Starting phenix.real_space_refine on Mon Apr 8 19:28:34 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz5_24083/04_2024/7mz5_24083_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz5_24083/04_2024/7mz5_24083.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.76 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz5_24083/04_2024/7mz5_24083.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz5_24083/04_2024/7mz5_24083.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz5_24083/04_2024/7mz5_24083_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7mz5_24083/04_2024/7mz5_24083_updated.pdb" } resolution = 2.76 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= 0.004 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 S 92 5.16 5 Na 3 4.78 5 C 9428 2.51 5 N 2252 2.21 5 O 2516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 309": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C ASP 654": "OD1" <-> "OD2" Time to flip residues: 0.07s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 14291 Number of models: 1 Model: "" Number of chains: 8 Chain: "A" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3526 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 2 Chain: "C" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3526 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 2 Chain: "D" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3526 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 2 Chain: "B" Number of atoms: 3526 Number of conformers: 1 Conformer: "" Number of residues, atoms: 431, 3526 Classifications: {'peptide': 431} Link IDs: {'PCIS': 1, 'PTRANS': 9, 'TRANS': 420} Chain breaks: 2 Chain: "A" Number of atoms: 49 Number of conformers: 1 Conformer: "" Number of residues, atoms: 4, 49 Unusual residues: {' NA': 3, '6EU': 1} Classifications: {'undetermined': 4} Link IDs: {None: 3} Chain: "C" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "D" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 46 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 46 Unusual residues: {'6EU': 1} Classifications: {'undetermined': 1} Time building chain proxies: 7.41, per 1000 atoms: 0.52 Number of scatterers: 14291 At special positions: 0 Unit cell: (122.808, 122.808, 102.168, 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 92 16.00 Na 3 11.00 O 2516 8.00 N 2252 7.00 C 9428 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: 6.29 Conformation dependent library (CDL) restraints added in 2.7 seconds 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 3280 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 72 helices and 4 sheets defined 62.8% alpha, 2.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 2.62 Creating SS restraints... Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 299 through 319 Processing helix chain 'A' and resid 325 through 327 No H-bonds generated for 'chain 'A' and resid 325 through 327' Processing helix chain 'A' and resid 336 through 342 Processing helix chain 'A' and resid 346 through 353 Processing helix chain 'A' and resid 363 through 365 No H-bonds generated for 'chain 'A' and resid 363 through 365' Processing helix chain 'A' and resid 395 through 400 Processing helix chain 'A' and resid 412 through 414 No H-bonds generated for 'chain 'A' and resid 412 through 414' Processing helix chain 'A' and resid 416 through 428 Processing helix chain 'A' and resid 430 through 453 Processing helix chain 'A' and resid 469 through 499 Processing helix chain 'A' and resid 511 through 531 Processing helix chain 'A' and resid 535 through 556 removed outlier: 4.177A pdb=" N VAL A 542 " --> pdb=" O ALA A 539 " (cutoff:3.500A) Processing helix chain 'A' and resid 563 through 575 Processing helix chain 'A' and resid 577 through 598 Processing helix chain 'A' and resid 630 through 641 removed outlier: 3.908A pdb=" N PHE A 640 " --> pdb=" O GLU A 636 " (cutoff:3.500A) removed outlier: 4.107A pdb=" N THR A 641 " --> pdb=" O LEU A 637 " (cutoff:3.500A) Processing helix chain 'A' and resid 656 through 684 removed outlier: 3.789A pdb=" N GLU A 684 " --> pdb=" O ALA A 680 " (cutoff:3.500A) Processing helix chain 'A' and resid 689 through 711 Processing helix chain 'C' and resid 287 through 294 Processing helix chain 'C' and resid 299 through 319 Processing helix chain 'C' and resid 325 through 327 No H-bonds generated for 'chain 'C' and resid 325 through 327' Processing helix chain 'C' and resid 336 through 342 Processing helix chain 'C' and resid 346 through 353 Processing helix chain 'C' and resid 363 through 365 No H-bonds generated for 'chain 'C' and resid 363 through 365' Processing helix chain 'C' and resid 395 through 400 Processing helix chain 'C' and resid 410 through 414 removed outlier: 4.210A pdb=" N LEU C 413 " --> pdb=" O HIS C 410 " (cutoff:3.500A) Processing helix chain 'C' and resid 416 through 428 Processing helix chain 'C' and resid 430 through 453 Processing helix chain 'C' and resid 469 through 499 Processing helix chain 'C' and resid 511 through 531 Processing helix chain 'C' and resid 535 through 556 removed outlier: 4.166A pdb=" N VAL C 542 " --> pdb=" O ALA C 539 " (cutoff:3.500A) removed outlier: 3.984A pdb=" N MET C 547 " --> pdb=" O SER C 544 " (cutoff:3.500A) Processing helix chain 'C' and resid 563 through 575 Processing helix chain 'C' and resid 577 through 598 Processing helix chain 'C' and resid 630 through 641 removed outlier: 3.929A pdb=" N PHE C 640 " --> pdb=" O GLU C 636 " (cutoff:3.500A) removed outlier: 4.114A pdb=" N THR C 641 " --> pdb=" O LEU C 637 " (cutoff:3.500A) Processing helix chain 'C' and resid 656 through 684 removed outlier: 3.890A pdb=" N GLU C 684 " --> pdb=" O ALA C 680 " (cutoff:3.500A) Processing helix chain 'C' and resid 689 through 711 Processing helix chain 'D' and resid 287 through 294 Processing helix chain 'D' and resid 299 through 319 Processing helix chain 'D' and resid 325 through 327 No H-bonds generated for 'chain 'D' and resid 325 through 327' Processing helix chain 'D' and resid 336 through 343 Processing helix chain 'D' and resid 346 through 353 Processing helix chain 'D' and resid 363 through 365 No H-bonds generated for 'chain 'D' and resid 363 through 365' Processing helix chain 'D' and resid 395 through 400 Processing helix chain 'D' and resid 409 through 414 removed outlier: 4.279A pdb=" N LEU D 413 " --> pdb=" O HIS D 410 " (cutoff:3.500A) Processing helix chain 'D' and resid 416 through 428 Processing helix chain 'D' and resid 430 through 453 Processing helix chain 'D' and resid 469 through 499 Processing helix chain 'D' and resid 511 through 531 Processing helix chain 'D' and resid 535 through 556 removed outlier: 4.158A pdb=" N VAL D 542 " --> pdb=" O ALA D 539 " (cutoff:3.500A) Processing helix chain 'D' and resid 563 through 575 Processing helix chain 'D' and resid 577 through 598 Processing helix chain 'D' and resid 630 through 641 removed outlier: 3.916A pdb=" N PHE D 640 " --> pdb=" O GLU D 636 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N THR D 641 " --> pdb=" O LEU D 637 " (cutoff:3.500A) Processing helix chain 'D' and resid 656 through 684 removed outlier: 3.839A pdb=" N GLU D 684 " --> pdb=" O ALA D 680 " (cutoff:3.500A) Processing helix chain 'D' and resid 688 through 711 Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 299 through 319 Processing helix chain 'B' and resid 325 through 327 No H-bonds generated for 'chain 'B' and resid 325 through 327' Processing helix chain 'B' and resid 336 through 342 Processing helix chain 'B' and resid 346 through 353 Processing helix chain 'B' and resid 363 through 365 No H-bonds generated for 'chain 'B' and resid 363 through 365' Processing helix chain 'B' and resid 395 through 400 Processing helix chain 'B' and resid 412 through 414 No H-bonds generated for 'chain 'B' and resid 412 through 414' Processing helix chain 'B' and resid 416 through 428 Processing helix chain 'B' and resid 430 through 453 Processing helix chain 'B' and resid 469 through 499 Processing helix chain 'B' and resid 511 through 531 Processing helix chain 'B' and resid 535 through 556 removed outlier: 4.152A pdb=" N VAL B 542 " --> pdb=" O ALA B 539 " (cutoff:3.500A) Processing helix chain 'B' and resid 563 through 574 removed outlier: 3.628A pdb=" N GLU B 570 " --> pdb=" O ALA B 566 " (cutoff:3.500A) Processing helix chain 'B' and resid 577 through 598 Processing helix chain 'B' and resid 630 through 641 removed outlier: 3.928A pdb=" N PHE B 640 " --> pdb=" O GLU B 636 " (cutoff:3.500A) removed outlier: 4.117A pdb=" N THR B 641 " --> pdb=" O LEU B 637 " (cutoff:3.500A) Processing helix chain 'B' and resid 656 through 684 removed outlier: 3.836A pdb=" N GLU B 684 " --> pdb=" O ALA B 680 " (cutoff:3.500A) Processing helix chain 'B' and resid 689 through 711 Processing sheet with id= A, first strand: chain 'A' and resid 741 through 744 removed outlier: 6.395A pdb=" N LEU A 381 " --> pdb=" O THR A 370 " (cutoff:3.500A) removed outlier: 5.239A pdb=" N THR A 370 " --> pdb=" O LEU A 381 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'C' and resid 741 through 744 removed outlier: 6.186A pdb=" N LEU C 381 " --> pdb=" O THR C 370 " (cutoff:3.500A) removed outlier: 5.337A pdb=" N THR C 370 " --> pdb=" O LEU C 381 " (cutoff:3.500A) Processing sheet with id= C, first strand: chain 'D' and resid 741 through 744 removed outlier: 6.170A pdb=" N LEU D 381 " --> pdb=" O THR D 370 " (cutoff:3.500A) removed outlier: 5.262A pdb=" N THR D 370 " --> pdb=" O LEU D 381 " (cutoff:3.500A) Processing sheet with id= D, first strand: chain 'B' and resid 741 through 744 removed outlier: 6.361A pdb=" N LEU B 381 " --> pdb=" O THR B 370 " (cutoff:3.500A) removed outlier: 5.159A pdb=" N THR B 370 " --> pdb=" O LEU B 381 " (cutoff:3.500A) 814 hydrogen bonds defined for protein. 2220 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: 4.07 Time building geometry restraints manager: 6.70 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 3081 1.33 - 1.45: 3430 1.45 - 1.57: 7981 1.57 - 1.69: 0 1.69 - 1.81: 152 Bond restraints: 14644 Sorted by residual: bond pdb=" CBK 6EU B 901 " pdb=" OAF 6EU B 901 " ideal model delta sigma weight residual 1.329 1.456 -0.127 2.00e-02 2.50e+03 4.02e+01 bond pdb=" CBK 6EU D 901 " pdb=" OAF 6EU D 901 " ideal model delta sigma weight residual 1.329 1.455 -0.126 2.00e-02 2.50e+03 3.98e+01 bond pdb=" CBK 6EU A 901 " pdb=" OAF 6EU A 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" CBK 6EU C 901 " pdb=" OAF 6EU C 901 " ideal model delta sigma weight residual 1.329 1.454 -0.125 2.00e-02 2.50e+03 3.92e+01 bond pdb=" N PHE A 712 " pdb=" CA PHE A 712 " ideal model delta sigma weight residual 1.457 1.491 -0.034 1.29e-02 6.01e+03 6.75e+00 ... (remaining 14639 not shown) Histogram of bond angle deviations from ideal: 97.61 - 104.92: 178 104.92 - 112.22: 7215 112.22 - 119.53: 4908 119.53 - 126.84: 7406 126.84 - 134.15: 141 Bond angle restraints: 19848 Sorted by residual: angle pdb=" N ASP A 654 " pdb=" CA ASP A 654 " pdb=" C ASP A 654 " ideal model delta sigma weight residual 110.14 100.32 9.82 1.47e+00 4.63e-01 4.46e+01 angle pdb=" N ASP C 654 " pdb=" CA ASP C 654 " pdb=" C ASP C 654 " ideal model delta sigma weight residual 110.14 100.51 9.63 1.47e+00 4.63e-01 4.29e+01 angle pdb=" O TYR A 653 " pdb=" C TYR A 653 " pdb=" N ASP A 654 " ideal model delta sigma weight residual 123.26 126.73 -3.47 1.05e+00 9.07e-01 1.10e+01 angle pdb=" N LEU C 713 " pdb=" CA LEU C 713 " pdb=" C LEU C 713 " ideal model delta sigma weight residual 110.80 117.80 -7.00 2.13e+00 2.20e-01 1.08e+01 angle pdb=" N PHE A 712 " pdb=" CA PHE A 712 " pdb=" C PHE A 712 " ideal model delta sigma weight residual 110.80 117.69 -6.89 2.13e+00 2.20e-01 1.05e+01 ... (remaining 19843 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.77: 8395 17.77 - 35.55: 366 35.55 - 53.32: 80 53.32 - 71.09: 30 71.09 - 88.87: 5 Dihedral angle restraints: 8876 sinusoidal: 3776 harmonic: 5100 Sorted by residual: dihedral pdb=" N PHE A 712 " pdb=" C PHE A 712 " pdb=" CA PHE A 712 " pdb=" CB PHE A 712 " ideal model delta harmonic sigma weight residual 122.80 139.54 -16.74 0 2.50e+00 1.60e-01 4.48e+01 dihedral pdb=" C PHE A 712 " pdb=" N PHE A 712 " pdb=" CA PHE A 712 " pdb=" CB PHE A 712 " ideal model delta harmonic sigma weight residual -122.60 -139.00 16.40 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" N PHE D 712 " pdb=" C PHE D 712 " pdb=" CA PHE D 712 " pdb=" CB PHE D 712 " ideal model delta harmonic sigma weight residual 122.80 139.08 -16.28 0 2.50e+00 1.60e-01 4.24e+01 ... (remaining 8873 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.128: 2216 0.128 - 0.255: 14 0.255 - 0.383: 6 0.383 - 0.510: 0 0.510 - 0.638: 4 Chirality restraints: 2240 Sorted by residual: chirality pdb=" CA PHE A 712 " pdb=" N PHE A 712 " pdb=" C PHE A 712 " pdb=" CB PHE A 712 " both_signs ideal model delta sigma weight residual False 2.51 1.87 0.64 2.00e-01 2.50e+01 1.02e+01 chirality pdb=" CA PHE B 712 " pdb=" N PHE B 712 " pdb=" C PHE B 712 " pdb=" CB PHE B 712 " both_signs ideal model delta sigma weight residual False 2.51 1.89 0.62 2.00e-01 2.50e+01 9.52e+00 chirality pdb=" CA PHE D 712 " pdb=" N PHE D 712 " pdb=" C PHE D 712 " pdb=" CB PHE D 712 " both_signs ideal model delta sigma weight residual False 2.51 1.90 0.61 2.00e-01 2.50e+01 9.43e+00 ... (remaining 2237 not shown) Planarity restraints: 2412 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 546 " -0.012 2.00e-02 2.50e+03 2.43e-02 5.89e+00 pdb=" C ALA A 546 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA A 546 " -0.016 2.00e-02 2.50e+03 pdb=" N MET A 547 " -0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA B 546 " 0.012 2.00e-02 2.50e+03 2.41e-02 5.79e+00 pdb=" C ALA B 546 " -0.042 2.00e-02 2.50e+03 pdb=" O ALA B 546 " 0.016 2.00e-02 2.50e+03 pdb=" N MET B 547 " 0.014 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 546 " -0.012 2.00e-02 2.50e+03 2.40e-02 5.77e+00 pdb=" C ALA D 546 " 0.042 2.00e-02 2.50e+03 pdb=" O ALA D 546 " -0.016 2.00e-02 2.50e+03 pdb=" N MET D 547 " -0.014 2.00e-02 2.50e+03 ... (remaining 2409 not shown) Histogram of nonbonded interaction distances: 2.14 - 2.69: 228 2.69 - 3.24: 14568 3.24 - 3.80: 23284 3.80 - 4.35: 30488 4.35 - 4.90: 50687 Nonbonded interactions: 119255 Sorted by model distance: nonbonded pdb=" O LEU C 673 " pdb=" OH TYR D 565 " model vdw 2.138 2.440 nonbonded pdb=" OH TYR A 565 " pdb=" O LEU D 673 " model vdw 2.178 2.440 nonbonded pdb=" OH TYR C 565 " pdb=" O LEU B 673 " model vdw 2.185 2.440 nonbonded pdb=" OG SER C 379 " pdb=" OD1 ASP C 745 " model vdw 2.221 2.440 nonbonded pdb=" NH1 ARG C 557 " pdb=" OE1 GLU C 570 " model vdw 2.248 2.520 ... (remaining 119250 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' and (resid 282 through 745 or resid 901)) selection = chain 'B' selection = chain 'C' selection = chain 'D' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.120 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 6.140 Check model and map are aligned: 0.220 Set scattering table: 0.130 Process input model: 40.600 Find NCS groups from input model: 1.050 Set up NCS constraints: 0.100 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:11.880 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 61.260 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7777 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 0.127 14644 Z= 0.299 Angle : 0.721 9.820 19848 Z= 0.380 Chirality : 0.049 0.638 2240 Planarity : 0.004 0.030 2412 Dihedral : 11.209 88.866 5596 Min Nonbonded Distance : 2.138 Molprobity Statistics. All-atom Clashscore : 1.25 Ramachandran Plot: Outliers : 0.41 % Allowed : 4.12 % Favored : 95.47 % Rotamer: Outliers : 1.03 % Allowed : 0.84 % Favored : 98.13 % Cbeta Deviations : 0.24 % Peptide Plane: Cis-proline : 10.00 % 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: 1.27 (0.21), residues: 1700 helix: 1.82 (0.15), residues: 1100 sheet: -1.87 (0.74), residues: 64 loop : -0.87 (0.29), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 549 HIS 0.003 0.001 HIS B 410 PHE 0.016 0.002 PHE C 489 TYR 0.011 0.001 TYR D 309 ARG 0.003 0.000 ARG D 355 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 457 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 441 time to evaluate : 1.715 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 LYS cc_start: 0.8258 (mmtt) cc_final: 0.7408 (mmmt) REVERT: A 423 GLN cc_start: 0.8518 (tp40) cc_final: 0.8168 (mm-40) REVERT: A 424 ASP cc_start: 0.8351 (t70) cc_final: 0.8001 (t0) REVERT: A 427 ASP cc_start: 0.8410 (m-30) cc_final: 0.8157 (m-30) REVERT: A 536 GLU cc_start: 0.8158 (mp0) cc_final: 0.7568 (mp0) REVERT: A 559 PHE cc_start: 0.6945 (m-80) cc_final: 0.5459 (t80) REVERT: A 644 MET cc_start: 0.9102 (mmm) cc_final: 0.8877 (mmm) REVERT: C 308 MET cc_start: 0.8189 (mmm) cc_final: 0.7987 (mpp) REVERT: C 423 GLN cc_start: 0.8575 (tp40) cc_final: 0.8256 (mm-40) REVERT: C 424 ASP cc_start: 0.8425 (t70) cc_final: 0.8090 (t0) REVERT: C 536 GLU cc_start: 0.8188 (mp0) cc_final: 0.7651 (mp0) REVERT: C 559 PHE cc_start: 0.6856 (m-80) cc_final: 0.5709 (t80) REVERT: C 639 LYS cc_start: 0.8638 (mttt) cc_final: 0.8080 (mtmt) REVERT: C 644 MET cc_start: 0.9101 (mmm) cc_final: 0.8881 (mmm) REVERT: C 705 ILE cc_start: 0.9536 (mt) cc_final: 0.9326 (mp) REVERT: D 383 ASP cc_start: 0.7871 (t0) cc_final: 0.7579 (t0) REVERT: D 423 GLN cc_start: 0.8535 (tp40) cc_final: 0.8235 (mm-40) REVERT: D 424 ASP cc_start: 0.8386 (t70) cc_final: 0.8043 (t0) REVERT: D 427 ASP cc_start: 0.8422 (m-30) cc_final: 0.8220 (m-30) REVERT: D 536 GLU cc_start: 0.8157 (mp0) cc_final: 0.7540 (mp0) REVERT: D 639 LYS cc_start: 0.8634 (mttt) cc_final: 0.8363 (mmtp) REVERT: D 644 MET cc_start: 0.9109 (mmm) cc_final: 0.8880 (mmm) REVERT: B 285 ASN cc_start: 0.5795 (p0) cc_final: 0.5445 (p0) REVERT: B 308 MET cc_start: 0.8257 (mmt) cc_final: 0.7776 (mpp) REVERT: B 423 GLN cc_start: 0.8544 (tp40) cc_final: 0.8176 (mm-40) REVERT: B 424 ASP cc_start: 0.8399 (t70) cc_final: 0.7957 (t0) REVERT: B 427 ASP cc_start: 0.8449 (m-30) cc_final: 0.8248 (m-30) REVERT: B 478 GLU cc_start: 0.7831 (mt-10) cc_final: 0.7558 (mt-10) REVERT: B 536 GLU cc_start: 0.8154 (mp0) cc_final: 0.7537 (mp0) REVERT: B 644 MET cc_start: 0.9106 (mmm) cc_final: 0.8878 (mmm) outliers start: 16 outliers final: 8 residues processed: 453 average time/residue: 1.3774 time to fit residues: 678.8881 Evaluate side-chains 316 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 308 time to evaluate : 1.628 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 145 optimal weight: 0.8980 chunk 130 optimal weight: 20.0000 chunk 72 optimal weight: 0.5980 chunk 44 optimal weight: 6.9990 chunk 87 optimal weight: 9.9990 chunk 69 optimal weight: 0.5980 chunk 134 optimal weight: 5.9990 chunk 52 optimal weight: 9.9990 chunk 81 optimal weight: 0.2980 chunk 100 optimal weight: 0.8980 chunk 156 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 310 ASN A 419 ASN C 301 ASN C 419 ASN D 301 ASN D 419 ASN B 301 ASN B 419 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7842 moved from start: 0.2068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 14644 Z= 0.176 Angle : 0.508 7.097 19848 Z= 0.271 Chirality : 0.038 0.161 2240 Planarity : 0.003 0.045 2412 Dihedral : 7.651 57.830 2304 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 7.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.94 % Favored : 95.06 % Rotamer: Outliers : 2.51 % Allowed : 11.86 % Favored : 85.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.75 (0.21), residues: 1700 helix: 2.19 (0.15), residues: 1096 sheet: -1.70 (0.76), residues: 64 loop : -0.65 (0.30), residues: 540 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.001 TRP C 697 HIS 0.005 0.001 HIS B 410 PHE 0.028 0.001 PHE A 304 TYR 0.014 0.001 TYR A 351 ARG 0.008 0.000 ARG B 474 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 382 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 39 poor density : 343 time to evaluate : 1.717 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 345 LYS cc_start: 0.8535 (mmtt) cc_final: 0.7608 (mmmt) REVERT: A 423 GLN cc_start: 0.8518 (tp40) cc_final: 0.8152 (mm-40) REVERT: A 424 ASP cc_start: 0.8163 (t70) cc_final: 0.7914 (t0) REVERT: A 427 ASP cc_start: 0.8404 (m-30) cc_final: 0.8181 (m-30) REVERT: A 499 ARG cc_start: 0.7612 (mmm160) cc_final: 0.7400 (mmm160) REVERT: A 562 MET cc_start: 0.8558 (mtm) cc_final: 0.8335 (ttm) REVERT: C 423 GLN cc_start: 0.8538 (tp40) cc_final: 0.8165 (mm-40) REVERT: C 424 ASP cc_start: 0.8257 (t70) cc_final: 0.7900 (t0) REVERT: C 427 ASP cc_start: 0.8386 (m-30) cc_final: 0.8037 (m-30) REVERT: C 559 PHE cc_start: 0.6718 (m-80) cc_final: 0.5388 (t80) REVERT: C 639 LYS cc_start: 0.8625 (mttt) cc_final: 0.8097 (mtmt) REVERT: D 293 GLU cc_start: 0.8506 (mt-10) cc_final: 0.8136 (mt-10) REVERT: D 423 GLN cc_start: 0.8485 (tp40) cc_final: 0.8123 (mm-40) REVERT: D 467 ASN cc_start: 0.6908 (t0) cc_final: 0.6606 (t0) REVERT: D 535 LYS cc_start: 0.8633 (mtmm) cc_final: 0.8398 (mtpt) REVERT: D 636 GLU cc_start: 0.7997 (mm-30) cc_final: 0.7670 (mm-30) REVERT: B 293 GLU cc_start: 0.8307 (mt-10) cc_final: 0.8000 (mt-10) REVERT: B 308 MET cc_start: 0.8270 (mmt) cc_final: 0.7986 (mpp) REVERT: B 423 GLN cc_start: 0.8455 (tp40) cc_final: 0.8056 (mm-40) REVERT: B 424 ASP cc_start: 0.8287 (t70) cc_final: 0.7903 (t0) REVERT: B 467 ASN cc_start: 0.6927 (t0) cc_final: 0.6631 (t0) REVERT: B 535 LYS cc_start: 0.8604 (mtmm) cc_final: 0.8376 (mtpt) REVERT: B 564 ILE cc_start: 0.8634 (OUTLIER) cc_final: 0.8385 (tp) outliers start: 39 outliers final: 17 residues processed: 362 average time/residue: 1.2322 time to fit residues: 489.5233 Evaluate side-chains 315 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 297 time to evaluate : 1.507 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 714 LYS Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 571 LYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain B residue 285 ASN Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 714 LYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 86 optimal weight: 20.0000 chunk 48 optimal weight: 9.9990 chunk 129 optimal weight: 10.0000 chunk 106 optimal weight: 3.9990 chunk 43 optimal weight: 8.9990 chunk 156 optimal weight: 2.9990 chunk 169 optimal weight: 0.6980 chunk 139 optimal weight: 1.9990 chunk 155 optimal weight: 0.8980 chunk 53 optimal weight: 0.0170 chunk 125 optimal weight: 0.9980 overall best weight: 0.9220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 310 ASN A 419 ASN C 419 ASN D 301 ASN D 419 ASN D 561 GLN B 301 ASN B 419 ASN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7870 moved from start: 0.2572 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 14644 Z= 0.210 Angle : 0.515 6.880 19848 Z= 0.274 Chirality : 0.038 0.165 2240 Planarity : 0.003 0.030 2412 Dihedral : 7.526 59.466 2304 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 8.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 2.90 % Allowed : 15.21 % Favored : 81.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.67 (0.21), residues: 1700 helix: 2.09 (0.15), residues: 1100 sheet: -1.65 (0.76), residues: 64 loop : -0.62 (0.31), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP C 697 HIS 0.004 0.001 HIS C 289 PHE 0.021 0.002 PHE D 304 TYR 0.012 0.001 TYR A 351 ARG 0.007 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 357 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 45 poor density : 312 time to evaluate : 1.681 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 423 GLN cc_start: 0.8488 (tp40) cc_final: 0.8144 (mm-40) REVERT: A 424 ASP cc_start: 0.8179 (t70) cc_final: 0.7946 (t0) REVERT: A 499 ARG cc_start: 0.7681 (mmm160) cc_final: 0.7471 (mmm160) REVERT: A 562 MET cc_start: 0.8564 (mtm) cc_final: 0.8231 (mtt) REVERT: C 424 ASP cc_start: 0.8305 (t70) cc_final: 0.8005 (t0) REVERT: C 635 LEU cc_start: 0.8875 (OUTLIER) cc_final: 0.8669 (mm) REVERT: D 293 GLU cc_start: 0.8567 (mt-10) cc_final: 0.8194 (mt-10) REVERT: D 423 GLN cc_start: 0.8469 (tp40) cc_final: 0.8155 (mm-40) REVERT: D 427 ASP cc_start: 0.8374 (m-30) cc_final: 0.8104 (m-30) REVERT: D 467 ASN cc_start: 0.6939 (t0) cc_final: 0.6683 (t0) REVERT: D 535 LYS cc_start: 0.8655 (mtmm) cc_final: 0.8436 (mtpt) REVERT: B 293 GLU cc_start: 0.8269 (mt-10) cc_final: 0.7972 (mt-10) REVERT: B 308 MET cc_start: 0.8114 (mmt) cc_final: 0.7793 (mpp) REVERT: B 423 GLN cc_start: 0.8456 (tp40) cc_final: 0.8095 (mm-40) REVERT: B 424 ASP cc_start: 0.8293 (t70) cc_final: 0.7929 (t0) REVERT: B 427 ASP cc_start: 0.8455 (m-30) cc_final: 0.8173 (m-30) REVERT: B 467 ASN cc_start: 0.7083 (t0) cc_final: 0.6873 (t160) REVERT: B 513 GLU cc_start: 0.8123 (mm-30) cc_final: 0.7863 (tp30) REVERT: B 535 LYS cc_start: 0.8656 (mtmm) cc_final: 0.8320 (mtpt) REVERT: B 564 ILE cc_start: 0.8748 (OUTLIER) cc_final: 0.8526 (tp) REVERT: B 705 ILE cc_start: 0.9519 (mt) cc_final: 0.9245 (mp) REVERT: B 709 GLU cc_start: 0.8779 (tt0) cc_final: 0.8355 (mt-10) outliers start: 45 outliers final: 18 residues processed: 334 average time/residue: 1.2608 time to fit residues: 462.0132 Evaluate side-chains 314 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 294 time to evaluate : 1.592 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 635 LEU Chi-restraints excluded: chain C residue 678 LEU Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 571 LYS Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 714 LYS Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.9980 chunk 117 optimal weight: 0.7980 chunk 81 optimal weight: 0.0570 chunk 17 optimal weight: 0.9990 chunk 74 optimal weight: 0.6980 chunk 105 optimal weight: 0.9990 chunk 157 optimal weight: 0.9990 chunk 166 optimal weight: 0.5980 chunk 82 optimal weight: 0.5980 chunk 148 optimal weight: 2.9990 chunk 44 optimal weight: 8.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN ** A 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 419 ASN C 301 ASN C 467 ASN D 301 ASN B 301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7840 moved from start: 0.2816 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.025 14644 Z= 0.161 Angle : 0.496 8.340 19848 Z= 0.262 Chirality : 0.037 0.232 2240 Planarity : 0.003 0.034 2412 Dihedral : 6.959 57.916 2294 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 7.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 2.58 % Allowed : 15.85 % Favored : 81.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.73 (0.21), residues: 1700 helix: 2.22 (0.15), residues: 1092 sheet: -1.60 (0.75), residues: 64 loop : -0.77 (0.29), residues: 544 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP C 697 HIS 0.003 0.000 HIS C 289 PHE 0.016 0.001 PHE C 489 TYR 0.012 0.001 TYR A 627 ARG 0.009 0.000 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 40 poor density : 326 time to evaluate : 1.590 Fit side-chains revert: symmetry clash REVERT: A 308 MET cc_start: 0.7454 (OUTLIER) cc_final: 0.6633 (mpt) REVERT: A 424 ASP cc_start: 0.8123 (t70) cc_final: 0.7897 (t0) REVERT: A 499 ARG cc_start: 0.7613 (mmm160) cc_final: 0.7411 (mmm160) REVERT: A 561 GLN cc_start: 0.8086 (mm110) cc_final: 0.7765 (mp10) REVERT: A 562 MET cc_start: 0.8584 (mtm) cc_final: 0.8226 (ttm) REVERT: A 644 MET cc_start: 0.9049 (mmm) cc_final: 0.7710 (mmm) REVERT: A 709 GLU cc_start: 0.8709 (tt0) cc_final: 0.8227 (mt-10) REVERT: C 308 MET cc_start: 0.8299 (tpp) cc_final: 0.7810 (mpp) REVERT: C 423 GLN cc_start: 0.8421 (mm-40) cc_final: 0.8145 (mm-40) REVERT: C 424 ASP cc_start: 0.8151 (t70) cc_final: 0.7782 (t0) REVERT: D 293 GLU cc_start: 0.8623 (mt-10) cc_final: 0.8232 (mt-10) REVERT: D 467 ASN cc_start: 0.6881 (t0) cc_final: 0.6614 (t160) REVERT: D 709 GLU cc_start: 0.8748 (tt0) cc_final: 0.8494 (mt-10) REVERT: B 293 GLU cc_start: 0.8363 (mt-10) cc_final: 0.8053 (mt-10) REVERT: B 308 MET cc_start: 0.8096 (mmt) cc_final: 0.7863 (mpp) REVERT: B 424 ASP cc_start: 0.8232 (t70) cc_final: 0.7850 (t0) REVERT: B 467 ASN cc_start: 0.7084 (t0) cc_final: 0.6850 (t160) REVERT: B 513 GLU cc_start: 0.8080 (mm-30) cc_final: 0.7835 (tp30) REVERT: B 535 LYS cc_start: 0.8602 (mtmm) cc_final: 0.8392 (mtpt) REVERT: B 562 MET cc_start: 0.8712 (mmm) cc_final: 0.8226 (ttm) REVERT: B 564 ILE cc_start: 0.8762 (OUTLIER) cc_final: 0.8519 (tp) outliers start: 40 outliers final: 17 residues processed: 343 average time/residue: 1.2099 time to fit residues: 457.2980 Evaluate side-chains 314 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 295 time to evaluate : 1.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 714 LYS Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 443 LEU Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 460 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 138 optimal weight: 0.9990 chunk 94 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 123 optimal weight: 1.9990 chunk 68 optimal weight: 0.3980 chunk 141 optimal weight: 10.0000 chunk 114 optimal weight: 0.6980 chunk 0 optimal weight: 20.0000 chunk 84 optimal weight: 7.9990 chunk 149 optimal weight: 2.9990 chunk 41 optimal weight: 20.0000 overall best weight: 1.2186 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 301 ASN D 301 ASN B 301 ASN ** B 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7896 moved from start: 0.2997 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 14644 Z= 0.254 Angle : 0.530 8.198 19848 Z= 0.281 Chirality : 0.039 0.226 2240 Planarity : 0.004 0.040 2412 Dihedral : 7.054 59.927 2288 Min Nonbonded Distance : 2.187 Molprobity Statistics. All-atom Clashscore : 8.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 2.71 % Allowed : 17.72 % Favored : 79.57 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.53 (0.21), residues: 1700 helix: 2.02 (0.15), residues: 1100 sheet: -1.58 (0.76), residues: 64 loop : -0.77 (0.30), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.001 TRP B 697 HIS 0.003 0.001 HIS C 289 PHE 0.017 0.002 PHE C 489 TYR 0.011 0.001 TYR C 627 ARG 0.008 0.000 ARG D 575 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 355 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 42 poor density : 313 time to evaluate : 1.671 Fit side-chains revert: symmetry clash REVERT: A 308 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7106 (mpp) REVERT: A 423 GLN cc_start: 0.8430 (mm-40) cc_final: 0.7865 (tp-100) REVERT: A 499 ARG cc_start: 0.7723 (mmm160) cc_final: 0.7464 (mmm160) REVERT: A 562 MET cc_start: 0.8645 (mtm) cc_final: 0.8239 (mtt) REVERT: A 568 MET cc_start: 0.8937 (mtp) cc_final: 0.8718 (mtt) REVERT: C 423 GLN cc_start: 0.8450 (mm-40) cc_final: 0.8158 (mm-40) REVERT: C 424 ASP cc_start: 0.8290 (t70) cc_final: 0.7995 (t0) REVERT: C 559 PHE cc_start: 0.6724 (m-80) cc_final: 0.6367 (m-10) REVERT: D 293 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8311 (mt-10) REVERT: D 308 MET cc_start: 0.7778 (OUTLIER) cc_final: 0.7293 (mpp) REVERT: D 423 GLN cc_start: 0.8472 (mm-40) cc_final: 0.7894 (tp-100) REVERT: D 467 ASN cc_start: 0.6946 (t0) cc_final: 0.6703 (t160) REVERT: B 293 GLU cc_start: 0.8375 (mt-10) cc_final: 0.8064 (mt-10) REVERT: B 308 MET cc_start: 0.8086 (mmt) cc_final: 0.7803 (mpp) REVERT: B 423 GLN cc_start: 0.8490 (mm-40) cc_final: 0.7930 (tp-100) REVERT: B 424 ASP cc_start: 0.8188 (t70) cc_final: 0.7940 (t0) REVERT: B 427 ASP cc_start: 0.8425 (m-30) cc_final: 0.7859 (m-30) REVERT: B 467 ASN cc_start: 0.7135 (t0) cc_final: 0.6918 (t160) REVERT: B 644 MET cc_start: 0.9096 (mmm) cc_final: 0.7768 (mmm) outliers start: 42 outliers final: 15 residues processed: 332 average time/residue: 1.2107 time to fit residues: 443.3149 Evaluate side-chains 317 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 300 time to evaluate : 1.718 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 55 optimal weight: 8.9990 chunk 149 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 97 optimal weight: 7.9990 chunk 41 optimal weight: 0.9990 chunk 166 optimal weight: 0.6980 chunk 138 optimal weight: 0.8980 chunk 77 optimal weight: 3.9990 chunk 13 optimal weight: 7.9990 chunk 87 optimal weight: 8.9990 chunk 160 optimal weight: 0.8980 overall best weight: 1.2984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 301 ASN D 301 ASN B 301 ASN B 676 ASN B 691 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7902 moved from start: 0.3195 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 14644 Z= 0.266 Angle : 0.534 9.280 19848 Z= 0.282 Chirality : 0.039 0.256 2240 Planarity : 0.004 0.045 2412 Dihedral : 6.944 59.006 2284 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.06 % Favored : 93.94 % Rotamer: Outliers : 3.03 % Allowed : 17.33 % Favored : 79.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.41 (0.21), residues: 1700 helix: 1.88 (0.15), residues: 1108 sheet: -1.65 (0.76), residues: 64 loop : -0.75 (0.30), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.023 0.001 TRP B 697 HIS 0.002 0.001 HIS A 289 PHE 0.016 0.002 PHE C 489 TYR 0.011 0.001 TYR C 627 ARG 0.010 0.001 ARG C 575 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 366 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 47 poor density : 319 time to evaluate : 1.590 Fit side-chains REVERT: A 293 GLU cc_start: 0.8326 (mt-10) cc_final: 0.7981 (mt-10) REVERT: A 308 MET cc_start: 0.7650 (OUTLIER) cc_final: 0.7099 (mpp) REVERT: A 423 GLN cc_start: 0.8434 (mm-40) cc_final: 0.7862 (tp-100) REVERT: A 427 ASP cc_start: 0.8382 (m-30) cc_final: 0.7775 (m-30) REVERT: A 499 ARG cc_start: 0.7699 (mmm160) cc_final: 0.7464 (mmm160) REVERT: A 561 GLN cc_start: 0.8142 (mm110) cc_final: 0.7777 (mp10) REVERT: A 562 MET cc_start: 0.8589 (OUTLIER) cc_final: 0.8219 (mtt) REVERT: C 293 GLU cc_start: 0.8377 (mt-10) cc_final: 0.7785 (pm20) REVERT: C 308 MET cc_start: 0.8276 (tpp) cc_final: 0.7789 (mpp) REVERT: C 424 ASP cc_start: 0.8330 (t70) cc_final: 0.7963 (t0) REVERT: C 559 PHE cc_start: 0.6717 (m-80) cc_final: 0.6385 (m-10) REVERT: C 639 LYS cc_start: 0.8698 (OUTLIER) cc_final: 0.8434 (mmtp) REVERT: D 293 GLU cc_start: 0.8698 (mt-10) cc_final: 0.8311 (mt-10) REVERT: D 308 MET cc_start: 0.7654 (OUTLIER) cc_final: 0.7156 (mpp) REVERT: D 423 GLN cc_start: 0.8465 (mm-40) cc_final: 0.7918 (tp-100) REVERT: D 467 ASN cc_start: 0.6981 (t0) cc_final: 0.6750 (t160) REVERT: B 293 GLU cc_start: 0.8383 (mt-10) cc_final: 0.8069 (mt-10) REVERT: B 308 MET cc_start: 0.8062 (mmt) cc_final: 0.7775 (mpp) REVERT: B 423 GLN cc_start: 0.8492 (mm-40) cc_final: 0.7866 (tp-100) REVERT: B 424 ASP cc_start: 0.8205 (t70) cc_final: 0.7951 (t0) REVERT: B 467 ASN cc_start: 0.7078 (t0) cc_final: 0.6846 (t160) outliers start: 47 outliers final: 22 residues processed: 339 average time/residue: 1.2076 time to fit residues: 451.3306 Evaluate side-chains 333 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 307 time to evaluate : 1.624 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 413 LEU Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 601 ASP Chi-restraints excluded: chain C residue 639 LYS Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 678 LEU Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 601 ASP Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 18 optimal weight: 3.9990 chunk 94 optimal weight: 9.9990 chunk 121 optimal weight: 0.9980 chunk 140 optimal weight: 5.9990 chunk 92 optimal weight: 0.9990 chunk 165 optimal weight: 0.6980 chunk 103 optimal weight: 1.9990 chunk 101 optimal weight: 0.8980 chunk 76 optimal weight: 0.8980 chunk 102 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 301 ASN D 301 ASN B 301 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7881 moved from start: 0.3305 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 14644 Z= 0.205 Angle : 0.526 7.172 19848 Z= 0.276 Chirality : 0.038 0.191 2240 Planarity : 0.004 0.044 2412 Dihedral : 6.770 57.028 2284 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 3.22 % Allowed : 18.04 % Favored : 78.74 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.42 (0.21), residues: 1700 helix: 1.90 (0.15), residues: 1112 sheet: -1.67 (0.76), residues: 64 loop : -0.79 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.028 0.001 TRP B 697 HIS 0.002 0.000 HIS A 289 PHE 0.016 0.001 PHE C 489 TYR 0.011 0.001 TYR A 627 ARG 0.010 0.000 ARG A 575 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 377 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 50 poor density : 327 time to evaluate : 1.656 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8572 (mt-10) cc_final: 0.8208 (mt-10) REVERT: A 308 MET cc_start: 0.7635 (OUTLIER) cc_final: 0.7153 (mpp) REVERT: A 423 GLN cc_start: 0.8407 (mm-40) cc_final: 0.7790 (tp-100) REVERT: A 427 ASP cc_start: 0.8342 (m-30) cc_final: 0.7686 (m-30) REVERT: A 499 ARG cc_start: 0.7628 (mmm160) cc_final: 0.7332 (mmm160) REVERT: A 561 GLN cc_start: 0.8100 (mm110) cc_final: 0.7750 (mp10) REVERT: A 562 MET cc_start: 0.8605 (OUTLIER) cc_final: 0.8161 (mtt) REVERT: C 308 MET cc_start: 0.8281 (tpp) cc_final: 0.7854 (mpp) REVERT: C 424 ASP cc_start: 0.8247 (t70) cc_final: 0.7925 (t0) REVERT: C 559 PHE cc_start: 0.6610 (m-80) cc_final: 0.6344 (m-10) REVERT: D 293 GLU cc_start: 0.8670 (mt-10) cc_final: 0.8296 (mt-10) REVERT: D 308 MET cc_start: 0.7812 (OUTLIER) cc_final: 0.7307 (mpp) REVERT: D 423 GLN cc_start: 0.8450 (mm-40) cc_final: 0.7878 (tp-100) REVERT: D 427 ASP cc_start: 0.8428 (m-30) cc_final: 0.7793 (m-30) REVERT: D 467 ASN cc_start: 0.6951 (t0) cc_final: 0.6723 (t160) REVERT: B 293 GLU cc_start: 0.8411 (mt-10) cc_final: 0.8086 (mt-10) REVERT: B 308 MET cc_start: 0.8007 (mmt) cc_final: 0.7762 (mpp) REVERT: B 423 GLN cc_start: 0.8467 (mm-40) cc_final: 0.8211 (mm-40) REVERT: B 467 ASN cc_start: 0.7078 (t0) cc_final: 0.6849 (t160) outliers start: 50 outliers final: 19 residues processed: 348 average time/residue: 1.1645 time to fit residues: 447.7001 Evaluate side-chains 332 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 310 time to evaluate : 1.629 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 678 LEU Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 571 LYS Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 2.9990 chunk 49 optimal weight: 0.9990 chunk 32 optimal weight: 3.9990 chunk 105 optimal weight: 0.8980 chunk 112 optimal weight: 1.9990 chunk 81 optimal weight: 0.0980 chunk 15 optimal weight: 2.9990 chunk 130 optimal weight: 20.0000 chunk 150 optimal weight: 2.9990 chunk 158 optimal weight: 1.9990 chunk 144 optimal weight: 0.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 301 ASN D 301 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.3415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 14644 Z= 0.231 Angle : 0.541 8.676 19848 Z= 0.285 Chirality : 0.038 0.142 2240 Planarity : 0.004 0.048 2412 Dihedral : 6.767 57.720 2282 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.58 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.94 % Favored : 94.06 % Rotamer: Outliers : 2.64 % Allowed : 19.59 % Favored : 77.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.34 (0.21), residues: 1700 helix: 1.83 (0.15), residues: 1112 sheet: -1.73 (0.75), residues: 64 loop : -0.79 (0.29), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.033 0.001 TRP B 697 HIS 0.002 0.000 HIS D 289 PHE 0.018 0.001 PHE C 489 TYR 0.011 0.001 TYR A 627 ARG 0.011 0.001 ARG B 575 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 360 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 41 poor density : 319 time to evaluate : 1.709 Fit side-chains REVERT: A 293 GLU cc_start: 0.8613 (mt-10) cc_final: 0.8213 (mt-10) REVERT: A 308 MET cc_start: 0.7651 (OUTLIER) cc_final: 0.7211 (mpp) REVERT: A 423 GLN cc_start: 0.8414 (mm-40) cc_final: 0.7795 (tp-100) REVERT: A 427 ASP cc_start: 0.8340 (m-30) cc_final: 0.7746 (m-30) REVERT: A 499 ARG cc_start: 0.7655 (mmm160) cc_final: 0.7354 (mmm160) REVERT: A 561 GLN cc_start: 0.8095 (mm110) cc_final: 0.7743 (mp10) REVERT: A 562 MET cc_start: 0.8610 (OUTLIER) cc_final: 0.8099 (mtt) REVERT: C 308 MET cc_start: 0.8338 (tpp) cc_final: 0.7859 (mpp) REVERT: C 423 GLN cc_start: 0.8412 (mm-40) cc_final: 0.7853 (tp-100) REVERT: C 424 ASP cc_start: 0.8225 (t70) cc_final: 0.7937 (t0) REVERT: C 427 ASP cc_start: 0.8391 (m-30) cc_final: 0.7837 (m-30) REVERT: C 547 MET cc_start: 0.8749 (mtp) cc_final: 0.8484 (mtp) REVERT: C 559 PHE cc_start: 0.6474 (m-80) cc_final: 0.6260 (m-10) REVERT: D 293 GLU cc_start: 0.8687 (mt-10) cc_final: 0.8297 (mt-10) REVERT: D 308 MET cc_start: 0.7628 (OUTLIER) cc_final: 0.7133 (mpp) REVERT: D 423 GLN cc_start: 0.8439 (mm-40) cc_final: 0.7820 (tp-100) REVERT: D 427 ASP cc_start: 0.8394 (m-30) cc_final: 0.7681 (m-30) REVERT: D 467 ASN cc_start: 0.6975 (t0) cc_final: 0.6749 (t160) REVERT: B 293 GLU cc_start: 0.8427 (mt-10) cc_final: 0.8096 (mt-10) REVERT: B 308 MET cc_start: 0.8014 (mmt) cc_final: 0.7762 (mpp) REVERT: B 467 ASN cc_start: 0.7100 (t0) cc_final: 0.6864 (t160) REVERT: B 562 MET cc_start: 0.8986 (mmm) cc_final: 0.8481 (mmt) outliers start: 41 outliers final: 21 residues processed: 336 average time/residue: 1.1627 time to fit residues: 432.2005 Evaluate side-chains 336 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 312 time to evaluate : 1.669 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 562 MET Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 601 ASP Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 413 LEU Chi-restraints excluded: chain D residue 433 ILE Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 632 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 433 ILE Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE Chi-restraints excluded: chain B residue 632 SER Chi-restraints excluded: chain B residue 678 LEU Chi-restraints excluded: chain B residue 685 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 154 optimal weight: 0.8980 chunk 158 optimal weight: 0.0980 chunk 92 optimal weight: 0.8980 chunk 67 optimal weight: 0.8980 chunk 121 optimal weight: 0.9990 chunk 47 optimal weight: 10.0000 chunk 139 optimal weight: 0.0030 chunk 146 optimal weight: 0.0050 chunk 153 optimal weight: 0.7980 chunk 101 optimal weight: 0.8980 chunk 163 optimal weight: 0.0870 overall best weight: 0.1982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN C 301 ASN ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 301 ASN D 410 HIS B 301 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7816 moved from start: 0.3575 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.033 14644 Z= 0.149 Angle : 0.530 7.205 19848 Z= 0.275 Chirality : 0.037 0.158 2240 Planarity : 0.004 0.054 2412 Dihedral : 6.391 57.389 2280 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.88 % Favored : 94.12 % Rotamer: Outliers : 1.61 % Allowed : 20.75 % Favored : 77.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.54 (0.21), residues: 1700 helix: 2.02 (0.15), residues: 1108 sheet: -1.66 (0.74), residues: 64 loop : -0.79 (0.29), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.036 0.001 TRP D 697 HIS 0.004 0.000 HIS B 410 PHE 0.018 0.001 PHE C 489 TYR 0.008 0.001 TYR A 627 ARG 0.013 0.000 ARG D 575 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 374 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 25 poor density : 349 time to evaluate : 1.612 Fit side-chains REVERT: A 293 GLU cc_start: 0.8601 (mt-10) cc_final: 0.8221 (mt-10) REVERT: A 308 MET cc_start: 0.7687 (OUTLIER) cc_final: 0.7199 (mpp) REVERT: A 423 GLN cc_start: 0.8372 (mm-40) cc_final: 0.7726 (tp-100) REVERT: A 427 ASP cc_start: 0.8398 (m-30) cc_final: 0.7730 (m-30) REVERT: A 499 ARG cc_start: 0.7480 (mmm160) cc_final: 0.7255 (mmm160) REVERT: A 561 GLN cc_start: 0.8034 (mm110) cc_final: 0.7685 (mp10) REVERT: C 293 GLU cc_start: 0.8423 (mt-10) cc_final: 0.7941 (pm20) REVERT: C 308 MET cc_start: 0.8269 (tpp) cc_final: 0.7802 (mpp) REVERT: C 423 GLN cc_start: 0.8437 (mm-40) cc_final: 0.7950 (tp-100) REVERT: D 293 GLU cc_start: 0.8678 (mt-10) cc_final: 0.8305 (mt-10) REVERT: D 308 MET cc_start: 0.7606 (OUTLIER) cc_final: 0.7120 (mpp) REVERT: D 423 GLN cc_start: 0.8359 (mm-40) cc_final: 0.7769 (tp-100) REVERT: D 467 ASN cc_start: 0.6887 (t0) cc_final: 0.6611 (t160) REVERT: B 293 GLU cc_start: 0.8452 (mt-10) cc_final: 0.8129 (mt-10) REVERT: B 308 MET cc_start: 0.8045 (mmt) cc_final: 0.7802 (mpp) REVERT: B 423 GLN cc_start: 0.8369 (mm-40) cc_final: 0.7840 (tp-100) REVERT: B 467 ASN cc_start: 0.7051 (t0) cc_final: 0.6774 (t160) REVERT: B 562 MET cc_start: 0.8997 (mmm) cc_final: 0.8366 (mmt) outliers start: 25 outliers final: 12 residues processed: 359 average time/residue: 1.1092 time to fit residues: 441.7378 Evaluate side-chains 321 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 307 time to evaluate : 1.605 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 99 optimal weight: 0.9980 chunk 77 optimal weight: 1.9990 chunk 113 optimal weight: 0.0670 chunk 171 optimal weight: 9.9990 chunk 157 optimal weight: 1.9990 chunk 136 optimal weight: 0.5980 chunk 14 optimal weight: 0.6980 chunk 105 optimal weight: 1.9990 chunk 83 optimal weight: 5.9990 chunk 108 optimal weight: 0.2980 chunk 145 optimal weight: 2.9990 overall best weight: 0.5318 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 301 ASN B 419 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7836 moved from start: 0.3711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14644 Z= 0.180 Angle : 0.551 8.138 19848 Z= 0.287 Chirality : 0.038 0.189 2240 Planarity : 0.004 0.058 2412 Dihedral : 6.532 57.965 2280 Min Nonbonded Distance : 2.208 Molprobity Statistics. All-atom Clashscore : 9.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.59 % Favored : 94.41 % Rotamer: Outliers : 1.55 % Allowed : 22.16 % Favored : 76.29 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % 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: 1.45 (0.21), residues: 1700 helix: 1.95 (0.15), residues: 1108 sheet: -1.63 (0.74), residues: 64 loop : -0.83 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.039 0.001 TRP D 697 HIS 0.005 0.000 HIS B 410 PHE 0.019 0.001 PHE C 489 TYR 0.012 0.001 TYR D 584 ARG 0.013 0.000 ARG C 575 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 3400 Ramachandran restraints generated. 1700 Oldfield, 0 Emsley, 1700 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 335 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 311 time to evaluate : 1.667 Fit side-chains revert: symmetry clash REVERT: A 293 GLU cc_start: 0.8597 (mt-10) cc_final: 0.8238 (mt-10) REVERT: A 308 MET cc_start: 0.7786 (OUTLIER) cc_final: 0.7305 (mpp) REVERT: A 423 GLN cc_start: 0.8340 (mm-40) cc_final: 0.7657 (tp-100) REVERT: A 427 ASP cc_start: 0.8378 (m-30) cc_final: 0.7696 (m-30) REVERT: A 499 ARG cc_start: 0.7473 (mmm160) cc_final: 0.7229 (mmm160) REVERT: C 293 GLU cc_start: 0.8466 (mt-10) cc_final: 0.7986 (pm20) REVERT: C 308 MET cc_start: 0.8309 (tpp) cc_final: 0.7832 (mpp) REVERT: C 423 GLN cc_start: 0.8381 (mm-40) cc_final: 0.7864 (tp-100) REVERT: C 424 ASP cc_start: 0.8102 (t70) cc_final: 0.7743 (t0) REVERT: D 293 GLU cc_start: 0.8720 (mt-10) cc_final: 0.8278 (mt-10) REVERT: D 308 MET cc_start: 0.7586 (OUTLIER) cc_final: 0.7106 (mpp) REVERT: D 423 GLN cc_start: 0.8371 (mm-40) cc_final: 0.7793 (tp-100) REVERT: D 427 ASP cc_start: 0.8397 (m-30) cc_final: 0.7837 (m-30) REVERT: D 467 ASN cc_start: 0.6928 (t0) cc_final: 0.6664 (t160) REVERT: B 293 GLU cc_start: 0.8548 (mt-10) cc_final: 0.8190 (mt-10) REVERT: B 308 MET cc_start: 0.8023 (mmt) cc_final: 0.7785 (mpp) REVERT: B 467 ASN cc_start: 0.7078 (t0) cc_final: 0.6801 (t160) REVERT: B 535 LYS cc_start: 0.8524 (mtmm) cc_final: 0.8298 (mtmt) REVERT: B 562 MET cc_start: 0.9057 (mmm) cc_final: 0.8740 (mmp) REVERT: B 644 MET cc_start: 0.9093 (mmm) cc_final: 0.7748 (mmm) outliers start: 24 outliers final: 15 residues processed: 322 average time/residue: 1.1703 time to fit residues: 421.2364 Evaluate side-chains 324 residues out of total 1552 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 307 time to evaluate : 1.697 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 308 MET Chi-restraints excluded: chain A residue 443 LEU Chi-restraints excluded: chain A residue 483 SER Chi-restraints excluded: chain A residue 571 LYS Chi-restraints excluded: chain A residue 685 THR Chi-restraints excluded: chain C residue 330 ASN Chi-restraints excluded: chain C residue 413 LEU Chi-restraints excluded: chain C residue 443 LEU Chi-restraints excluded: chain C residue 483 SER Chi-restraints excluded: chain C residue 685 THR Chi-restraints excluded: chain D residue 308 MET Chi-restraints excluded: chain D residue 483 SER Chi-restraints excluded: chain D residue 685 THR Chi-restraints excluded: chain B residue 413 LEU Chi-restraints excluded: chain B residue 443 LEU Chi-restraints excluded: chain B residue 483 SER Chi-restraints excluded: chain B residue 564 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 172 random chunks: chunk 41 optimal weight: 9.9990 chunk 125 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 chunk 37 optimal weight: 0.7980 chunk 136 optimal weight: 0.8980 chunk 57 optimal weight: 2.9990 chunk 140 optimal weight: 0.5980 chunk 17 optimal weight: 2.9990 chunk 25 optimal weight: 0.8980 chunk 119 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 301 ASN A 419 ASN ** C 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 310 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 561 GLN ** C 676 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 301 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** D 408 ASN B 301 ASN B 419 ASN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4230 r_free = 0.4230 target = 0.196369 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 52)----------------| | r_work = 0.3471 r_free = 0.3471 target = 0.124526 restraints weight = 16937.915| |-----------------------------------------------------------------------------| r_work (start): 0.3391 rms_B_bonded: 2.03 r_work: 0.3242 rms_B_bonded: 2.63 restraints_weight: 0.5000 r_work: 0.3109 rms_B_bonded: 4.11 restraints_weight: 0.2500 r_work (final): 0.3109 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8072 moved from start: 0.3731 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 14644 Z= 0.195 Angle : 0.554 8.886 19848 Z= 0.288 Chirality : 0.038 0.152 2240 Planarity : 0.004 0.057 2412 Dihedral : 6.592 58.463 2280 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 9.96 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.24 % Favored : 93.76 % Rotamer: Outliers : 1.29 % Allowed : 22.81 % Favored : 75.90 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.37 (0.21), residues: 1700 helix: 1.89 (0.15), residues: 1108 sheet: -1.62 (0.74), residues: 64 loop : -0.88 (0.28), residues: 528 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.045 0.001 TRP D 697 HIS 0.005 0.000 HIS B 410 PHE 0.018 0.001 PHE C 489 TYR 0.011 0.001 TYR B 584 ARG 0.014 0.001 ARG B 575 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 7155.80 seconds wall clock time: 128 minutes 5.55 seconds (7685.55 seconds total)