.32), residues: 668 helix: 1.19 (0.37), residues: 214 sheet: 0.74 (0.48), residues: 130 loop : -0.55 (0.32), residues: 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 64 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 61 time to evaluate : 0.634 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 62 average time/residue: 0.2184 time to fit residues: 17.3319 Evaluate side-chains 59 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 57 time to evaluate : 0.623 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0538 time to fit residues: 1.0795 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 15 optimal weight: 0.9980 chunk 64 optimal weight: 9.9990 chunk 53 optimal weight: 3.9990 chunk 30 optimal weight: 4.9990 chunk 5 optimal weight: 10.0000 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 9.9990 chunk 62 optimal weight: 4.9990 chunk 7 optimal weight: 5.9990 chunk 36 optimal weight: 3.9990 chunk 47 optimal weight: 4.9990 overall best weight: 3.1988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 520 HIS A 579 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8162 moved from start: 0.2290 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.006 0.043 5487 Z= 0.415 Angle : 0.629 12.820 7427 Z= 0.321 Chirality : 0.046 0.148 837 Planarity : 0.005 0.042 958 Dihedral : 4.230 19.773 732 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 5.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 1.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.32), residues: 668 helix: 0.80 (0.36), residues: 214 sheet: 0.68 (0.48), residues: 130 loop : -0.75 (0.32), residues: 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 63 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 56 time to evaluate : 0.610 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 59 average time/residue: 0.2498 time to fit residues: 18.3627 Evaluate side-chains 54 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 50 time to evaluate : 0.632 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0530 time to fit residues: 1.2680 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 36 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 64 optimal weight: 10.0000 chunk 40 optimal weight: 0.9980 chunk 39 optimal weight: 0.8980 chunk 29 optimal weight: 3.9990 chunk 25 optimal weight: 3.9990 chunk 38 optimal weight: 0.7980 chunk 19 optimal weight: 1.9990 chunk 12 optimal weight: 5.9990 chunk 41 optimal weight: 0.7980 overall best weight: 1.0982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8089 moved from start: 0.2471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.023 5487 Z= 0.178 Angle : 0.508 8.677 7427 Z= 0.260 Chirality : 0.042 0.203 837 Planarity : 0.004 0.038 958 Dihedral : 3.980 19.851 732 Min Nonbonded Distance : 2.281 Molprobity Statistics. All-atom Clashscore : 5.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.25 % Favored : 97.75 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.30 (0.33), residues: 668 helix: 1.14 (0.37), residues: 214 sheet: 0.61 (0.49), residues: 128 loop : -0.56 (0.33), residues: 326 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 51 time to evaluate : 0.588 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 54 average time/residue: 0.2240 time to fit residues: 15.6337 Evaluate side-chains 53 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 50 time to evaluate : 0.675 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.2090 time to fit residues: 1.6641 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 4.9990 chunk 6 optimal weight: 0.8980 chunk 50 optimal weight: 0.6980 chunk 58 optimal weight: 1.9990 chunk 61 optimal weight: 0.7980 chunk 56 optimal weight: 3.9990 chunk 60 optimal weight: 1.9990 chunk 36 optimal weight: 3.9990 chunk 26 optimal weight: 0.5980 chunk 47 optimal weight: 6.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8050 moved from start: 0.2669 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 5487 Z= 0.154 Angle : 0.481 7.129 7427 Z= 0.244 Chirality : 0.041 0.151 837 Planarity : 0.004 0.038 958 Dihedral : 3.754 20.479 732 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 4.73 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.40 % Favored : 97.60 % Rotamer Outliers : 0.17 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.43 (0.33), residues: 668 helix: 1.20 (0.37), residues: 220 sheet: 0.84 (0.50), residues: 121 loop : -0.53 (0.33), residues: 327 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 59 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 58 time to evaluate : 0.586 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 59 average time/residue: 0.2067 time to fit residues: 15.9086 Evaluate side-chains 51 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.620 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8888 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 18 optimal weight: 1.9990 chunk 54 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 59 optimal weight: 10.0000 chunk 39 optimal weight: 6.9990 chunk 63 optimal weight: 8.9990 chunk 38 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 44 optimal weight: 4.9990 chunk 66 optimal weight: 0.0870 chunk 61 optimal weight: 5.9990 overall best weight: 2.4166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8130 moved from start: 0.2591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.037 5487 Z= 0.329 Angle : 0.571 9.442 7427 Z= 0.292 Chirality : 0.045 0.194 837 Planarity : 0.004 0.045 958 Dihedral : 4.030 20.237 732 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 5.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.25 (0.33), residues: 668 helix: 0.99 (0.37), residues: 220 sheet: 0.76 (0.50), residues: 121 loop : -0.60 (0.33), residues: 327 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 48 time to evaluate : 0.623 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 51 average time/residue: 0.1974 time to fit residues: 13.4136 Evaluate side-chains 50 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.638 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0539 time to fit residues: 1.1086 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 53 optimal weight: 0.0170 chunk 5 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 32 optimal weight: 5.9990 chunk 42 optimal weight: 2.9990 chunk 56 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 0.2980 chunk 7 optimal weight: 5.9990 chunk 14 optimal weight: 0.0020 chunk 22 optimal weight: 1.9990 overall best weight: 0.6028 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8048 moved from start: 0.2779 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 5487 Z= 0.144 Angle : 0.486 7.233 7427 Z= 0.247 Chirality : 0.041 0.137 837 Planarity : 0.004 0.041 958 Dihedral : 3.783 20.439 732 Min Nonbonded Distance : 2.288 Molprobity Statistics. All-atom Clashscore : 5.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.95 % Favored : 98.05 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.48 (0.33), residues: 668 helix: 1.20 (0.37), residues: 220 sheet: 0.92 (0.48), residues: 129 loop : -0.54 (0.34), residues: 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1336 Ramachandran restraints generated. 668 Oldfield, 0 Emsley, 668 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 53 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 53 time to evaluate : 0.652 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 53 average time/residue: 0.2316 time to fit residues: 15.7624 Evaluate side-chains 51 residues out of total 593 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 51 time to evaluate : 0.622 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.8716 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 67 random chunks: chunk 54 optimal weight: 6.9990 chunk 6 optimal weight: 10.0000 chunk 9 optimal weight: 0.8980 chunk 46 optimal weight: 5.9990 chunk 3 optimal weight: 9.9990 chunk 38 optimal weight: 0.2980 chunk 60 optimal weight: 6.9990 chunk 35 optimal weight: 0.9980 chunk 45 optimal weight: 7.9990 chunk 1 optimal weight: 3.9990 chunk 42 optimal weight: 0.8980 overall best weight: 1.4182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3768 r_free = 0.3768 target = 0.144649 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.3249 r_free = 0.3249 target = 0.100451 restraints weight = 7510.644| |-----------------------------------------------------------------------------| r_work (start): 0.3229 rms_B_bonded: 3.05 r_work: 0.3082 rms_B_bonded: 3.55 restraints_weight: 0.5000 r_work (final): 0.3082 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8132 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 5487 Z= 0.215 Angle : 0.519 7.747 7427 Z= 0.265 Chirality : 0.042 0.135 837 Planarity : 0.004 0.046 958 Dihedral : 3.843 20.438 732 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 5.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.54 % Favored : 97.46 % Rotamer Outliers : 0.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.41 (0.33), residues: 668 helix: 1.13 (0.37), residues: 220 sheet: 0.89 (0.48), residues: 129 loop : -0.56 (0.34), residues: 319 =============================================================================== Job complete usr+sys time: 1460.07 seconds wall clock time: 26 minutes 56.79 seconds (1616.79 seconds total)