Starting phenix.real_space_refine on Tue Feb 11 23:03:31 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8f7e_28904/02_2025/8f7e_28904.cif Found real_map, /net/cci-nas-00/data/ceres_data/8f7e_28904/02_2025/8f7e_28904.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.13 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8f7e_28904/02_2025/8f7e_28904.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8f7e_28904/02_2025/8f7e_28904.map" model { file = "/net/cci-nas-00/data/ceres_data/8f7e_28904/02_2025/8f7e_28904.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8f7e_28904/02_2025/8f7e_28904.cif" } resolution = 4.13 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= 0.003 sd= 0.045 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 16 5.16 5 C 4270 2.51 5 N 1166 2.21 5 O 1190 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 15 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/chem_data/mon_lib" Total number of atoms: 6642 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Chain: "C" Number of atoms: 3321 Number of conformers: 1 Conformer: "" Number of residues, atoms: 407, 3321 Classifications: {'peptide': 407} Link IDs: {'PTRANS': 18, 'TRANS': 388} Time building chain proxies: 5.62, per 1000 atoms: 0.85 Number of scatterers: 6642 At special positions: 0 Unit cell: (86.984, 101.656, 92.224, 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 1190 8.00 N 1166 7.00 C 4270 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.56 Conformation dependent library (CDL) restraints added in 931.9 milliseconds 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 36 helices and 5 sheets defined 32.9% alpha, 11.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.69 Creating SS restraints... Processing helix chain 'B' and resid 402 through 411 Processing helix chain 'B' and resid 412 through 419 Processing helix chain 'B' and resid 439 through 445 removed outlier: 3.843A pdb=" N PHE B 443 " --> pdb=" O PRO B 439 " (cutoff:3.500A) Processing helix chain 'B' and resid 462 through 467 Processing helix chain 'B' and resid 484 through 495 removed outlier: 3.740A pdb=" N GLU B 493 " --> pdb=" O ALA B 489 " (cutoff:3.500A) Processing helix chain 'B' and resid 503 through 508 removed outlier: 3.854A pdb=" N GLU B 507 " --> pdb=" O ASP B 504 " (cutoff:3.500A) Processing helix chain 'B' and resid 510 through 515 removed outlier: 4.279A pdb=" N SER B 514 " --> pdb=" O LEU B 510 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LEU B 515 " --> pdb=" O TRP B 511 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 510 through 515' Processing helix chain 'B' and resid 535 through 543 removed outlier: 3.532A pdb=" N ASP B 538 " --> pdb=" O ILE B 535 " (cutoff:3.500A) removed outlier: 3.912A pdb=" N GLY B 539 " --> pdb=" O VAL B 536 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N ARG B 541 " --> pdb=" O ASP B 538 " (cutoff:3.500A) removed outlier: 4.149A pdb=" N GLU B 542 " --> pdb=" O GLY B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 559 through 566 Processing helix chain 'B' and resid 567 through 569 No H-bonds generated for 'chain 'B' and resid 567 through 569' Processing helix chain 'B' and resid 634 through 638 Processing helix chain 'B' and resid 655 through 661 removed outlier: 3.684A pdb=" N ILE B 658 " --> pdb=" O PRO B 655 " (cutoff:3.500A) Processing helix chain 'B' and resid 679 through 684 removed outlier: 3.508A pdb=" N TYR B 683 " --> pdb=" O GLN B 680 " (cutoff:3.500A) removed outlier: 4.333A pdb=" N CYS B 684 " --> pdb=" O LEU B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 701 through 707 Processing helix chain 'B' and resid 724 through 730 removed outlier: 3.638A pdb=" N CYS B 730 " --> pdb=" O GLU B 726 " (cutoff:3.500A) Processing helix chain 'B' and resid 747 through 752 removed outlier: 3.508A pdb=" N GLY B 751 " --> pdb=" O PRO B 747 " (cutoff:3.500A) Processing helix chain 'B' and resid 770 through 774 removed outlier: 3.776A pdb=" N LEU B 773 " --> pdb=" O PRO B 770 " (cutoff:3.500A) Processing helix chain 'B' and resid 787 through 792 removed outlier: 3.557A pdb=" N SER B 792 " --> pdb=" O GLU B 788 " (cutoff:3.500A) Processing helix chain 'B' and resid 795 through 808 Processing helix chain 'C' and resid 403 through 411 Processing helix chain 'C' and resid 412 through 419 removed outlier: 4.003A pdb=" N GLN C 418 " --> pdb=" O ASP C 414 " (cutoff:3.500A) removed outlier: 3.708A pdb=" N ARG C 419 " --> pdb=" O LYS C 415 " (cutoff:3.500A) Processing helix chain 'C' and resid 439 through 444 removed outlier: 3.635A pdb=" N PHE C 443 " --> pdb=" O PRO C 439 " (cutoff:3.500A) Processing helix chain 'C' and resid 462 through 468 Processing helix chain 'C' and resid 484 through 494 Processing helix chain 'C' and resid 535 through 541 removed outlier: 3.755A pdb=" N ASP C 538 " --> pdb=" O ILE C 535 " (cutoff:3.500A) removed outlier: 4.415A pdb=" N GLY C 539 " --> pdb=" O VAL C 536 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N ARG C 541 " --> pdb=" O ASP C 538 " (cutoff:3.500A) Processing helix chain 'C' and resid 559 through 566 Processing helix chain 'C' and resid 607 through 612 removed outlier: 4.247A pdb=" N PHE C 611 " --> pdb=" O PRO C 607 " (cutoff:3.500A) Processing helix chain 'C' and resid 629 through 638 removed outlier: 3.525A pdb=" N ILE C 632 " --> pdb=" O ILE C 629 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N ILE C 633 " --> pdb=" O GLU C 630 " (cutoff:3.500A) removed outlier: 3.745A pdb=" N GLN C 636 " --> pdb=" O ILE C 633 " (cutoff:3.500A) removed outlier: 3.732A pdb=" N HIS C 637 " --> pdb=" O SER C 634 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 661 removed outlier: 3.823A pdb=" N LEU C 661 " --> pdb=" O ILE C 658 " (cutoff:3.500A) Processing helix chain 'C' and resid 678 through 684 removed outlier: 3.750A pdb=" N CYS C 684 " --> pdb=" O LEU C 681 " (cutoff:3.500A) Processing helix chain 'C' and resid 701 through 707 removed outlier: 3.662A pdb=" N ILE C 704 " --> pdb=" O PRO C 701 " (cutoff:3.500A) Processing helix chain 'C' and resid 725 through 730 removed outlier: 3.762A pdb=" N CYS C 730 " --> pdb=" O LEU C 727 " (cutoff:3.500A) Processing helix chain 'C' and resid 747 through 753 Processing helix chain 'C' and resid 770 through 775 Processing helix chain 'C' and resid 787 through 792 Processing helix chain 'C' and resid 795 through 807 Processing sheet with id=AA1, first strand: chain 'B' and resid 420 through 422 removed outlier: 6.966A pdb=" N LEU B 451 " --> pdb=" O TRP B 475 " (cutoff:3.500A) removed outlier: 7.180A pdb=" N TYR B 477 " --> pdb=" O LEU B 451 " (cutoff:3.500A) removed outlier: 6.717A pdb=" N LEU B 453 " --> pdb=" O TYR B 477 " (cutoff:3.500A) removed outlier: 6.473A pdb=" N LEU B 474 " --> pdb=" O HIS B 499 " (cutoff:3.500A) removed outlier: 7.938A pdb=" N LYS B 501 " --> pdb=" O LEU B 474 " (cutoff:3.500A) removed outlier: 6.609A pdb=" N LEU B 476 " --> pdb=" O LYS B 501 " (cutoff:3.500A) removed outlier: 3.820A pdb=" N ARG B 550 " --> pdb=" O LEU B 521 " (cutoff:3.500A) removed outlier: 3.600A pdb=" N LEU B 523 " --> pdb=" O ARG B 550 " (cutoff:3.500A) removed outlier: 3.765A pdb=" N LYS B 552 " --> pdb=" O LEU B 523 " (cutoff:3.500A) removed outlier: 3.581A pdb=" N SER B 573 " --> pdb=" O LEU B 549 " (cutoff:3.500A) removed outlier: 3.504A pdb=" N ASP B 620 " --> pdb=" O LEU B 596 " (cutoff:3.500A) removed outlier: 3.615A pdb=" N ILE B 619 " --> pdb=" O CYS B 643 " (cutoff:3.500A) removed outlier: 7.803A pdb=" N LEU B 644 " --> pdb=" O TYR B 668 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'B' and resid 736 through 737 removed outlier: 6.611A pdb=" N LEU B 736 " --> pdb=" O GLU B 760 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'C' and resid 421 through 422 removed outlier: 5.953A pdb=" N LEU C 451 " --> pdb=" O TRP C 475 " (cutoff:3.500A) removed outlier: 6.757A pdb=" N TYR C 477 " --> pdb=" O LEU C 451 " (cutoff:3.500A) removed outlier: 6.126A pdb=" N LEU C 453 " --> pdb=" O TYR C 477 " (cutoff:3.500A) removed outlier: 4.277A pdb=" N HIS C 522 " --> pdb=" O LEU C 498 " (cutoff:3.500A) removed outlier: 3.725A pdb=" N SER C 573 " --> pdb=" O LEU C 549 " (cutoff:3.500A) removed outlier: 4.171A pdb=" N LEU C 572 " --> pdb=" O GLU C 595 " (cutoff:3.500A) removed outlier: 3.509A pdb=" N LYS C 645 " --> pdb=" O ILE C 619 " (cutoff:3.500A) removed outlier: 6.410A pdb=" N LEU C 644 " --> pdb=" O TYR C 668 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 459 through 461 removed outlier: 6.032A pdb=" N VAL C 459 " --> pdb=" O LYS C 482 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'C' and resid 735 through 736 removed outlier: 8.155A pdb=" N LEU C 736 " --> pdb=" O GLU C 760 " (cutoff:3.500A) removed outlier: 6.179A pdb=" N ILE C 759 " --> pdb=" O VAL C 785 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 163 hydrogen bonds defined for protein. 351 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: 1.75 Time building geometry restraints manager: 1.82 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2144 1.34 - 1.46: 654 1.46 - 1.57: 3936 1.57 - 1.69: 2 1.69 - 1.81: 20 Bond restraints: 6756 Sorted by residual: bond pdb=" CA HIS C 522 " pdb=" CB HIS C 522 " ideal model delta sigma weight residual 1.533 1.597 -0.064 2.29e-02 1.91e+03 7.70e+00 bond pdb=" N THR B 412 " pdb=" CA THR B 412 " ideal model delta sigma weight residual 1.453 1.487 -0.034 1.31e-02 5.83e+03 6.83e+00 bond pdb=" N THR C 412 " pdb=" CA THR C 412 " ideal model delta sigma weight residual 1.453 1.488 -0.035 1.37e-02 5.33e+03 6.51e+00 bond pdb=" N LEU B 407 " pdb=" CA LEU B 407 " ideal model delta sigma weight residual 1.459 1.489 -0.030 1.21e-02 6.83e+03 6.07e+00 bond pdb=" C ILE C 508 " pdb=" N PRO C 509 " ideal model delta sigma weight residual 1.329 1.358 -0.030 1.20e-02 6.94e+03 6.07e+00 ... (remaining 6751 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.93: 8674 1.93 - 3.87: 399 3.87 - 5.80: 57 5.80 - 7.73: 19 7.73 - 9.66: 11 Bond angle restraints: 9160 Sorted by residual: angle pdb=" C ASP B 703 " pdb=" CA ASP B 703 " pdb=" CB ASP B 703 " ideal model delta sigma weight residual 110.01 117.16 -7.15 1.80e+00 3.09e-01 1.58e+01 angle pdb=" N HIS C 522 " pdb=" CA HIS C 522 " pdb=" CB HIS C 522 " ideal model delta sigma weight residual 110.83 117.62 -6.79 1.74e+00 3.30e-01 1.52e+01 angle pdb=" CA LYS B 472 " pdb=" CB LYS B 472 " pdb=" CG LYS B 472 " ideal model delta sigma weight residual 114.10 121.88 -7.78 2.00e+00 2.50e-01 1.51e+01 angle pdb=" CB LYS B 472 " pdb=" CG LYS B 472 " pdb=" CD LYS B 472 " ideal model delta sigma weight residual 111.30 119.95 -8.65 2.30e+00 1.89e-01 1.42e+01 angle pdb=" CB ARG B 781 " pdb=" CG ARG B 781 " pdb=" CD ARG B 781 " ideal model delta sigma weight residual 111.30 119.82 -8.52 2.30e+00 1.89e-01 1.37e+01 ... (remaining 9155 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.46: 3639 16.46 - 32.92: 428 32.92 - 49.38: 91 49.38 - 65.85: 25 65.85 - 82.31: 5 Dihedral angle restraints: 4188 sinusoidal: 1784 harmonic: 2404 Sorted by residual: dihedral pdb=" CA LYS B 589 " pdb=" C LYS B 589 " pdb=" N MET B 590 " pdb=" CA MET B 590 " ideal model delta harmonic sigma weight residual -180.00 -155.49 -24.51 0 5.00e+00 4.00e-02 2.40e+01 dihedral pdb=" CA GLY B 774 " pdb=" C GLY B 774 " pdb=" N GLU B 775 " pdb=" CA GLU B 775 " ideal model delta harmonic sigma weight residual -180.00 -156.86 -23.14 0 5.00e+00 4.00e-02 2.14e+01 dihedral pdb=" CA THR B 679 " pdb=" C THR B 679 " pdb=" N GLN B 680 " pdb=" CA GLN B 680 " ideal model delta harmonic sigma weight residual 180.00 -157.41 -22.59 0 5.00e+00 4.00e-02 2.04e+01 ... (remaining 4185 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 727 0.043 - 0.085: 278 0.085 - 0.128: 72 0.128 - 0.170: 15 0.170 - 0.213: 6 Chirality restraints: 1098 Sorted by residual: chirality pdb=" CA LEU C 407 " pdb=" N LEU C 407 " pdb=" C LEU C 407 " pdb=" CB LEU C 407 " both_signs ideal model delta sigma weight residual False 2.51 2.72 -0.21 2.00e-01 2.50e+01 1.13e+00 chirality pdb=" CB ILE B 677 " pdb=" CA ILE B 677 " pdb=" CG1 ILE B 677 " pdb=" CG2 ILE B 677 " both_signs ideal model delta sigma weight residual False 2.64 2.45 0.20 2.00e-01 2.50e+01 9.85e-01 chirality pdb=" CG LEU C 416 " pdb=" CB LEU C 416 " pdb=" CD1 LEU C 416 " pdb=" CD2 LEU C 416 " both_signs ideal model delta sigma weight residual False -2.59 -2.40 -0.19 2.00e-01 2.50e+01 8.88e-01 ... (remaining 1095 not shown) Planarity restraints: 1156 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PRO C 462 " 0.062 5.00e-02 4.00e+02 9.32e-02 1.39e+01 pdb=" N PRO C 463 " -0.161 5.00e-02 4.00e+02 pdb=" CA PRO C 463 " 0.049 5.00e-02 4.00e+02 pdb=" CD PRO C 463 " 0.050 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO B 724 " 0.055 5.00e-02 4.00e+02 8.35e-02 1.12e+01 pdb=" N PRO B 725 " -0.144 5.00e-02 4.00e+02 pdb=" CA PRO B 725 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 725 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 682 " -0.014 2.00e-02 2.50e+03 1.77e-02 5.47e+00 pdb=" CG PHE B 682 " 0.039 2.00e-02 2.50e+03 pdb=" CD1 PHE B 682 " -0.019 2.00e-02 2.50e+03 pdb=" CD2 PHE B 682 " -0.006 2.00e-02 2.50e+03 pdb=" CE1 PHE B 682 " 0.007 2.00e-02 2.50e+03 pdb=" CE2 PHE B 682 " -0.006 2.00e-02 2.50e+03 pdb=" CZ PHE B 682 " -0.001 2.00e-02 2.50e+03 ... (remaining 1153 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.79: 1462 2.79 - 3.32: 6280 3.32 - 3.85: 11061 3.85 - 4.37: 13743 4.37 - 4.90: 21617 Nonbonded interactions: 54163 Sorted by model distance: nonbonded pdb=" O GLN C 560 " pdb=" OG1 THR C 563 " model vdw 2.266 3.040 nonbonded pdb=" O ARG B 492 " pdb=" OG1 THR B 517 " model vdw 2.272 3.040 nonbonded pdb=" O PRO B 777 " pdb=" NZ LYS B 780 " model vdw 2.297 3.120 nonbonded pdb=" O GLN B 560 " pdb=" OG1 THR B 563 " model vdw 2.325 3.040 nonbonded pdb=" N HIS C 694 " pdb=" O THR C 716 " model vdw 2.365 3.120 ... (remaining 54158 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.03 Found NCS groups: ncs_group { reference = chain 'B' selection = chain 'C' } 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 group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.230 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: 0.000 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 19.900 Find NCS groups from input model: 0.210 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 26.670 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.5806 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 : 0.005 0.098 6756 Z= 0.297 Angle : 0.982 9.664 9160 Z= 0.557 Chirality : 0.049 0.213 1098 Planarity : 0.007 0.093 1156 Dihedral : 15.172 82.307 2612 Min Nonbonded Distance : 2.266 Molprobity Statistics. All-atom Clashscore : 14.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.41 % Favored : 92.59 % Rotamer: Outliers : 0.53 % Allowed : 18.78 % Favored : 80.69 % 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: -3.38 (0.27), residues: 810 helix: -2.83 (0.29), residues: 221 sheet: -2.57 (0.54), residues: 90 loop : -1.92 (0.27), residues: 499 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.003 TRP B 475 HIS 0.007 0.001 HIS B 522 PHE 0.039 0.002 PHE B 682 TYR 0.009 0.001 TYR C 668 ARG 0.008 0.001 ARG B 731 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 291 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 287 time to evaluate : 0.727 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 410 GLU cc_start: 0.8190 (tt0) cc_final: 0.7821 (tm-30) REVERT: B 412 THR cc_start: 0.9113 (p) cc_final: 0.8664 (p) REVERT: B 419 ARG cc_start: 0.7927 (ttt180) cc_final: 0.7560 (ttm110) REVERT: B 452 LYS cc_start: 0.8239 (ttpt) cc_final: 0.7982 (tttt) REVERT: B 571 LYS cc_start: 0.8553 (tttt) cc_final: 0.8185 (tptt) REVERT: B 590 MET cc_start: -0.1767 (tpt) cc_final: -0.4918 (mtm) REVERT: B 599 ILE cc_start: 0.5698 (mm) cc_final: 0.5423 (mm) REVERT: B 615 ASN cc_start: 0.7141 (m-40) cc_final: 0.6915 (t0) REVERT: B 656 ILE cc_start: 0.8564 (pt) cc_final: 0.7839 (pt) REVERT: B 682 PHE cc_start: 0.7736 (m-80) cc_final: 0.7506 (m-10) REVERT: B 688 ARG cc_start: 0.8144 (mtm180) cc_final: 0.7095 (mtm180) REVERT: B 784 LEU cc_start: 0.5851 (pp) cc_final: 0.5445 (pt) REVERT: C 413 LEU cc_start: 0.8044 (tt) cc_final: 0.7540 (tt) REVERT: C 426 ASP cc_start: 0.7291 (m-30) cc_final: 0.7051 (t0) REVERT: C 455 LEU cc_start: 0.8288 (mt) cc_final: 0.6806 (mt) REVERT: C 474 LEU cc_start: 0.8426 (tp) cc_final: 0.8144 (tp) REVERT: C 501 LYS cc_start: 0.8306 (tttt) cc_final: 0.6724 (tttt) REVERT: C 522 HIS cc_start: 0.7856 (p-80) cc_final: 0.6182 (p-80) REVERT: C 640 ARG cc_start: 0.6614 (mtm180) cc_final: 0.6201 (mmp80) REVERT: C 728 PHE cc_start: 0.7698 (m-80) cc_final: 0.7291 (m-80) REVERT: C 736 LEU cc_start: 0.7057 (mp) cc_final: 0.6802 (mt) REVERT: C 785 VAL cc_start: 0.6470 (t) cc_final: 0.5887 (t) REVERT: C 786 VAL cc_start: 0.7233 (p) cc_final: 0.6489 (m) outliers start: 4 outliers final: 0 residues processed: 290 average time/residue: 0.2441 time to fit residues: 87.5623 Evaluate side-chains 158 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 158 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 5.9990 chunk 60 optimal weight: 8.9990 chunk 33 optimal weight: 7.9990 chunk 20 optimal weight: 0.7980 chunk 40 optimal weight: 3.9990 chunk 32 optimal weight: 8.9990 chunk 62 optimal weight: 2.9990 chunk 24 optimal weight: 9.9990 chunk 38 optimal weight: 3.9990 chunk 46 optimal weight: 0.2980 chunk 72 optimal weight: 0.1980 overall best weight: 1.6584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 617 GLN C 478 HIS C 650 HIS C 696 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4537 r_free = 0.4537 target = 0.139945 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4294 r_free = 0.4294 target = 0.123103 restraints weight = 30371.558| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.4333 r_free = 0.4333 target = 0.125698 restraints weight = 20700.306| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 45)----------------| | r_work = 0.4360 r_free = 0.4360 target = 0.127588 restraints weight = 15064.777| |-----------------------------------------------------------------------------| r_work (final): 0.4352 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6109 moved from start: 0.5013 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.052 6756 Z= 0.280 Angle : 0.824 9.382 9160 Z= 0.411 Chirality : 0.047 0.206 1098 Planarity : 0.007 0.079 1156 Dihedral : 6.037 26.987 878 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 20.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.91 % Favored : 93.09 % Rotamer: Outliers : 0.13 % Allowed : 4.23 % Favored : 95.63 % 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: -3.07 (0.28), residues: 810 helix: -2.75 (0.31), residues: 210 sheet: -2.42 (0.59), residues: 88 loop : -1.66 (0.27), residues: 512 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP C 475 HIS 0.013 0.001 HIS C 608 PHE 0.020 0.003 PHE B 682 TYR 0.031 0.003 TYR C 477 ARG 0.011 0.001 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 210 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 209 time to evaluate : 0.662 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 411 TRP cc_start: 0.7040 (m100) cc_final: 0.6837 (m100) REVERT: B 434 MET cc_start: 0.7117 (mmp) cc_final: 0.6664 (mmm) REVERT: B 440 ASP cc_start: 0.7227 (t0) cc_final: 0.6823 (t0) REVERT: B 511 TRP cc_start: 0.6792 (p-90) cc_final: 0.4753 (p-90) REVERT: B 517 THR cc_start: 0.6505 (p) cc_final: 0.6303 (t) REVERT: B 571 LYS cc_start: 0.8883 (tttt) cc_final: 0.8552 (tptt) REVERT: B 572 LEU cc_start: 0.7817 (tp) cc_final: 0.7314 (tt) REVERT: B 590 MET cc_start: -0.2197 (tpt) cc_final: -0.5293 (mtm) REVERT: B 600 ARG cc_start: 0.6066 (ttt180) cc_final: 0.5384 (mmt90) REVERT: B 611 PHE cc_start: 0.5919 (m-80) cc_final: 0.5550 (m-10) REVERT: B 617 GLN cc_start: 0.7793 (mt0) cc_final: 0.7543 (mm110) REVERT: B 682 PHE cc_start: 0.7666 (m-80) cc_final: 0.7390 (m-80) REVERT: B 688 ARG cc_start: 0.7261 (mtm180) cc_final: 0.7030 (mtp180) REVERT: C 455 LEU cc_start: 0.7438 (mt) cc_final: 0.6948 (mt) REVERT: C 465 ILE cc_start: 0.7709 (tt) cc_final: 0.6939 (tt) REVERT: C 501 LYS cc_start: 0.8326 (tttt) cc_final: 0.7005 (tttt) REVERT: C 537 ILE cc_start: 0.8103 (tp) cc_final: 0.7441 (tp) REVERT: C 603 LEU cc_start: 0.6217 (mp) cc_final: 0.5991 (mp) REVERT: C 666 ARG cc_start: 0.8782 (mtp85) cc_final: 0.7945 (mtp85) REVERT: C 689 TYR cc_start: 0.6483 (m-80) cc_final: 0.6273 (m-80) REVERT: C 734 ARG cc_start: 0.7566 (mmt180) cc_final: 0.7200 (mmm160) outliers start: 1 outliers final: 0 residues processed: 210 average time/residue: 0.2221 time to fit residues: 59.4881 Evaluate side-chains 144 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 144 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 22 optimal weight: 1.9990 chunk 3 optimal weight: 2.9990 chunk 57 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 65 optimal weight: 2.9990 chunk 66 optimal weight: 0.7980 chunk 37 optimal weight: 4.9990 chunk 42 optimal weight: 0.4980 chunk 52 optimal weight: 3.9990 chunk 76 optimal weight: 5.9990 chunk 77 optimal weight: 8.9990 overall best weight: 1.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 467 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 649 ASN C 709 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4495 r_free = 0.4495 target = 0.137049 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.121954 restraints weight = 30579.447| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4314 r_free = 0.4314 target = 0.124465 restraints weight = 20715.346| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 39)----------------| | r_work = 0.4340 r_free = 0.4340 target = 0.126197 restraints weight = 14999.371| |-----------------------------------------------------------------------------| r_work (final): 0.4339 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6170 moved from start: 0.6271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6756 Z= 0.247 Angle : 0.753 10.159 9160 Z= 0.376 Chirality : 0.046 0.168 1098 Planarity : 0.006 0.068 1156 Dihedral : 5.763 24.420 878 Min Nonbonded Distance : 2.459 Molprobity Statistics. All-atom Clashscore : 18.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.04 % Favored : 92.96 % Rotamer: Outliers : 0.13 % Allowed : 3.84 % Favored : 96.03 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.87 (0.29), residues: 810 helix: -2.71 (0.33), residues: 199 sheet: -2.37 (0.49), residues: 118 loop : -1.41 (0.28), residues: 493 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 647 HIS 0.011 0.002 HIS C 499 PHE 0.017 0.002 PHE B 682 TYR 0.027 0.003 TYR C 513 ARG 0.019 0.001 ARG C 801 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 192 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 191 time to evaluate : 0.836 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 434 MET cc_start: 0.7233 (mmp) cc_final: 0.6995 (mmp) REVERT: B 567 VAL cc_start: 0.8282 (p) cc_final: 0.7953 (t) REVERT: B 571 LYS cc_start: 0.8883 (tttt) cc_final: 0.8559 (tptt) REVERT: B 572 LEU cc_start: 0.7874 (tp) cc_final: 0.7438 (tt) REVERT: B 590 MET cc_start: -0.2168 (tpt) cc_final: -0.5384 (mtm) REVERT: B 600 ARG cc_start: 0.6896 (ttt180) cc_final: 0.6517 (mmt180) REVERT: B 611 PHE cc_start: 0.5721 (m-80) cc_final: 0.5519 (m-10) REVERT: B 698 THR cc_start: 0.6927 (p) cc_final: 0.6589 (p) REVERT: C 455 LEU cc_start: 0.7340 (mt) cc_final: 0.6778 (mt) REVERT: C 501 LYS cc_start: 0.8238 (tttt) cc_final: 0.7784 (tttt) REVERT: C 524 THR cc_start: 0.7930 (m) cc_final: 0.7631 (m) REVERT: C 548 VAL cc_start: 0.7653 (t) cc_final: 0.5382 (t) REVERT: C 666 ARG cc_start: 0.8736 (mtp85) cc_final: 0.7907 (mtp85) REVERT: C 734 ARG cc_start: 0.7650 (mmt180) cc_final: 0.7183 (mmt-90) outliers start: 1 outliers final: 1 residues processed: 192 average time/residue: 0.2314 time to fit residues: 56.4430 Evaluate side-chains 134 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 133 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 42 optimal weight: 0.7980 chunk 55 optimal weight: 0.4980 chunk 6 optimal weight: 0.0070 chunk 18 optimal weight: 0.3980 chunk 58 optimal weight: 5.9990 chunk 57 optimal weight: 6.9990 chunk 41 optimal weight: 0.7980 chunk 3 optimal weight: 10.0000 chunk 1 optimal weight: 1.9990 chunk 30 optimal weight: 9.9990 chunk 17 optimal weight: 10.0000 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 404 GLN B 636 GLN B 649 ASN ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4531 r_free = 0.4531 target = 0.138897 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.4309 r_free = 0.4309 target = 0.123687 restraints weight = 30952.519| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 42)----------------| | r_work = 0.4347 r_free = 0.4347 target = 0.126210 restraints weight = 21192.145| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 43)----------------| | r_work = 0.4373 r_free = 0.4373 target = 0.127917 restraints weight = 15394.119| |-----------------------------------------------------------------------------| r_work (final): 0.4370 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6114 moved from start: 0.6738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6756 Z= 0.180 Angle : 0.690 8.820 9160 Z= 0.342 Chirality : 0.046 0.268 1098 Planarity : 0.005 0.050 1156 Dihedral : 5.412 23.526 878 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 15.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.05 % Favored : 93.95 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: -2.93 (0.29), residues: 810 helix: -2.71 (0.32), residues: 208 sheet: -2.47 (0.45), residues: 141 loop : -1.32 (0.30), residues: 461 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.035 0.002 TRP B 647 HIS 0.007 0.001 HIS C 608 PHE 0.017 0.002 PHE B 682 TYR 0.021 0.002 TYR C 513 ARG 0.007 0.001 ARG B 417 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 186 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 186 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 450 VAL cc_start: 0.8510 (t) cc_final: 0.7252 (t) REVERT: B 567 VAL cc_start: 0.8241 (p) cc_final: 0.7888 (t) REVERT: B 568 HIS cc_start: 0.3965 (p-80) cc_final: 0.3388 (p-80) REVERT: B 571 LYS cc_start: 0.8936 (tttt) cc_final: 0.8554 (tptt) REVERT: B 572 LEU cc_start: 0.7944 (tp) cc_final: 0.7447 (tt) REVERT: B 590 MET cc_start: -0.1976 (tpt) cc_final: -0.5337 (mtm) REVERT: B 611 PHE cc_start: 0.5612 (m-80) cc_final: 0.5410 (m-10) REVERT: C 455 LEU cc_start: 0.7332 (mt) cc_final: 0.6957 (mt) REVERT: C 501 LYS cc_start: 0.8252 (tttt) cc_final: 0.7728 (tttt) REVERT: C 524 THR cc_start: 0.7856 (m) cc_final: 0.7305 (m) REVERT: C 610 ILE cc_start: 0.8383 (pt) cc_final: 0.8068 (mp) REVERT: C 666 ARG cc_start: 0.8619 (mtp85) cc_final: 0.7815 (mtp85) REVERT: C 670 ASN cc_start: 0.7257 (p0) cc_final: 0.6860 (p0) REVERT: C 734 ARG cc_start: 0.7601 (mmt180) cc_final: 0.7198 (mmt-90) outliers start: 0 outliers final: 0 residues processed: 186 average time/residue: 0.2214 time to fit residues: 52.9960 Evaluate side-chains 136 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 136 time to evaluate : 0.842 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 52 optimal weight: 7.9990 chunk 46 optimal weight: 0.9990 chunk 47 optimal weight: 4.9990 chunk 53 optimal weight: 0.3980 chunk 70 optimal weight: 0.0870 chunk 59 optimal weight: 10.0000 chunk 73 optimal weight: 9.9990 chunk 3 optimal weight: 2.9990 chunk 9 optimal weight: 7.9990 chunk 28 optimal weight: 8.9990 chunk 19 optimal weight: 4.9990 overall best weight: 1.8964 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 649 ASN B 729 GLN ** C 431 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** C 568 HIS C 657 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4477 r_free = 0.4477 target = 0.136022 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.4307 r_free = 0.4307 target = 0.124533 restraints weight = 33583.191| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 29)----------------| | r_work = 0.4329 r_free = 0.4329 target = 0.126411 restraints weight = 25259.715| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.4346 r_free = 0.4346 target = 0.127247 restraints weight = 18554.282| |-----------------------------------------------------------------------------| r_work (final): 0.4309 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6354 moved from start: 0.7859 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.054 6756 Z= 0.285 Angle : 0.775 8.020 9160 Z= 0.388 Chirality : 0.048 0.222 1098 Planarity : 0.006 0.050 1156 Dihedral : 5.668 23.714 878 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 20.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.27 % Favored : 91.73 % Rotamer: Outliers : 0.00 % Allowed : 2.78 % Favored : 97.22 % 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: -3.00 (0.28), residues: 810 helix: -2.71 (0.33), residues: 199 sheet: -2.46 (0.42), residues: 142 loop : -1.44 (0.29), residues: 469 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.003 TRP B 475 HIS 0.011 0.002 HIS B 737 PHE 0.018 0.002 PHE B 682 TYR 0.019 0.003 TYR C 477 ARG 0.006 0.001 ARG C 688 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1620 Ramachandran restraints generated. 810 Oldfield, 0 Emsley, 810 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 160 time to evaluate : 0.767 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 412 THR cc_start: 0.8961 (p) cc_final: 0.8539 (p) REVERT: B 567 VAL cc_start: 0.8235 (p) cc_final: 0.7683 (t) REVERT: B 571 LYS cc_start: 0.8947 (tttt) cc_final: 0.8521 (tptt) REVERT: B 572 LEU cc_start: 0.7847 (tp) cc_final: 0.7257 (tt) REVERT: B 590 MET cc_start: -0.1657 (tpt) cc_final: -0.5412 (mtm) REVERT: C 455 LEU cc_start: 0.7427 (mt) cc_final: 0.7221 (mt) REVERT: C 499 HIS cc_start: 0.5008 (m-70) cc_final: 0.4182 (m-70) REVERT: C 522 HIS cc_start: 0.7325 (p-80) cc_final: 0.5813 (p-80) REVERT: C 666 ARG cc_start: 0.8753 (mtp85) cc_final: 0.7749 (mtp85) REVERT: C 734 ARG cc_start: 0.7655 (mmt180) cc_final: 0.7221 (mmt-90) REVERT: C 797 GLU cc_start: 0.7247 (tt0) cc_final: 0.6997 (tp30) REVERT: C 801 ARG cc_start: 0.7145 (ptp-170) cc_final: 0.6803 (ptm160) outliers start: 0 outliers final: 0 residues processed: 160 average time/residue: 0.1941 time to fit residues: 40.8634 Evaluate side-chains 117 residues out of total 756 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 117 time to evaluate : 0.902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Traceback (most recent call last): File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/build/../modules/phenix/phenix/command_line/real_space_refine.py", line 8, in run_program(real_space_refine.Program) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/iotbx/cli_parser.py", line 946, in run_program task.run() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/programs/real_space_refine.py", line 210, in run log = self.logger) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/rsr/wrappers.py", line 58, in __init__ log = log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 306, in __init__ self.caller(self.refine_xyz) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 321, in caller func() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 702, in refine_xyz self.minimization_no_ncs() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/phenix/phenix/refinement/macro_cycle_real_space.py", line 767, in minimization_no_ncs log = self.log) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 51, in __init__ gradients_method = gradients_method) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/weight.py", line 87, in __init__ rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 368, in refine rms_angles_limit = rms_angles_limit) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 235, in __init__ weight = weight) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/mmtbx/refinement/real_space/individual_sites.py", line 112, in refine states_collector = self.states_accumulator) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 174, in __init__ exception_handling_params=lbfgs_exception_handling_params) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 278, in run line_search) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/scitbx/lbfgs/__init__.py", line 131, in run_c_plus_plus f, g = target_evaluator.compute_functional_and_gradients() File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/maptbx/real_space_refinement_simple.py", line 245, in compute_functional_and_gradients compute_gradients=True) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1525, in energies_sites flags=flags, sites_cart=sites_cart, site_labels=site_labels) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1427, in pair_proxies check_bonded_distance_cutoff(sites_frac=sites_frac) File "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5592/modules/cctbx_project/cctbx/geometry_restraints/manager.py", line 1308, in check_bonded_distance_cutoff raise RuntimeError(msg) RuntimeError: Bond distance > max_reasonable_bond_distance: 58.6268 > 50: distance: 29 - 35: 10.475 distance: 35 - 36: 13.094 distance: 36 - 37: 16.047 distance: 36 - 39: 22.222 distance: 37 - 38: 22.231 distance: 37 - 43: 21.961 distance: 39 - 40: 16.242 distance: 40 - 41: 17.587 distance: 40 - 42: 16.611 distance: 43 - 44: 12.022 distance: 44 - 45: 14.702 distance: 44 - 47: 10.231 distance: 45 - 46: 21.259 distance: 45 - 51: 39.210 distance: 47 - 48: 22.419 distance: 48 - 49: 26.583 distance: 48 - 50: 30.113 distance: 51 - 52: 6.417 distance: 52 - 53: 18.671 distance: 52 - 55: 13.679 distance: 53 - 54: 25.931 distance: 53 - 62: 37.044 distance: 55 - 56: 9.278 distance: 56 - 57: 12.796 distance: 57 - 58: 9.107 distance: 58 - 59: 15.404 distance: 59 - 60: 9.394 distance: 59 - 61: 14.584 distance: 62 - 63: 4.152 distance: 63 - 64: 6.978 distance: 63 - 66: 3.834 distance: 64 - 65: 20.869 distance: 64 - 74: 30.097 distance: 66 - 67: 4.231 distance: 67 - 68: 23.410 distance: 67 - 69: 3.861 distance: 68 - 70: 23.718 distance: 69 - 71: 4.715 distance: 70 - 72: 9.157 distance: 71 - 72: 33.628 distance: 72 - 73: 20.979 distance: 74 - 75: 10.388 distance: 75 - 76: 15.293 distance: 75 - 78: 5.261 distance: 76 - 77: 19.740 distance: 76 - 82: 12.955 distance: 78 - 79: 6.626 distance: 78 - 80: 9.999 distance: 79 - 81: 11.706 distance: 82 - 83: 24.744 distance: 83 - 84: 33.053 distance: 83 - 86: 8.159 distance: 84 - 85: 12.316 distance: 84 - 89: 33.723 distance: 86 - 87: 19.589 distance: 86 - 88: 9.943 distance: 89 - 90: 20.019 distance: 90 - 91: 22.607 distance: 90 - 93: 14.028 distance: 91 - 92: 5.992 distance: 91 - 97: 10.940 distance: 92 - 109: 23.196 distance: 93 - 94: 32.264 distance: 93 - 95: 17.945 distance: 94 - 96: 8.635 distance: 97 - 98: 40.078 distance: 98 - 99: 21.294 distance: 98 - 101: 21.416 distance: 99 - 100: 29.632 distance: 99 - 105: 11.172 distance: 101 - 102: 20.786 distance: 102 - 103: 25.878 distance: 102 - 104: 13.120 distance: 105 - 106: 5.955 distance: 106 - 107: 19.293 distance: 107 - 108: 15.014 distance: 107 - 109: 20.385 distance: 109 - 110: 10.640 distance: 110 - 111: 12.651 distance: 110 - 113: 18.318 distance: 111 - 112: 24.680 distance: 111 - 117: 6.510 distance: 113 - 114: 5.756 distance: 114 - 115: 24.399 distance: 114 - 116: 17.024