Starting phenix.real_space_refine on Fri Dec 8 23:41:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/12_2023/8fwk_29511.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/12_2023/8fwk_29511.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/12_2023/8fwk_29511.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/12_2023/8fwk_29511.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/12_2023/8fwk_29511.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fwk_29511/12_2023/8fwk_29511.pdb" } resolution = 3.5 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= 0.005 sd= 0.078 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 34 5.16 5 C 6072 2.51 5 N 1640 2.21 5 O 1716 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B ARG 240": "NH1" <-> "NH2" Residue "B ARG 247": "NH1" <-> "NH2" Residue "B ARG 256": "NH1" <-> "NH2" Residue "B ARG 276": "NH1" <-> "NH2" Residue "B ARG 287": "NH1" <-> "NH2" Residue "B ARG 344": "NH1" <-> "NH2" Residue "B ARG 371": "NH1" <-> "NH2" Residue "B ARG 440": "NH1" <-> "NH2" Residue "B ARG 450": "NH1" <-> "NH2" Residue "B PHE 460": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 477": "NH1" <-> "NH2" Residue "B ARG 584": "NH1" <-> "NH2" Residue "B ARG 589": "NH1" <-> "NH2" Residue "B ARG 603": "NH1" <-> "NH2" Residue "B TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ARG 648": "NH1" <-> "NH2" Residue "B ARG 685": "NH1" <-> "NH2" Residue "B ARG 717": "NH1" <-> "NH2" Residue "B ARG 763": "NH1" <-> "NH2" Residue "B ARG 805": "NH1" <-> "NH2" Residue "B ARG 807": "NH1" <-> "NH2" Residue "A ARG 240": "NH1" <-> "NH2" Residue "A ARG 247": "NH1" <-> "NH2" Residue "A ARG 256": "NH1" <-> "NH2" Residue "A ARG 276": "NH1" <-> "NH2" Residue "A ARG 287": "NH1" <-> "NH2" Residue "A ARG 344": "NH1" <-> "NH2" Residue "A ARG 371": "NH1" <-> "NH2" Residue "A ARG 440": "NH1" <-> "NH2" Residue "A ARG 450": "NH1" <-> "NH2" Residue "A ARG 477": "NH1" <-> "NH2" Residue "A ARG 584": "NH1" <-> "NH2" Residue "A ARG 589": "NH1" <-> "NH2" Residue "A ARG 603": "NH1" <-> "NH2" Residue "A TYR 640": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ARG 648": "NH1" <-> "NH2" Residue "A ARG 685": "NH1" <-> "NH2" Residue "A ARG 717": "NH1" <-> "NH2" Residue "A ARG 763": "NH1" <-> "NH2" Residue "A ARG 805": "NH1" <-> "NH2" Residue "A ARG 807": "NH1" <-> "NH2" Time to flip residues: 0.04s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 9462 Number of models: 1 Model: "" Number of chains: 2 Chain: "B" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4731 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 13, 'TRANS': 583} Chain: "A" Number of atoms: 4731 Number of conformers: 1 Conformer: "" Number of residues, atoms: 597, 4731 Classifications: {'peptide': 597} Link IDs: {'PTRANS': 13, 'TRANS': 583} Time building chain proxies: 5.41, per 1000 atoms: 0.57 Number of scatterers: 9462 At special positions: 0 Unit cell: (104.76, 87.48, 137.16, 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 34 16.00 O 1716 8.00 N 1640 7.00 C 6072 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: 3.57 Conformation dependent library (CDL) restraints added in 1.9 seconds 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 2196 Finding SS restraints... Secondary structure from input PDB file: 47 helices and 4 sheets defined 59.2% alpha, 2.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'B' and resid 239 through 245 Processing helix chain 'B' and resid 261 through 294 removed outlier: 3.500A pdb=" N VAL B 265 " --> pdb=" O LEU B 261 " (cutoff:3.500A) removed outlier: 3.876A pdb=" N VAL B 280 " --> pdb=" O ARG B 276 " (cutoff:3.500A) Proline residue: B 283 - end of helix Processing helix chain 'B' and resid 298 through 301 Processing helix chain 'B' and resid 302 through 315 Processing helix chain 'B' and resid 326 through 353 removed outlier: 4.770A pdb=" N ARG B 336 " --> pdb=" O PHE B 332 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL B 337 " --> pdb=" O LEU B 333 " (cutoff:3.500A) Processing helix chain 'B' and resid 366 through 390 Processing helix chain 'B' and resid 391 through 408 Processing helix chain 'B' and resid 412 through 458 removed outlier: 3.969A pdb=" N ILE B 416 " --> pdb=" O TRP B 412 " (cutoff:3.500A) removed outlier: 4.712A pdb=" N LYS B 437 " --> pdb=" O GLU B 433 " (cutoff:3.500A) removed outlier: 4.468A pdb=" N PHE B 438 " --> pdb=" O TRP B 434 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N ALA B 453 " --> pdb=" O THR B 449 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP B 455 " --> pdb=" O ALA B 451 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER B 456 " --> pdb=" O ARG B 452 " (cutoff:3.500A) Processing helix chain 'B' and resid 459 through 465 Processing helix chain 'B' and resid 468 through 510 removed outlier: 3.645A pdb=" N GLU B 472 " --> pdb=" O ALA B 468 " (cutoff:3.500A) Processing helix chain 'B' and resid 511 through 516 removed outlier: 3.844A pdb=" N CYS B 516 " --> pdb=" O SER B 513 " (cutoff:3.500A) Processing helix chain 'B' and resid 527 through 541 removed outlier: 4.081A pdb=" N VAL B 531 " --> pdb=" O VAL B 527 " (cutoff:3.500A) removed outlier: 3.544A pdb=" N PHE B 533 " --> pdb=" O ASP B 529 " (cutoff:3.500A) removed outlier: 4.379A pdb=" N ILE B 538 " --> pdb=" O GLY B 534 " (cutoff:3.500A) Processing helix chain 'B' and resid 544 through 548 removed outlier: 3.765A pdb=" N PHE B 547 " --> pdb=" O LEU B 544 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY B 548 " --> pdb=" O ASN B 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 544 through 548' Processing helix chain 'B' and resid 550 through 567 removed outlier: 3.504A pdb=" N LEU B 567 " --> pdb=" O ASN B 563 " (cutoff:3.500A) Processing helix chain 'B' and resid 627 through 634 removed outlier: 3.660A pdb=" N ILE B 632 " --> pdb=" O GLY B 628 " (cutoff:3.500A) removed outlier: 3.870A pdb=" N LEU B 633 " --> pdb=" O LYS B 629 " (cutoff:3.500A) Processing helix chain 'B' and resid 659 through 665 Processing helix chain 'B' and resid 680 through 685 removed outlier: 3.546A pdb=" N ARG B 685 " --> pdb=" O ALA B 681 " (cutoff:3.500A) Processing helix chain 'B' and resid 686 through 688 No H-bonds generated for 'chain 'B' and resid 686 through 688' Processing helix chain 'B' and resid 698 through 703 Processing helix chain 'B' and resid 705 through 710 Processing helix chain 'B' and resid 729 through 742 removed outlier: 4.086A pdb=" N GLN B 733 " --> pdb=" O GLY B 729 " (cutoff:3.500A) Processing helix chain 'B' and resid 758 through 770 removed outlier: 4.121A pdb=" N GLU B 762 " --> pdb=" O ASP B 758 " (cutoff:3.500A) removed outlier: 3.514A pdb=" N ALA B 764 " --> pdb=" O SER B 760 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA B 767 " --> pdb=" O ARG B 763 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER B 768 " --> pdb=" O ALA B 764 " (cutoff:3.500A) Processing helix chain 'B' and resid 807 through 814 Processing helix chain 'B' and resid 817 through 829 Processing helix chain 'A' and resid 239 through 245 Processing helix chain 'A' and resid 261 through 294 removed outlier: 3.876A pdb=" N VAL A 280 " --> pdb=" O ARG A 276 " (cutoff:3.500A) Proline residue: A 283 - end of helix Processing helix chain 'A' and resid 298 through 301 Processing helix chain 'A' and resid 302 through 315 Processing helix chain 'A' and resid 326 through 353 removed outlier: 4.770A pdb=" N ARG A 336 " --> pdb=" O PHE A 332 " (cutoff:3.500A) removed outlier: 4.432A pdb=" N VAL A 337 " --> pdb=" O LEU A 333 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 390 Processing helix chain 'A' and resid 391 through 408 Processing helix chain 'A' and resid 412 through 458 removed outlier: 3.970A pdb=" N ILE A 416 " --> pdb=" O TRP A 412 " (cutoff:3.500A) removed outlier: 4.711A pdb=" N LYS A 437 " --> pdb=" O GLU A 433 " (cutoff:3.500A) removed outlier: 4.469A pdb=" N PHE A 438 " --> pdb=" O TRP A 434 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N ALA A 453 " --> pdb=" O THR A 449 " (cutoff:3.500A) removed outlier: 3.877A pdb=" N ASP A 455 " --> pdb=" O ALA A 451 " (cutoff:3.500A) removed outlier: 4.005A pdb=" N SER A 456 " --> pdb=" O ARG A 452 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 465 Processing helix chain 'A' and resid 468 through 510 removed outlier: 3.645A pdb=" N GLU A 472 " --> pdb=" O ALA A 468 " (cutoff:3.500A) Processing helix chain 'A' and resid 511 through 516 removed outlier: 3.845A pdb=" N CYS A 516 " --> pdb=" O SER A 513 " (cutoff:3.500A) Processing helix chain 'A' and resid 527 through 541 removed outlier: 4.080A pdb=" N VAL A 531 " --> pdb=" O VAL A 527 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N PHE A 533 " --> pdb=" O ASP A 529 " (cutoff:3.500A) removed outlier: 4.378A pdb=" N ILE A 538 " --> pdb=" O GLY A 534 " (cutoff:3.500A) Processing helix chain 'A' and resid 544 through 548 removed outlier: 3.764A pdb=" N PHE A 547 " --> pdb=" O LEU A 544 " (cutoff:3.500A) removed outlier: 3.727A pdb=" N GLY A 548 " --> pdb=" O ASN A 545 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 544 through 548' Processing helix chain 'A' and resid 550 through 567 removed outlier: 3.504A pdb=" N LEU A 567 " --> pdb=" O ASN A 563 " (cutoff:3.500A) Processing helix chain 'A' and resid 630 through 637 removed outlier: 4.335A pdb=" N ARG A 634 " --> pdb=" O SER A 630 " (cutoff:3.500A) Processing helix chain 'A' and resid 659 through 665 Processing helix chain 'A' and resid 680 through 685 Processing helix chain 'A' and resid 698 through 703 Processing helix chain 'A' and resid 705 through 710 Processing helix chain 'A' and resid 729 through 742 removed outlier: 4.086A pdb=" N GLN A 733 " --> pdb=" O GLY A 729 " (cutoff:3.500A) Processing helix chain 'A' and resid 758 through 770 removed outlier: 4.120A pdb=" N GLU A 762 " --> pdb=" O ASP A 758 " (cutoff:3.500A) removed outlier: 3.515A pdb=" N ALA A 764 " --> pdb=" O SER A 760 " (cutoff:3.500A) removed outlier: 5.758A pdb=" N ALA A 767 " --> pdb=" O ARG A 763 " (cutoff:3.500A) removed outlier: 5.988A pdb=" N SER A 768 " --> pdb=" O ALA A 764 " (cutoff:3.500A) Processing helix chain 'A' and resid 807 through 814 Processing helix chain 'A' and resid 817 through 829 Processing sheet with id=AA1, first strand: chain 'B' and resid 590 through 591 Processing sheet with id=AA2, first strand: chain 'B' and resid 617 through 620 removed outlier: 5.516A pdb=" N GLN B 617 " --> pdb=" O THR B 778 " (cutoff:3.500A) removed outlier: 7.022A pdb=" N VAL B 780 " --> pdb=" O GLN B 617 " (cutoff:3.500A) removed outlier: 5.928A pdb=" N LEU B 619 " --> pdb=" O VAL B 780 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 590 through 591 Processing sheet with id=AA4, first strand: chain 'A' and resid 617 through 620 removed outlier: 5.517A pdb=" N GLN A 617 " --> pdb=" O THR A 778 " (cutoff:3.500A) removed outlier: 7.023A pdb=" N VAL A 780 " --> pdb=" O GLN A 617 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N LEU A 619 " --> pdb=" O VAL A 780 " (cutoff:3.500A) removed outlier: 6.960A pdb=" N ILE A 748 " --> pdb=" O ILE A 779 " (cutoff:3.500A) removed outlier: 8.658A pdb=" N VAL A 781 " --> pdb=" O ILE A 748 " (cutoff:3.500A) removed outlier: 7.145A pdb=" N LEU A 750 " --> pdb=" O VAL A 781 " (cutoff:3.500A) 485 hydrogen bonds defined for protein. 1431 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: 2.40 Time building geometry restraints manager: 3.73 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.17 - 1.30: 1520 1.30 - 1.43: 2556 1.43 - 1.55: 5510 1.55 - 1.68: 6 1.68 - 1.81: 56 Bond restraints: 9648 Sorted by residual: bond pdb=" C TRP B 360 " pdb=" O TRP B 360 " ideal model delta sigma weight residual 1.235 1.170 0.065 1.33e-02 5.65e+03 2.42e+01 bond pdb=" CA TRP B 360 " pdb=" C TRP B 360 " ideal model delta sigma weight residual 1.523 1.455 0.068 1.56e-02 4.11e+03 1.90e+01 bond pdb=" N ARG B 364 " pdb=" CA ARG B 364 " ideal model delta sigma weight residual 1.457 1.504 -0.046 1.29e-02 6.01e+03 1.30e+01 bond pdb=" C HIS B 361 " pdb=" O HIS B 361 " ideal model delta sigma weight residual 1.236 1.191 0.045 1.47e-02 4.63e+03 9.40e+00 bond pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta sigma weight residual 1.531 1.486 0.045 1.62e-02 3.81e+03 7.62e+00 ... (remaining 9643 not shown) Histogram of bond angle deviations from ideal: 99.17 - 106.28: 166 106.28 - 113.39: 5100 113.39 - 120.50: 4356 120.50 - 127.61: 3368 127.61 - 134.72: 92 Bond angle restraints: 13082 Sorted by residual: angle pdb=" N ARG B 359 " pdb=" CA ARG B 359 " pdb=" C ARG B 359 " ideal model delta sigma weight residual 111.28 100.04 11.24 1.09e+00 8.42e-01 1.06e+02 angle pdb=" N ILE A 632 " pdb=" CA ILE A 632 " pdb=" C ILE A 632 " ideal model delta sigma weight residual 110.62 119.69 -9.07 1.02e+00 9.61e-01 7.90e+01 angle pdb=" N GLY A 687 " pdb=" CA GLY A 687 " pdb=" C GLY A 687 " ideal model delta sigma weight residual 112.73 120.21 -7.48 1.20e+00 6.94e-01 3.88e+01 angle pdb=" N LEU B 750 " pdb=" CA LEU B 750 " pdb=" C LEU B 750 " ideal model delta sigma weight residual 110.23 101.25 8.98 1.45e+00 4.76e-01 3.84e+01 angle pdb=" N ARG B 688 " pdb=" CA ARG B 688 " pdb=" C ARG B 688 " ideal model delta sigma weight residual 111.14 117.73 -6.59 1.08e+00 8.57e-01 3.72e+01 ... (remaining 13077 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.16: 5245 15.16 - 30.32: 312 30.32 - 45.48: 95 45.48 - 60.64: 16 60.64 - 75.81: 20 Dihedral angle restraints: 5688 sinusoidal: 2256 harmonic: 3432 Sorted by residual: dihedral pdb=" C HIS B 361 " pdb=" N HIS B 361 " pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta harmonic sigma weight residual -122.60 -138.34 15.74 0 2.50e+00 1.60e-01 3.96e+01 dihedral pdb=" N HIS B 361 " pdb=" C HIS B 361 " pdb=" CA HIS B 361 " pdb=" CB HIS B 361 " ideal model delta harmonic sigma weight residual 122.80 138.44 -15.64 0 2.50e+00 1.60e-01 3.91e+01 dihedral pdb=" CA ARG B 685 " pdb=" C ARG B 685 " pdb=" N TYR B 686 " pdb=" CA TYR B 686 " ideal model delta harmonic sigma weight residual -180.00 -155.58 -24.42 0 5.00e+00 4.00e-02 2.39e+01 ... (remaining 5685 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.159: 1468 0.159 - 0.319: 30 0.319 - 0.478: 3 0.478 - 0.637: 0 0.637 - 0.797: 1 Chirality restraints: 1502 Sorted by residual: chirality pdb=" CA HIS B 361 " pdb=" N HIS B 361 " pdb=" C HIS B 361 " pdb=" CB HIS B 361 " both_signs ideal model delta sigma weight residual False 2.51 1.71 0.80 2.00e-01 2.50e+01 1.59e+01 chirality pdb=" CA LEU A 356 " pdb=" N LEU A 356 " pdb=" C LEU A 356 " pdb=" CB LEU A 356 " both_signs ideal model delta sigma weight residual False 2.51 2.10 0.41 2.00e-01 2.50e+01 4.11e+00 chirality pdb=" CA SER B 357 " pdb=" N SER B 357 " pdb=" C SER B 357 " pdb=" CB SER B 357 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.04e+00 ... (remaining 1499 not shown) Planarity restraints: 1658 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA GLY B 687 " 0.028 2.00e-02 2.50e+03 5.56e-02 3.09e+01 pdb=" C GLY B 687 " -0.096 2.00e-02 2.50e+03 pdb=" O GLY B 687 " 0.036 2.00e-02 2.50e+03 pdb=" N ARG B 688 " 0.032 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA LEU B 356 " 0.022 2.00e-02 2.50e+03 4.55e-02 2.07e+01 pdb=" C LEU B 356 " -0.079 2.00e-02 2.50e+03 pdb=" O LEU B 356 " 0.030 2.00e-02 2.50e+03 pdb=" N SER B 357 " 0.026 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 360 " 0.022 2.00e-02 2.50e+03 4.24e-02 1.80e+01 pdb=" C TRP B 360 " -0.073 2.00e-02 2.50e+03 pdb=" O TRP B 360 " 0.027 2.00e-02 2.50e+03 pdb=" N HIS B 361 " 0.024 2.00e-02 2.50e+03 ... (remaining 1655 not shown) Histogram of nonbonded interaction distances: 2.29 - 2.81: 2620 2.81 - 3.33: 9011 3.33 - 3.86: 15034 3.86 - 4.38: 16342 4.38 - 4.90: 27933 Nonbonded interactions: 70940 Sorted by model distance: nonbonded pdb=" O THR B 323 " pdb=" OG SER B 327 " model vdw 2.289 2.440 nonbonded pdb=" O THR A 323 " pdb=" OG SER A 327 " model vdw 2.290 2.440 nonbonded pdb=" O GLY B 588 " pdb=" OG1 THR B 777 " model vdw 2.296 2.440 nonbonded pdb=" O GLY A 588 " pdb=" OG1 THR A 777 " model vdw 2.296 2.440 nonbonded pdb=" O GLY A 692 " pdb=" CB ASN A 693 " model vdw 2.305 3.440 ... (remaining 70935 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } 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: 1.270 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: 5.370 Check model and map are aligned: 0.130 Set scattering table: 0.090 Process input model: 27.410 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.050 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:2.530 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 37.320 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7143 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 0.068 9648 Z= 0.309 Angle : 1.070 11.590 13082 Z= 0.619 Chirality : 0.065 0.797 1502 Planarity : 0.007 0.056 1658 Dihedral : 12.403 75.806 3492 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 13.87 Ramachandran Plot: Outliers : 1.18 % Allowed : 11.60 % Favored : 87.23 % Rotamer: Outliers : 1.29 % Allowed : 2.38 % Favored : 96.34 % Cbeta Deviations : 0.18 % 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: -4.60 (0.18), residues: 1190 helix: -2.26 (0.15), residues: 696 sheet: -1.84 (1.02), residues: 24 loop : -4.34 (0.20), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.002 TRP B 360 HIS 0.009 0.001 HIS B 352 PHE 0.017 0.002 PHE A 611 TYR 0.024 0.002 TYR B 536 ARG 0.004 0.000 ARG A 807 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 222 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 209 time to evaluate : 1.042 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 13 outliers final: 4 residues processed: 217 average time/residue: 0.2487 time to fit residues: 72.2965 Evaluate side-chains 107 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 103 time to evaluate : 1.027 Switching outliers to nearest non-outliers revert: symmetry clash outliers start: 4 outliers final: 1 residues processed: 4 average time/residue: 0.2188 time to fit residues: 2.6115 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 99 optimal weight: 0.9990 chunk 89 optimal weight: 0.9990 chunk 49 optimal weight: 10.0000 chunk 30 optimal weight: 3.9990 chunk 60 optimal weight: 2.9990 chunk 47 optimal weight: 0.1980 chunk 92 optimal weight: 0.0040 chunk 35 optimal weight: 0.9980 chunk 56 optimal weight: 5.9990 chunk 68 optimal weight: 2.9990 chunk 107 optimal weight: 6.9990 overall best weight: 0.6396 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 354 HIS B 410 ASN B 445 GLN B 484 GLN B 617 GLN B 683 ASN B 693 ASN B 706 HIS ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 808 HIS B 823 GLN A 410 ASN A 445 GLN A 793 GLN ** A 823 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 13 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7337 moved from start: 0.3001 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9648 Z= 0.188 Angle : 0.701 10.231 13082 Z= 0.363 Chirality : 0.042 0.178 1502 Planarity : 0.004 0.031 1658 Dihedral : 5.340 23.230 1320 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.40 Ramachandran Plot: Outliers : 0.59 % Allowed : 10.76 % Favored : 88.66 % Rotamer: Outliers : 3.37 % Allowed : 12.57 % Favored : 84.06 % 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: -2.73 (0.22), residues: 1190 helix: -0.44 (0.19), residues: 688 sheet: -1.96 (0.72), residues: 44 loop : -4.06 (0.22), residues: 458 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP B 822 HIS 0.004 0.001 HIS A 352 PHE 0.020 0.001 PHE A 597 TYR 0.027 0.002 TYR B 716 ARG 0.005 0.000 ARG B 814 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 137 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 34 poor density : 103 time to evaluate : 1.006 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 34 outliers final: 21 residues processed: 127 average time/residue: 0.2011 time to fit residues: 36.6875 Evaluate side-chains 101 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 80 time to evaluate : 0.971 Switching outliers to nearest non-outliers outliers start: 21 outliers final: 0 residues processed: 21 average time/residue: 0.0973 time to fit residues: 5.1923 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 59 optimal weight: 30.0000 chunk 33 optimal weight: 0.8980 chunk 89 optimal weight: 0.7980 chunk 72 optimal weight: 0.1980 chunk 29 optimal weight: 0.0670 chunk 107 optimal weight: 1.9990 chunk 115 optimal weight: 5.9990 chunk 95 optimal weight: 0.9990 chunk 106 optimal weight: 0.0370 chunk 36 optimal weight: 5.9990 chunk 86 optimal weight: 0.6980 overall best weight: 0.3596 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 484 GLN B 683 ASN ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 617 GLN A 823 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7347 moved from start: 0.3659 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 9648 Z= 0.149 Angle : 0.636 8.661 13082 Z= 0.332 Chirality : 0.041 0.174 1502 Planarity : 0.003 0.029 1658 Dihedral : 4.914 21.440 1320 Min Nonbonded Distance : 2.162 Molprobity Statistics. All-atom Clashscore : 11.03 Ramachandran Plot: Outliers : 0.50 % Allowed : 10.50 % Favored : 88.99 % Rotamer: Outliers : 1.39 % Allowed : 14.55 % Favored : 84.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.83 (0.24), residues: 1190 helix: 0.40 (0.20), residues: 682 sheet: -1.38 (0.79), residues: 44 loop : -3.85 (0.24), residues: 464 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 239 HIS 0.005 0.001 HIS A 352 PHE 0.011 0.001 PHE A 597 TYR 0.016 0.001 TYR B 716 ARG 0.002 0.000 ARG B 634 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 93 time to evaluate : 0.971 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 14 outliers final: 4 residues processed: 101 average time/residue: 0.1858 time to fit residues: 27.5357 Evaluate side-chains 82 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 78 time to evaluate : 0.978 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0858 time to fit residues: 1.9580 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 106 optimal weight: 0.3980 chunk 80 optimal weight: 0.9990 chunk 55 optimal weight: 5.9990 chunk 11 optimal weight: 1.9990 chunk 51 optimal weight: 1.9990 chunk 72 optimal weight: 3.9990 chunk 107 optimal weight: 0.9990 chunk 114 optimal weight: 10.0000 chunk 56 optimal weight: 0.6980 chunk 102 optimal weight: 0.0770 chunk 30 optimal weight: 3.9990 overall best weight: 0.6342 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7442 moved from start: 0.4279 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 9648 Z= 0.161 Angle : 0.620 9.274 13082 Z= 0.325 Chirality : 0.041 0.152 1502 Planarity : 0.003 0.025 1658 Dihedral : 4.717 21.070 1320 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 10.77 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.76 % Favored : 88.82 % Rotamer: Outliers : 1.88 % Allowed : 15.74 % Favored : 82.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.35 (0.25), residues: 1190 helix: 0.87 (0.20), residues: 680 sheet: -1.18 (0.81), residues: 44 loop : -3.75 (0.24), residues: 466 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.025 0.001 TRP A 239 HIS 0.003 0.001 HIS A 352 PHE 0.025 0.001 PHE B 597 TYR 0.017 0.001 TYR B 530 ARG 0.003 0.000 ARG A 589 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 86 time to evaluate : 1.139 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 19 outliers final: 8 residues processed: 97 average time/residue: 0.2230 time to fit residues: 30.9242 Evaluate side-chains 83 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 1.067 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.1050 time to fit residues: 2.9124 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 94 optimal weight: 2.9990 chunk 64 optimal weight: 0.7980 chunk 1 optimal weight: 20.0000 chunk 84 optimal weight: 0.8980 chunk 47 optimal weight: 0.1980 chunk 97 optimal weight: 0.9980 chunk 78 optimal weight: 2.9990 chunk 0 optimal weight: 9.9990 chunk 58 optimal weight: 0.0030 chunk 102 optimal weight: 5.9990 chunk 28 optimal weight: 0.5980 overall best weight: 0.4990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 484 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7454 moved from start: 0.4660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.027 9648 Z= 0.146 Angle : 0.609 9.563 13082 Z= 0.316 Chirality : 0.040 0.147 1502 Planarity : 0.003 0.071 1658 Dihedral : 4.615 20.826 1320 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 10.93 Ramachandran Plot: Outliers : 0.42 % Allowed : 10.59 % Favored : 88.99 % Rotamer: Outliers : 1.09 % Allowed : 17.72 % Favored : 81.19 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.08 (0.25), residues: 1190 helix: 1.12 (0.20), residues: 676 sheet: -0.86 (0.84), residues: 44 loop : -3.68 (0.25), residues: 470 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.030 0.001 TRP A 239 HIS 0.004 0.001 HIS B 352 PHE 0.019 0.001 PHE B 597 TYR 0.018 0.001 TYR A 716 ARG 0.006 0.000 ARG A 552 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 83 time to evaluate : 1.019 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 11 outliers final: 4 residues processed: 87 average time/residue: 0.2230 time to fit residues: 27.9119 Evaluate side-chains 78 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 74 time to evaluate : 1.141 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1047 time to fit residues: 2.1579 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 38 optimal weight: 6.9990 chunk 102 optimal weight: 0.9990 chunk 22 optimal weight: 0.3980 chunk 66 optimal weight: 0.3980 chunk 28 optimal weight: 0.7980 chunk 114 optimal weight: 8.9990 chunk 94 optimal weight: 5.9990 chunk 52 optimal weight: 0.9980 chunk 9 optimal weight: 3.9990 chunk 37 optimal weight: 0.9980 chunk 59 optimal weight: 20.0000 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7502 moved from start: 0.5087 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 9648 Z= 0.164 Angle : 0.620 10.066 13082 Z= 0.321 Chirality : 0.040 0.148 1502 Planarity : 0.003 0.029 1658 Dihedral : 4.583 20.688 1320 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.26 % Favored : 88.32 % Rotamer: Outliers : 2.67 % Allowed : 17.52 % Favored : 79.80 % 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: -0.98 (0.25), residues: 1190 helix: 1.22 (0.21), residues: 680 sheet: -1.20 (0.94), residues: 34 loop : -3.64 (0.24), residues: 476 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 239 HIS 0.003 0.001 HIS A 352 PHE 0.013 0.001 PHE B 460 TYR 0.017 0.001 TYR B 530 ARG 0.011 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 27 poor density : 76 time to evaluate : 1.158 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 27 outliers final: 10 residues processed: 95 average time/residue: 0.2215 time to fit residues: 30.1594 Evaluate side-chains 80 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 70 time to evaluate : 0.987 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 0 residues processed: 10 average time/residue: 0.1029 time to fit residues: 3.1607 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 110 optimal weight: 2.9990 chunk 12 optimal weight: 6.9990 chunk 65 optimal weight: 0.9980 chunk 83 optimal weight: 1.9990 chunk 64 optimal weight: 0.7980 chunk 96 optimal weight: 3.9990 chunk 63 optimal weight: 0.7980 chunk 113 optimal weight: 1.9990 chunk 71 optimal weight: 4.9990 chunk 69 optimal weight: 0.9980 chunk 52 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 656 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7567 moved from start: 0.5660 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 9648 Z= 0.199 Angle : 0.650 10.491 13082 Z= 0.336 Chirality : 0.042 0.152 1502 Planarity : 0.004 0.065 1658 Dihedral : 4.760 21.697 1320 Min Nonbonded Distance : 2.149 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.42 % Allowed : 11.60 % Favored : 87.98 % Rotamer: Outliers : 1.98 % Allowed : 17.62 % Favored : 80.40 % 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: -0.96 (0.25), residues: 1190 helix: 1.23 (0.21), residues: 682 sheet: -1.15 (0.95), residues: 34 loop : -3.64 (0.24), residues: 474 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.001 TRP B 488 HIS 0.004 0.001 HIS B 352 PHE 0.012 0.001 PHE B 460 TYR 0.015 0.001 TYR A 541 ARG 0.009 0.000 ARG B 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 77 time to evaluate : 0.998 Fit side-chains revert: symmetry clash outliers start: 20 outliers final: 5 residues processed: 92 average time/residue: 0.2215 time to fit residues: 29.8276 Evaluate side-chains 71 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 66 time to evaluate : 1.134 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.1028 time to fit residues: 2.5551 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 70 optimal weight: 0.7980 chunk 45 optimal weight: 4.9990 chunk 67 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 22 optimal weight: 2.9990 chunk 72 optimal weight: 0.0970 chunk 77 optimal weight: 0.9980 chunk 56 optimal weight: 1.9990 chunk 10 optimal weight: 3.9990 chunk 89 optimal weight: 0.6980 chunk 103 optimal weight: 2.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 557 ASN ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7566 moved from start: 0.5934 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.053 9648 Z= 0.188 Angle : 0.669 10.763 13082 Z= 0.343 Chirality : 0.042 0.151 1502 Planarity : 0.003 0.027 1658 Dihedral : 4.697 21.955 1320 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 12.35 Ramachandran Plot: Outliers : 0.34 % Allowed : 11.76 % Favored : 87.90 % Rotamer: Outliers : 1.29 % Allowed : 18.51 % Favored : 80.20 % 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: -0.87 (0.25), residues: 1190 helix: 1.26 (0.21), residues: 684 sheet: -1.26 (0.93), residues: 34 loop : -3.52 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP A 239 HIS 0.004 0.001 HIS A 352 PHE 0.011 0.001 PHE B 460 TYR 0.018 0.001 TYR A 541 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 68 time to evaluate : 1.192 Fit side-chains outliers start: 13 outliers final: 4 residues processed: 76 average time/residue: 0.1921 time to fit residues: 22.2999 Evaluate side-chains 68 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 64 time to evaluate : 1.155 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.1189 time to fit residues: 2.3010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 108 optimal weight: 0.9990 chunk 99 optimal weight: 0.8980 chunk 105 optimal weight: 5.9990 chunk 63 optimal weight: 0.7980 chunk 46 optimal weight: 1.9990 chunk 83 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 95 optimal weight: 0.0770 chunk 100 optimal weight: 0.6980 chunk 69 optimal weight: 1.9990 chunk 112 optimal weight: 0.8980 overall best weight: 0.6738 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 823 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7550 moved from start: 0.6035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9648 Z= 0.169 Angle : 0.668 11.156 13082 Z= 0.340 Chirality : 0.041 0.153 1502 Planarity : 0.003 0.028 1658 Dihedral : 4.678 21.130 1320 Min Nonbonded Distance : 2.141 Molprobity Statistics. All-atom Clashscore : 11.61 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.85 % Favored : 87.90 % Rotamer: Outliers : 0.59 % Allowed : 18.51 % Favored : 80.89 % 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: -0.79 (0.25), residues: 1190 helix: 1.33 (0.21), residues: 684 sheet: -1.33 (0.91), residues: 34 loop : -3.51 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP A 239 HIS 0.004 0.001 HIS A 352 PHE 0.011 0.001 PHE B 460 TYR 0.016 0.001 TYR A 541 ARG 0.005 0.000 ARG A 365 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 1.131 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 74 average time/residue: 0.2176 time to fit residues: 23.7612 Evaluate side-chains 70 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 65 time to evaluate : 1.005 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0955 time to fit residues: 2.1892 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 68 optimal weight: 2.9990 chunk 53 optimal weight: 5.9990 chunk 77 optimal weight: 0.6980 chunk 117 optimal weight: 4.9990 chunk 108 optimal weight: 0.9980 chunk 93 optimal weight: 0.9990 chunk 9 optimal weight: 1.9990 chunk 72 optimal weight: 6.9990 chunk 57 optimal weight: 0.0040 chunk 74 optimal weight: 0.9980 chunk 99 optimal weight: 1.9990 overall best weight: 0.7394 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7557 moved from start: 0.6197 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 9648 Z= 0.176 Angle : 0.675 11.973 13082 Z= 0.344 Chirality : 0.041 0.147 1502 Planarity : 0.003 0.033 1658 Dihedral : 4.661 21.561 1320 Min Nonbonded Distance : 2.126 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.85 % Favored : 87.90 % Rotamer: Outliers : 0.40 % Allowed : 18.32 % Favored : 81.29 % 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: -0.81 (0.25), residues: 1190 helix: 1.31 (0.21), residues: 684 sheet: -1.34 (0.91), residues: 34 loop : -3.50 (0.25), residues: 472 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP A 239 HIS 0.004 0.001 HIS A 352 PHE 0.011 0.001 PHE B 460 TYR 0.017 0.001 TYR B 530 ARG 0.010 0.000 ARG A 371 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 2380 Ramachandran restraints generated. 1190 Oldfield, 0 Emsley, 1190 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 70 time to evaluate : 1.200 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 73 average time/residue: 0.2082 time to fit residues: 22.7149 Evaluate side-chains 70 residues out of total 1010 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 67 time to evaluate : 1.092 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.1245 time to fit residues: 2.0745 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 118 random chunks: chunk 28 optimal weight: 2.9990 chunk 86 optimal weight: 0.8980 chunk 13 optimal weight: 0.9990 chunk 26 optimal weight: 0.7980 chunk 93 optimal weight: 0.3980 chunk 39 optimal weight: 2.9990 chunk 96 optimal weight: 0.9990 chunk 11 optimal weight: 0.7980 chunk 17 optimal weight: 0.8980 chunk 82 optimal weight: 0.9990 chunk 5 optimal weight: 0.5980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 793 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3869 r_free = 0.3869 target = 0.096706 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3459 r_free = 0.3459 target = 0.075083 restraints weight = 30538.735| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3514 r_free = 0.3514 target = 0.077787 restraints weight = 15420.631| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 38)----------------| | r_work = 0.3550 r_free = 0.3550 target = 0.079618 restraints weight = 9954.871| |-----------------------------------------------------------------------------| r_work (final): 0.3538 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7647 moved from start: 0.6286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 9648 Z= 0.174 Angle : 0.675 11.089 13082 Z= 0.343 Chirality : 0.041 0.149 1502 Planarity : 0.003 0.041 1658 Dihedral : 4.644 21.571 1320 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 11.92 Ramachandran Plot: Outliers : 0.25 % Allowed : 11.60 % Favored : 88.15 % Rotamer: Outliers : 0.20 % Allowed : 18.81 % Favored : 80.99 % 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: -0.86 (0.25), residues: 1190 helix: 1.27 (0.21), residues: 688 sheet: -1.30 (0.92), residues: 34 loop : -3.57 (0.25), residues: 468 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 488 HIS 0.004 0.001 HIS A 352 PHE 0.011 0.001 PHE B 460 TYR 0.017 0.001 TYR A 716 ARG 0.009 0.000 ARG A 371 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1865.52 seconds wall clock time: 34 minutes 42.05 seconds (2082.05 seconds total)