Starting phenix.real_space_refine on Thu Nov 14 20:52:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3i_36852/11_2024/8k3i_36852.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3i_36852/11_2024/8k3i_36852.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.83 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3i_36852/11_2024/8k3i_36852.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3i_36852/11_2024/8k3i_36852.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3i_36852/11_2024/8k3i_36852.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8k3i_36852/11_2024/8k3i_36852.cif" } resolution = 2.83 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= 0.000 sd= 0.005 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 24 5.16 5 C 4682 2.51 5 N 1300 2.21 5 O 1364 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 7372 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3686 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'HIS:plan': 1, 'LLP:plan-2': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Chain: "B" Number of atoms: 3686 Number of conformers: 1 Conformer: "" Number of residues, atoms: 480, 3686 Classifications: {'peptide': 480} Incomplete info: {'truncation_to_alanine': 22} Link IDs: {'PCIS': 2, 'PTRANS': 21, 'TRANS': 456} Unresolved non-hydrogen bonds: 95 Unresolved non-hydrogen angles: 117 Unresolved non-hydrogen dihedrals: 75 Planarities with less than four sites: {'GLN:plan1': 4, 'ASP:plan': 4, 'HIS:plan': 1, 'LLP:plan-2': 1, 'GLU:plan': 7, 'ARG:plan': 4} Unresolved non-hydrogen planarities: 82 Time building chain proxies: 4.96, per 1000 atoms: 0.67 Number of scatterers: 7372 At special positions: 0 Unit cell: (102.09, 77.19, 78.02, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 24 16.00 P 2 15.00 O 1364 8.00 N 1300 7.00 C 4682 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: 1.88 Conformation dependent library (CDL) restraints added in 1.0 seconds 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1788 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 8 sheets defined 55.2% alpha, 8.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.88 Creating SS restraints... Processing helix chain 'A' and resid 337 through 347 removed outlier: 4.226A pdb=" N VAL A 343 " --> pdb=" O ARG A 339 " (cutoff:3.500A) removed outlier: 3.724A pdb=" N PHE A 344 " --> pdb=" O THR A 340 " (cutoff:3.500A) Processing helix chain 'A' and resid 352 through 368 Processing helix chain 'A' and resid 374 through 384 removed outlier: 3.775A pdb=" N ALA A 378 " --> pdb=" O ARG A 374 " (cutoff:3.500A) Processing helix chain 'A' and resid 391 through 397 Processing helix chain 'A' and resid 398 through 415 removed outlier: 4.002A pdb=" N VAL A 402 " --> pdb=" O SER A 398 " (cutoff:3.500A) removed outlier: 3.548A pdb=" N PHE A 413 " --> pdb=" O PHE A 409 " (cutoff:3.500A) Processing helix chain 'A' and resid 442 through 455 Processing helix chain 'A' and resid 466 through 479 Processing helix chain 'A' and resid 487 through 489 No H-bonds generated for 'chain 'A' and resid 487 through 489' Processing helix chain 'A' and resid 496 through 509 Processing helix chain 'A' and resid 525 through 536 removed outlier: 4.068A pdb=" N ARG A 535 " --> pdb=" O SER A 531 " (cutoff:3.500A) Processing helix chain 'A' and resid 552 through 559 removed outlier: 3.628A pdb=" N ARG A 557 " --> pdb=" O GLN A 553 " (cutoff:3.500A) Processing helix chain 'A' and resid 580 through 590 Processing helix chain 'A' and resid 613 through 618 Processing helix chain 'A' and resid 644 through 659 removed outlier: 4.359A pdb=" N GLU A 653 " --> pdb=" O SER A 649 " (cutoff:3.500A) removed outlier: 3.843A pdb=" N PHE A 654 " --> pdb=" O ARG A 650 " (cutoff:3.500A) Processing helix chain 'A' and resid 663 through 665 No H-bonds generated for 'chain 'A' and resid 663 through 665' Processing helix chain 'A' and resid 666 through 682 Processing helix chain 'A' and resid 688 through 693 removed outlier: 3.634A pdb=" N LEU A 692 " --> pdb=" O ASP A 688 " (cutoff:3.500A) Processing helix chain 'A' and resid 694 through 695 No H-bonds generated for 'chain 'A' and resid 694 through 695' Processing helix chain 'A' and resid 696 through 700 Processing helix chain 'A' and resid 702 through 738 Processing helix chain 'A' and resid 760 through 773 Processing helix chain 'A' and resid 780 through 783 Processing helix chain 'A' and resid 797 through 811 Processing helix chain 'B' and resid 337 through 347 removed outlier: 4.223A pdb=" N VAL B 343 " --> pdb=" O ARG B 339 " (cutoff:3.500A) removed outlier: 3.722A pdb=" N PHE B 344 " --> pdb=" O THR B 340 " (cutoff:3.500A) Processing helix chain 'B' and resid 352 through 368 Processing helix chain 'B' and resid 374 through 384 removed outlier: 3.777A pdb=" N ALA B 378 " --> pdb=" O ARG B 374 " (cutoff:3.500A) Processing helix chain 'B' and resid 391 through 397 Processing helix chain 'B' and resid 398 through 415 removed outlier: 4.002A pdb=" N VAL B 402 " --> pdb=" O SER B 398 " (cutoff:3.500A) removed outlier: 3.549A pdb=" N PHE B 413 " --> pdb=" O PHE B 409 " (cutoff:3.500A) Processing helix chain 'B' and resid 442 through 455 Processing helix chain 'B' and resid 466 through 479 Processing helix chain 'B' and resid 487 through 489 No H-bonds generated for 'chain 'B' and resid 487 through 489' Processing helix chain 'B' and resid 496 through 509 Processing helix chain 'B' and resid 525 through 536 removed outlier: 4.068A pdb=" N ARG B 535 " --> pdb=" O SER B 531 " (cutoff:3.500A) Processing helix chain 'B' and resid 552 through 559 removed outlier: 3.627A pdb=" N ARG B 557 " --> pdb=" O GLN B 553 " (cutoff:3.500A) Processing helix chain 'B' and resid 580 through 590 Processing helix chain 'B' and resid 613 through 618 Processing helix chain 'B' and resid 644 through 659 removed outlier: 4.357A pdb=" N GLU B 653 " --> pdb=" O SER B 649 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N PHE B 654 " --> pdb=" O ARG B 650 " (cutoff:3.500A) Processing helix chain 'B' and resid 663 through 665 No H-bonds generated for 'chain 'B' and resid 663 through 665' Processing helix chain 'B' and resid 666 through 682 Processing helix chain 'B' and resid 688 through 693 removed outlier: 3.638A pdb=" N LEU B 692 " --> pdb=" O ASP B 688 " (cutoff:3.500A) removed outlier: 3.502A pdb=" N ARG B 693 " --> pdb=" O GLN B 689 " (cutoff:3.500A) No H-bonds generated for 'chain 'B' and resid 688 through 693' Processing helix chain 'B' and resid 694 through 695 No H-bonds generated for 'chain 'B' and resid 694 through 695' Processing helix chain 'B' and resid 696 through 700 Processing helix chain 'B' and resid 702 through 738 Processing helix chain 'B' and resid 760 through 773 Processing helix chain 'B' and resid 780 through 783 Processing helix chain 'B' and resid 797 through 811 Processing sheet with id=AA1, first strand: chain 'A' and resid 427 through 428 removed outlier: 6.582A pdb=" N ILE A 427 " --> pdb=" O SER A 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 491 through 494 removed outlier: 6.071A pdb=" N ILE A 597 " --> pdb=" O ILE A 622 " (cutoff:3.500A) removed outlier: 7.086A pdb=" N VAL A 624 " --> pdb=" O ILE A 597 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU A 599 " --> pdb=" O VAL A 624 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N SER A 626 " --> pdb=" O LEU A 599 " (cutoff:3.500A) removed outlier: 6.415A pdb=" N VAL A 566 " --> pdb=" O ILE A 598 " (cutoff:3.500A) removed outlier: 7.158A pdb=" N ASP A 600 " --> pdb=" O VAL A 566 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU A 568 " --> pdb=" O ASP A 600 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE A 519 " --> pdb=" O LEU A 567 " (cutoff:3.500A) removed outlier: 8.461A pdb=" N GLN A 569 " --> pdb=" O ILE A 519 " (cutoff:3.500A) removed outlier: 8.377A pdb=" N ALA A 521 " --> pdb=" O GLN A 569 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 545 through 546 Processing sheet with id=AA4, first strand: chain 'A' and resid 741 through 742 Processing sheet with id=AA5, first strand: chain 'B' and resid 427 through 428 removed outlier: 6.583A pdb=" N ILE B 427 " --> pdb=" O SER B 775 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'B' and resid 491 through 494 removed outlier: 6.071A pdb=" N ILE B 597 " --> pdb=" O ILE B 622 " (cutoff:3.500A) removed outlier: 7.085A pdb=" N VAL B 624 " --> pdb=" O ILE B 597 " (cutoff:3.500A) removed outlier: 6.350A pdb=" N LEU B 599 " --> pdb=" O VAL B 624 " (cutoff:3.500A) removed outlier: 8.312A pdb=" N SER B 626 " --> pdb=" O LEU B 599 " (cutoff:3.500A) removed outlier: 6.414A pdb=" N VAL B 566 " --> pdb=" O ILE B 598 " (cutoff:3.500A) removed outlier: 7.157A pdb=" N ASP B 600 " --> pdb=" O VAL B 566 " (cutoff:3.500A) removed outlier: 6.721A pdb=" N LEU B 568 " --> pdb=" O ASP B 600 " (cutoff:3.500A) removed outlier: 6.786A pdb=" N ILE B 519 " --> pdb=" O LEU B 567 " (cutoff:3.500A) removed outlier: 8.462A pdb=" N GLN B 569 " --> pdb=" O ILE B 519 " (cutoff:3.500A) removed outlier: 8.376A pdb=" N ALA B 521 " --> pdb=" O GLN B 569 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 545 through 546 Processing sheet with id=AA8, first strand: chain 'B' and resid 741 through 742 385 hydrogen bonds defined for protein. 1089 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: 2.37 Time building geometry restraints manager: 2.16 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: 2327 1.34 - 1.45: 1161 1.45 - 1.57: 4014 1.57 - 1.69: 2 1.69 - 1.81: 38 Bond restraints: 7542 Sorted by residual: bond pdb=" OP4 LLP A 629 " pdb=" P LLP A 629 " ideal model delta sigma weight residual 1.726 1.540 0.186 2.00e-02 2.50e+03 8.64e+01 bond pdb=" OP4 LLP B 629 " pdb=" P LLP B 629 " ideal model delta sigma weight residual 1.726 1.540 0.186 2.00e-02 2.50e+03 8.61e+01 bond pdb=" NZ LLP B 629 " pdb=" C4' LLP B 629 " ideal model delta sigma weight residual 1.273 1.430 -0.157 2.00e-02 2.50e+03 6.19e+01 bond pdb=" NZ LLP A 629 " pdb=" C4' LLP A 629 " ideal model delta sigma weight residual 1.273 1.429 -0.156 2.00e-02 2.50e+03 6.08e+01 bond pdb=" C4 LLP A 629 " pdb=" C4' LLP A 629 " ideal model delta sigma weight residual 1.464 1.614 -0.150 2.00e-02 2.50e+03 5.63e+01 ... (remaining 7537 not shown) Histogram of bond angle deviations from ideal: 0.00 - 2.19: 10129 2.19 - 4.37: 113 4.37 - 6.56: 24 6.56 - 8.75: 7 8.75 - 10.93: 5 Bond angle restraints: 10278 Sorted by residual: angle pdb=" NZ LLP B 629 " pdb=" C4' LLP B 629 " pdb=" C4 LLP B 629 " ideal model delta sigma weight residual 120.09 109.16 10.93 3.00e+00 1.11e-01 1.33e+01 angle pdb=" NZ LLP A 629 " pdb=" C4' LLP A 629 " pdb=" C4 LLP A 629 " ideal model delta sigma weight residual 120.09 109.17 10.92 3.00e+00 1.11e-01 1.32e+01 angle pdb=" CE LLP B 629 " pdb=" NZ LLP B 629 " pdb=" C4' LLP B 629 " ideal model delta sigma weight residual 119.26 109.80 9.46 3.00e+00 1.11e-01 9.94e+00 angle pdb=" CE LLP A 629 " pdb=" NZ LLP A 629 " pdb=" C4' LLP A 629 " ideal model delta sigma weight residual 119.26 109.85 9.41 3.00e+00 1.11e-01 9.84e+00 angle pdb=" OP1 LLP A 629 " pdb=" P LLP A 629 " pdb=" OP4 LLP A 629 " ideal model delta sigma weight residual 100.47 109.23 -8.76 3.00e+00 1.11e-01 8.53e+00 ... (remaining 10273 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.32: 4050 17.32 - 34.64: 346 34.64 - 51.95: 48 51.95 - 69.27: 22 69.27 - 86.59: 4 Dihedral angle restraints: 4470 sinusoidal: 1688 harmonic: 2782 Sorted by residual: dihedral pdb=" CA GLU B 367 " pdb=" C GLU B 367 " pdb=" N LEU B 368 " pdb=" CA LEU B 368 " ideal model delta harmonic sigma weight residual 180.00 159.62 20.38 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA GLU A 367 " pdb=" C GLU A 367 " pdb=" N LEU A 368 " pdb=" CA LEU A 368 " ideal model delta harmonic sigma weight residual 180.00 159.64 20.36 0 5.00e+00 4.00e-02 1.66e+01 dihedral pdb=" CA SER B 748 " pdb=" C SER B 748 " pdb=" N ILE B 749 " pdb=" CA ILE B 749 " ideal model delta harmonic sigma weight residual -180.00 -164.46 -15.54 0 5.00e+00 4.00e-02 9.67e+00 ... (remaining 4467 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.034: 695 0.034 - 0.068: 332 0.068 - 0.101: 100 0.101 - 0.135: 35 0.135 - 0.169: 2 Chirality restraints: 1164 Sorted by residual: chirality pdb=" CA GLU A 367 " pdb=" N GLU A 367 " pdb=" C GLU A 367 " pdb=" CB GLU A 367 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.12e-01 chirality pdb=" CA GLU B 367 " pdb=" N GLU B 367 " pdb=" C GLU B 367 " pdb=" CB GLU B 367 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 6.89e-01 chirality pdb=" CA ILE A 687 " pdb=" N ILE A 687 " pdb=" C ILE A 687 " pdb=" CB ILE A 687 " both_signs ideal model delta sigma weight residual False 2.43 2.56 -0.12 2.00e-01 2.50e+01 3.82e-01 ... (remaining 1161 not shown) Planarity restraints: 1324 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CE LLP B 629 " 0.191 2.00e-02 2.50e+03 3.31e-01 1.10e+03 pdb=" NZ LLP B 629 " -0.485 2.00e-02 2.50e+03 pdb=" C4 LLP B 629 " -0.102 2.00e-02 2.50e+03 pdb=" C4' LLP B 629 " 0.396 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CE LLP A 629 " -0.192 2.00e-02 2.50e+03 3.31e-01 1.10e+03 pdb=" NZ LLP A 629 " 0.486 2.00e-02 2.50e+03 pdb=" C4 LLP A 629 " 0.101 2.00e-02 2.50e+03 pdb=" C4' LLP A 629 " -0.395 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 670 " 0.009 2.00e-02 2.50e+03 1.78e-02 3.16e+00 pdb=" C VAL A 670 " -0.031 2.00e-02 2.50e+03 pdb=" O VAL A 670 " 0.012 2.00e-02 2.50e+03 pdb=" N GLU A 671 " 0.010 2.00e-02 2.50e+03 ... (remaining 1321 not shown) Histogram of nonbonded interaction distances: 2.06 - 2.63: 48 2.63 - 3.20: 6519 3.20 - 3.76: 11642 3.76 - 4.33: 16620 4.33 - 4.90: 27399 Nonbonded interactions: 62228 Sorted by model distance: nonbonded pdb=" OD2 ASP B 416 " pdb=" OH TYR B 762 " model vdw 2.060 3.040 nonbonded pdb=" OD2 ASP A 416 " pdb=" OH TYR A 762 " model vdw 2.060 3.040 nonbonded pdb=" O ILE B 588 " pdb=" OG1 THR B 591 " model vdw 2.338 3.040 nonbonded pdb=" O ILE A 588 " pdb=" OG1 THR A 591 " model vdw 2.340 3.040 nonbonded pdb=" NE2 HIS A 485 " pdb=" OE2 GLU A 487 " model vdw 2.353 3.120 ... (remaining 62223 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: 0.00 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 individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.190 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: 0.020 Extract box with map and model: 0.260 Check model and map are aligned: 0.050 Set scattering table: 0.070 Process input model: 20.730 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.060 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: 0.010 Load rotamer database and sin/cos tables:13.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8418 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 : 0.007 0.186 7542 Z= 0.423 Angle : 0.666 10.934 10278 Z= 0.323 Chirality : 0.044 0.169 1164 Planarity : 0.014 0.331 1324 Dihedral : 13.366 86.588 2682 Min Nonbonded Distance : 2.060 Molprobity Statistics. All-atom Clashscore : 6.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.84 % Favored : 97.16 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 0.64 (0.27), residues: 950 helix: 1.52 (0.25), residues: 450 sheet: 0.26 (0.45), residues: 126 loop : -0.85 (0.30), residues: 374 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 631 HIS 0.003 0.001 HIS B 485 PHE 0.023 0.002 PHE B 641 TYR 0.023 0.002 TYR B 458 ARG 0.004 0.000 ARG A 616 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.832 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 93 average time/residue: 1.9174 time to fit residues: 185.1500 Evaluate side-chains 58 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 58 time to evaluate : 0.806 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 81 optimal weight: 2.9990 chunk 72 optimal weight: 2.9990 chunk 40 optimal weight: 7.9990 chunk 24 optimal weight: 3.9990 chunk 49 optimal weight: 7.9990 chunk 38 optimal weight: 0.8980 chunk 75 optimal weight: 1.9990 chunk 29 optimal weight: 4.9990 chunk 45 optimal weight: 4.9990 chunk 56 optimal weight: 1.9990 chunk 87 optimal weight: 0.7980 overall best weight: 1.7386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 349 ASN A 553 GLN B 349 ASN B 553 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8433 moved from start: 0.0993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.039 7542 Z= 0.246 Angle : 0.566 7.476 10278 Z= 0.292 Chirality : 0.043 0.131 1164 Planarity : 0.005 0.046 1324 Dihedral : 6.169 77.959 1084 Min Nonbonded Distance : 2.625 Molprobity Statistics. All-atom Clashscore : 4.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.58 % Allowed : 7.12 % Favored : 91.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.15 (0.27), residues: 950 helix: 2.02 (0.24), residues: 462 sheet: 0.40 (0.45), residues: 124 loop : -0.76 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 631 HIS 0.003 0.001 HIS B 712 PHE 0.022 0.002 PHE B 641 TYR 0.012 0.002 TYR B 514 ARG 0.006 0.000 ARG A 693 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 64 time to evaluate : 0.873 Fit side-chains REVERT: A 447 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5867 (tt0) REVERT: A 721 GLU cc_start: 0.7419 (OUTLIER) cc_final: 0.6882 (tm-30) REVERT: A 722 GLN cc_start: 0.7726 (OUTLIER) cc_final: 0.7046 (mp10) REVERT: A 806 GLU cc_start: 0.6848 (mm-30) cc_final: 0.6557 (mm-30) REVERT: B 447 GLU cc_start: 0.6582 (OUTLIER) cc_final: 0.5879 (tt0) outliers start: 12 outliers final: 0 residues processed: 74 average time/residue: 1.7534 time to fit residues: 135.6863 Evaluate side-chains 62 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 0.840 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 48 optimal weight: 10.0000 chunk 27 optimal weight: 6.9990 chunk 72 optimal weight: 4.9990 chunk 59 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 87 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 77 optimal weight: 4.9990 chunk 86 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 70 optimal weight: 1.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN B 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8412 moved from start: 0.1183 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7542 Z= 0.183 Angle : 0.500 6.838 10278 Z= 0.259 Chirality : 0.041 0.129 1164 Planarity : 0.004 0.046 1324 Dihedral : 6.028 80.195 1084 Min Nonbonded Distance : 2.639 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.72 % Allowed : 9.37 % Favored : 88.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.48 (0.27), residues: 950 helix: 2.29 (0.24), residues: 462 sheet: 0.44 (0.45), residues: 120 loop : -0.53 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 631 HIS 0.002 0.001 HIS A 712 PHE 0.019 0.002 PHE B 641 TYR 0.010 0.001 TYR B 514 ARG 0.002 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 64 time to evaluate : 0.860 Fit side-chains REVERT: A 357 ARG cc_start: 0.8461 (ttp80) cc_final: 0.8196 (ttp-170) REVERT: A 387 ARG cc_start: 0.7617 (OUTLIER) cc_final: 0.7416 (mtt-85) REVERT: A 447 GLU cc_start: 0.6560 (OUTLIER) cc_final: 0.5788 (tt0) REVERT: A 722 GLN cc_start: 0.7718 (OUTLIER) cc_final: 0.7138 (mp10) REVERT: B 357 ARG cc_start: 0.8470 (ttp80) cc_final: 0.8198 (ttp-170) REVERT: B 447 GLU cc_start: 0.6581 (OUTLIER) cc_final: 0.5843 (tt0) outliers start: 13 outliers final: 0 residues processed: 75 average time/residue: 1.8660 time to fit residues: 145.8717 Evaluate side-chains 67 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 63 time to evaluate : 0.864 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.9980 chunk 65 optimal weight: 0.0970 chunk 45 optimal weight: 5.9990 chunk 9 optimal weight: 10.0000 chunk 41 optimal weight: 0.4980 chunk 58 optimal weight: 4.9990 chunk 87 optimal weight: 2.9990 chunk 92 optimal weight: 20.0000 chunk 83 optimal weight: 4.9990 chunk 25 optimal weight: 1.9990 chunk 77 optimal weight: 6.9990 overall best weight: 1.3182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN B 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1224 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7542 Z= 0.195 Angle : 0.509 6.843 10278 Z= 0.262 Chirality : 0.041 0.130 1164 Planarity : 0.005 0.046 1324 Dihedral : 6.014 80.013 1084 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.32 % Allowed : 10.16 % Favored : 88.52 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.27), residues: 950 helix: 2.36 (0.24), residues: 462 sheet: 0.45 (0.45), residues: 120 loop : -0.54 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 631 HIS 0.004 0.001 HIS B 485 PHE 0.020 0.002 PHE A 641 TYR 0.010 0.001 TYR B 514 ARG 0.002 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 67 time to evaluate : 0.862 Fit side-chains REVERT: A 387 ARG cc_start: 0.7641 (OUTLIER) cc_final: 0.6933 (ptm160) REVERT: A 447 GLU cc_start: 0.6525 (OUTLIER) cc_final: 0.5799 (tt0) REVERT: A 722 GLN cc_start: 0.7731 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: B 447 GLU cc_start: 0.6550 (OUTLIER) cc_final: 0.5826 (tt0) outliers start: 10 outliers final: 0 residues processed: 74 average time/residue: 1.9928 time to fit residues: 153.6625 Evaluate side-chains 63 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 59 time to evaluate : 0.773 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 52 optimal weight: 2.9990 chunk 1 optimal weight: 4.9990 chunk 69 optimal weight: 4.9990 chunk 38 optimal weight: 0.9980 chunk 79 optimal weight: 0.8980 chunk 64 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 47 optimal weight: 0.8980 chunk 83 optimal weight: 3.9990 chunk 23 optimal weight: 0.6980 chunk 31 optimal weight: 3.9990 overall best weight: 0.8580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN B 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8392 moved from start: 0.1443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7542 Z= 0.149 Angle : 0.467 6.166 10278 Z= 0.242 Chirality : 0.040 0.127 1164 Planarity : 0.004 0.045 1324 Dihedral : 5.932 81.839 1084 Min Nonbonded Distance : 2.641 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.72 % Allowed : 10.82 % Favored : 87.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.71 (0.27), residues: 950 helix: 2.49 (0.24), residues: 464 sheet: 0.54 (0.45), residues: 120 loop : -0.46 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 631 HIS 0.005 0.001 HIS A 485 PHE 0.018 0.001 PHE B 641 TYR 0.009 0.001 TYR B 514 ARG 0.004 0.000 ARG B 357 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 62 time to evaluate : 0.781 Fit side-chains REVERT: A 387 ARG cc_start: 0.7659 (OUTLIER) cc_final: 0.6879 (ptm160) REVERT: A 447 GLU cc_start: 0.6569 (OUTLIER) cc_final: 0.5802 (tt0) REVERT: A 485 HIS cc_start: 0.7123 (t70) cc_final: 0.6769 (t-90) REVERT: A 722 GLN cc_start: 0.7724 (OUTLIER) cc_final: 0.7154 (mp10) REVERT: B 447 GLU cc_start: 0.6481 (OUTLIER) cc_final: 0.5716 (tt0) outliers start: 13 outliers final: 0 residues processed: 73 average time/residue: 1.8809 time to fit residues: 143.0764 Evaluate side-chains 62 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 58 time to evaluate : 1.027 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 83 optimal weight: 3.9990 chunk 18 optimal weight: 7.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 1.9990 chunk 92 optimal weight: 8.9990 chunk 77 optimal weight: 7.9990 chunk 43 optimal weight: 4.9990 chunk 7 optimal weight: 0.9980 chunk 30 optimal weight: 0.5980 chunk 48 optimal weight: 10.0000 chunk 89 optimal weight: 4.9990 overall best weight: 1.7184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN B 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8431 moved from start: 0.1245 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 7542 Z= 0.239 Angle : 0.535 7.353 10278 Z= 0.276 Chirality : 0.042 0.133 1164 Planarity : 0.005 0.047 1324 Dihedral : 6.038 79.163 1084 Min Nonbonded Distance : 2.582 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.32 % Allowed : 11.61 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.50 (0.27), residues: 950 helix: 2.39 (0.24), residues: 462 sheet: 0.41 (0.45), residues: 124 loop : -0.65 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 631 HIS 0.007 0.001 HIS B 485 PHE 0.021 0.002 PHE A 641 TYR 0.010 0.001 TYR B 514 ARG 0.002 0.000 ARG A 510 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 61 time to evaluate : 0.862 Fit side-chains REVERT: A 387 ARG cc_start: 0.7703 (OUTLIER) cc_final: 0.6864 (ptm160) REVERT: A 447 GLU cc_start: 0.6342 (OUTLIER) cc_final: 0.5655 (tt0) REVERT: B 447 GLU cc_start: 0.6384 (OUTLIER) cc_final: 0.5669 (tt0) REVERT: B 487 GLU cc_start: 0.7084 (mm-30) cc_final: 0.6795 (mm-30) outliers start: 10 outliers final: 0 residues processed: 67 average time/residue: 1.9697 time to fit residues: 137.3695 Evaluate side-chains 60 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 57 time to evaluate : 0.871 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 10 optimal weight: 6.9990 chunk 52 optimal weight: 4.9990 chunk 67 optimal weight: 0.7980 chunk 78 optimal weight: 1.9990 chunk 51 optimal weight: 0.9980 chunk 92 optimal weight: 1.9990 chunk 57 optimal weight: 7.9990 chunk 56 optimal weight: 3.9990 chunk 42 optimal weight: 3.9990 chunk 36 optimal weight: 0.4980 chunk 55 optimal weight: 0.9990 overall best weight: 1.0584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN B 553 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1400 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 7542 Z= 0.171 Angle : 0.489 6.600 10278 Z= 0.253 Chirality : 0.041 0.128 1164 Planarity : 0.004 0.046 1324 Dihedral : 5.970 81.033 1084 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 4.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.11 % Favored : 97.89 % Rotamer: Outliers : 1.32 % Allowed : 11.48 % Favored : 87.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.69 (0.27), residues: 950 helix: 2.52 (0.24), residues: 462 sheet: 0.49 (0.45), residues: 120 loop : -0.49 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 631 HIS 0.007 0.001 HIS A 485 PHE 0.019 0.002 PHE A 641 TYR 0.009 0.001 TYR B 514 ARG 0.002 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 59 time to evaluate : 0.867 Fit side-chains revert: symmetry clash REVERT: A 387 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6902 (ptm160) REVERT: A 447 GLU cc_start: 0.6386 (OUTLIER) cc_final: 0.5638 (tt0) REVERT: A 722 GLN cc_start: 0.7716 (OUTLIER) cc_final: 0.7137 (mp10) REVERT: B 447 GLU cc_start: 0.6400 (OUTLIER) cc_final: 0.5673 (tt0) REVERT: B 487 GLU cc_start: 0.7041 (mm-30) cc_final: 0.6730 (mm-30) outliers start: 10 outliers final: 0 residues processed: 67 average time/residue: 1.9985 time to fit residues: 139.2363 Evaluate side-chains 61 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 57 time to evaluate : 0.878 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 27 optimal weight: 3.9990 chunk 18 optimal weight: 8.9990 chunk 17 optimal weight: 0.9980 chunk 58 optimal weight: 0.5980 chunk 63 optimal weight: 3.9990 chunk 45 optimal weight: 5.9990 chunk 8 optimal weight: 3.9990 chunk 72 optimal weight: 5.9990 chunk 84 optimal weight: 7.9990 chunk 88 optimal weight: 7.9990 chunk 80 optimal weight: 1.9990 overall best weight: 2.3186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 553 GLN B 485 HIS B 553 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8446 moved from start: 0.1285 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.051 7542 Z= 0.302 Angle : 0.576 7.668 10278 Z= 0.297 Chirality : 0.044 0.140 1164 Planarity : 0.005 0.056 1324 Dihedral : 6.147 78.240 1084 Min Nonbonded Distance : 2.624 Molprobity Statistics. All-atom Clashscore : 4.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.95 % Favored : 97.05 % Rotamer: Outliers : 1.72 % Allowed : 11.21 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % 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: 1.36 (0.27), residues: 950 helix: 2.27 (0.24), residues: 462 sheet: 0.40 (0.45), residues: 124 loop : -0.72 (0.31), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 631 HIS 0.003 0.001 HIS B 712 PHE 0.023 0.002 PHE A 641 TYR 0.012 0.002 TYR B 652 ARG 0.003 0.000 ARG B 510 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 56 time to evaluate : 0.807 Fit side-chains REVERT: A 387 ARG cc_start: 0.7708 (OUTLIER) cc_final: 0.6898 (ptm160) REVERT: A 447 GLU cc_start: 0.6325 (OUTLIER) cc_final: 0.5711 (tt0) REVERT: A 721 GLU cc_start: 0.7399 (OUTLIER) cc_final: 0.6870 (tm-30) REVERT: A 722 GLN cc_start: 0.7720 (OUTLIER) cc_final: 0.7012 (mp10) REVERT: B 447 GLU cc_start: 0.6345 (OUTLIER) cc_final: 0.5705 (tt0) outliers start: 13 outliers final: 0 residues processed: 67 average time/residue: 2.0148 time to fit residues: 140.4273 Evaluate side-chains 60 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 55 time to evaluate : 0.764 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 447 GLU Chi-restraints excluded: chain A residue 721 GLU Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 86 optimal weight: 0.8980 chunk 88 optimal weight: 6.9990 chunk 51 optimal weight: 6.9990 chunk 37 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 26 optimal weight: 0.0770 chunk 77 optimal weight: 5.9990 chunk 81 optimal weight: 0.7980 chunk 85 optimal weight: 4.9990 chunk 56 optimal weight: 4.9990 chunk 91 optimal weight: 0.7980 overall best weight: 0.6938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS A 553 GLN B 485 HIS B 553 GLN B 802 HIS Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8385 moved from start: 0.1527 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 7542 Z= 0.137 Angle : 0.463 5.697 10278 Z= 0.241 Chirality : 0.040 0.128 1164 Planarity : 0.004 0.047 1324 Dihedral : 6.003 82.813 1084 Min Nonbonded Distance : 2.642 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.89 % Favored : 98.11 % Rotamer: Outliers : 1.06 % Allowed : 12.01 % Favored : 86.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.76 (0.28), residues: 950 helix: 2.54 (0.24), residues: 464 sheet: 0.59 (0.45), residues: 120 loop : -0.44 (0.32), residues: 366 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 631 HIS 0.004 0.001 HIS A 485 PHE 0.018 0.001 PHE A 641 TYR 0.008 0.001 TYR B 514 ARG 0.002 0.000 ARG B 388 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 61 time to evaluate : 0.856 Fit side-chains REVERT: A 387 ARG cc_start: 0.7671 (OUTLIER) cc_final: 0.6865 (ptm160) REVERT: A 722 GLN cc_start: 0.7694 (OUTLIER) cc_final: 0.7099 (mp10) REVERT: B 447 GLU cc_start: 0.6443 (OUTLIER) cc_final: 0.5652 (tt0) outliers start: 8 outliers final: 0 residues processed: 66 average time/residue: 1.9902 time to fit residues: 136.8092 Evaluate side-chains 63 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 60 time to evaluate : 0.799 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 55 optimal weight: 4.9990 chunk 43 optimal weight: 1.9990 chunk 63 optimal weight: 2.9990 chunk 95 optimal weight: 2.9990 chunk 88 optimal weight: 6.9990 chunk 76 optimal weight: 0.7980 chunk 7 optimal weight: 4.9990 chunk 58 optimal weight: 1.9990 chunk 46 optimal weight: 10.0000 chunk 60 optimal weight: 5.9990 chunk 81 optimal weight: 5.9990 overall best weight: 2.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS A 553 GLN A 802 HIS B 485 HIS B 553 GLN B 802 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8442 moved from start: 0.1302 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 7542 Z= 0.285 Angle : 0.566 7.385 10278 Z= 0.293 Chirality : 0.043 0.142 1164 Planarity : 0.005 0.054 1324 Dihedral : 6.137 78.486 1084 Min Nonbonded Distance : 2.632 Molprobity Statistics. All-atom Clashscore : 4.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer: Outliers : 1.06 % Allowed : 12.53 % Favored : 86.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.46 (0.27), residues: 950 helix: 2.35 (0.24), residues: 462 sheet: 0.47 (0.45), residues: 124 loop : -0.70 (0.32), residues: 364 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP A 631 HIS 0.004 0.001 HIS B 485 PHE 0.023 0.002 PHE A 641 TYR 0.013 0.002 TYR A 652 ARG 0.003 0.000 ARG B 357 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1900 Ramachandran restraints generated. 950 Oldfield, 0 Emsley, 950 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 66 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 58 time to evaluate : 0.929 Fit side-chains REVERT: A 387 ARG cc_start: 0.7730 (OUTLIER) cc_final: 0.6905 (ptm160) REVERT: A 722 GLN cc_start: 0.7723 (OUTLIER) cc_final: 0.7101 (mp10) REVERT: B 447 GLU cc_start: 0.6354 (OUTLIER) cc_final: 0.5706 (tt0) outliers start: 8 outliers final: 0 residues processed: 63 average time/residue: 1.9629 time to fit residues: 128.9073 Evaluate side-chains 59 residues out of total 802 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 3 poor density : 56 time to evaluate : 0.915 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 387 ARG Chi-restraints excluded: chain A residue 722 GLN Chi-restraints excluded: chain B residue 447 GLU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 96 random chunks: chunk 23 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 76 optimal weight: 3.9990 chunk 31 optimal weight: 0.7980 chunk 78 optimal weight: 0.8980 chunk 9 optimal weight: 7.9990 chunk 14 optimal weight: 4.9990 chunk 66 optimal weight: 5.9990 chunk 4 optimal weight: 2.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 485 HIS A 553 GLN A 802 HIS B 485 HIS B 553 GLN B 802 HIS Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3264 r_free = 0.3264 target = 0.117687 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3003 r_free = 0.3003 target = 0.098611 restraints weight = 8244.397| |-----------------------------------------------------------------------------| r_work (start): 0.2990 rms_B_bonded: 1.17 r_work: 0.2874 rms_B_bonded: 1.86 restraints_weight: 0.5000 r_work: 0.2744 rms_B_bonded: 3.15 restraints_weight: 0.2500 r_work (final): 0.2744 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8596 moved from start: 0.1391 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 7542 Z= 0.198 Angle : 0.508 6.522 10278 Z= 0.264 Chirality : 0.041 0.135 1164 Planarity : 0.005 0.047 1324 Dihedral : 6.067 80.406 1084 Min Nonbonded Distance : 2.638 Molprobity Statistics. All-atom Clashscore : 4.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 1.19 % Allowed : 12.27 % Favored : 86.54 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 8.70 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.59 (0.27), residues: 950 helix: 2.44 (0.24), residues: 462 sheet: 0.52 (0.45), residues: 120 loop : -0.58 (0.32), residues: 368 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 631 HIS 0.003 0.001 HIS B 485 PHE 0.020 0.002 PHE A 641 TYR 0.011 0.001 TYR A 652 ARG 0.002 0.000 ARG B 387 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2828.72 seconds wall clock time: 51 minutes 29.22 seconds (3089.22 seconds total)