Starting phenix.real_space_refine on Fri Aug 2 19:11:32 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm1_41374/08_2024/8tm1_41374.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm1_41374/08_2024/8tm1_41374.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.79 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm1_41374/08_2024/8tm1_41374.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm1_41374/08_2024/8tm1_41374.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm1_41374/08_2024/8tm1_41374.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8tm1_41374/08_2024/8tm1_41374.cif" } resolution = 2.79 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= -0.008 sd= 0.167 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2908 2.51 5 N 754 2.21 5 O 859 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 400": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 4536 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 1407 Number of conformers: 1 Conformer: "" Number of residues, atoms: 175, 1407 Classifications: {'peptide': 175} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 8, 'TRANS': 166} Chain breaks: 1 Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Chain: "B" Number of atoms: 1282 Number of conformers: 1 Conformer: "" Number of residues, atoms: 159, 1282 Classifications: {'peptide': 159} Link IDs: {'PTRANS': 7, 'TRANS': 151} Chain breaks: 2 Chain: "H" Number of atoms: 1015 Number of conformers: 1 Conformer: "" Number of residues, atoms: 127, 1015 Classifications: {'peptide': 127} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 6, 'TRANS': 120} Chain: "L" Number of atoms: 832 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 832 Classifications: {'peptide': 108} Modifications used: {'COO': 1} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 1 Unresolved non-hydrogen dihedrals: 1 Time building chain proxies: 4.64, per 1000 atoms: 1.02 Number of scatterers: 4536 At special positions: 0 Unit cell: (96.8, 74.8, 92.4, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 859 8.00 N 754 7.00 C 2908 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.04 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.57 Conformation dependent library (CDL) restraints added in 818.0 milliseconds 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1044 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 12 sheets defined 14.8% alpha, 32.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.62 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.528A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 366 through 370 Processing helix chain 'A' and resid 383 through 390 removed outlier: 4.450A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.526A pdb=" N LEU A 390 " --> pdb=" O LEU A 387 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.408A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 505 Processing helix chain 'B' and resid 339 through 343 Processing helix chain 'B' and resid 349 through 353 removed outlier: 3.653A pdb=" N TRP B 353 " --> pdb=" O VAL B 350 " (cutoff:3.500A) Processing helix chain 'B' and resid 367 through 371 Processing helix chain 'B' and resid 405 through 410 removed outlier: 4.074A pdb=" N ARG B 408 " --> pdb=" O ASP B 405 " (cutoff:3.500A) Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 438 through 443 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'H' and resid 83 through 87 removed outlier: 3.703A pdb=" N THR H 87 " --> pdb=" O ALA H 84 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 354 through 357 Processing sheet with id=AA2, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA3, first strand: chain 'B' and resid 356 through 357 Processing sheet with id=AA4, first strand: chain 'B' and resid 376 through 379 removed outlier: 3.522A pdb=" N PHE B 400 " --> pdb=" O VAL B 510 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA6, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA7, first strand: chain 'H' and resid 3 through 7 removed outlier: 3.715A pdb=" N GLN H 3 " --> pdb=" O SER H 25 " (cutoff:3.500A) removed outlier: 3.595A pdb=" N SER H 70 " --> pdb=" O SER H 79 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'H' and resid 11 through 12 removed outlier: 3.500A pdb=" N VAL H 109 " --> pdb=" O ALA H 88 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N ALA H 88 " --> pdb=" O VAL H 109 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'H' and resid 57 through 59 removed outlier: 6.909A pdb=" N TRP H 36 " --> pdb=" O ILE H 48 " (cutoff:3.500A) removed outlier: 4.543A pdb=" N ASN H 50 " --> pdb=" O TRP H 35A" (cutoff:3.500A) removed outlier: 6.884A pdb=" N TRP H 35A" --> pdb=" O ASN H 50 " (cutoff:3.500A) removed outlier: 6.119A pdb=" N TYR H 52 " --> pdb=" O TYR H 34 " (cutoff:3.500A) removed outlier: 8.953A pdb=" N TYR H 34 " --> pdb=" O TYR H 52 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N TYR H 35 " --> pdb=" O GLY H 95 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG H 94 " --> pdb=" O ILE H 102 " (cutoff:3.500A) removed outlier: 4.093A pdb=" N ILE H 102 " --> pdb=" O ARG H 94 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.516A pdb=" N SER L 7 " --> pdb=" O THR L 22 " (cutoff:3.500A) removed outlier: 3.614A pdb=" N THR L 22 " --> pdb=" O SER L 7 " (cutoff:3.500A) removed outlier: 3.510A pdb=" N VAL L 19 " --> pdb=" O ILE L 75 " (cutoff:3.500A) removed outlier: 6.242A pdb=" N THR L 69 " --> pdb=" O ALA L 25 " (cutoff:3.500A) removed outlier: 10.386A pdb=" N GLN L 27 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 10.177A pdb=" N SER L 67 " --> pdb=" O GLN L 27 " (cutoff:3.500A) removed outlier: 12.189A pdb=" N ILE L 29 " --> pdb=" O SER L 65 " (cutoff:3.500A) removed outlier: 12.128A pdb=" N SER L 65 " --> pdb=" O ILE L 29 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.675A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.572A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.630A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'L' and resid 10 through 13 removed outlier: 3.812A pdb=" N THR L 97 " --> pdb=" O GLN L 90 " (cutoff:3.500A) 133 hydrogen bonds defined for protein. 315 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 1.75 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: 1430 1.34 - 1.47: 1322 1.47 - 1.59: 1896 1.59 - 1.71: 0 1.71 - 1.83: 17 Bond restraints: 4665 Sorted by residual: bond pdb=" CB PRO A 337 " pdb=" CG PRO A 337 " ideal model delta sigma weight residual 1.492 1.539 -0.047 5.00e-02 4.00e+02 8.83e-01 bond pdb=" CB MET L 4 " pdb=" CG MET L 4 " ideal model delta sigma weight residual 1.520 1.493 0.027 3.00e-02 1.11e+03 8.31e-01 bond pdb=" SD MET L 4 " pdb=" CE MET L 4 " ideal model delta sigma weight residual 1.791 1.769 0.022 2.50e-02 1.60e+03 7.51e-01 bond pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta sigma weight residual 1.460 1.472 -0.012 1.54e-02 4.22e+03 5.98e-01 bond pdb=" N SER H 54 " pdb=" CA SER H 54 " ideal model delta sigma weight residual 1.460 1.474 -0.015 1.95e-02 2.63e+03 5.86e-01 ... (remaining 4660 not shown) Histogram of bond angle deviations from ideal: 100.77 - 107.42: 166 107.42 - 114.06: 2386 114.06 - 120.71: 1845 120.71 - 127.35: 1893 127.35 - 133.99: 51 Bond angle restraints: 6341 Sorted by residual: angle pdb=" C ASN H 64 " pdb=" N ASN H 65 " pdb=" CA ASN H 65 " ideal model delta sigma weight residual 122.46 126.03 -3.57 1.41e+00 5.03e-01 6.42e+00 angle pdb=" C ASP L 50 " pdb=" N ALA L 51 " pdb=" CA ALA L 51 " ideal model delta sigma weight residual 121.54 126.32 -4.78 1.91e+00 2.74e-01 6.27e+00 angle pdb=" CB MET L 4 " pdb=" CG MET L 4 " pdb=" SD MET L 4 " ideal model delta sigma weight residual 112.70 105.35 7.35 3.00e+00 1.11e-01 6.01e+00 angle pdb=" C ASN B 354 " pdb=" N ARG B 355 " pdb=" CA ARG B 355 " ideal model delta sigma weight residual 122.81 126.20 -3.39 1.57e+00 4.06e-01 4.65e+00 angle pdb=" N ASN B 370 " pdb=" CA ASN B 370 " pdb=" C ASN B 370 " ideal model delta sigma weight residual 112.23 114.67 -2.44 1.26e+00 6.30e-01 3.74e+00 ... (remaining 6336 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.90: 2475 16.90 - 33.81: 193 33.81 - 50.71: 24 50.71 - 67.61: 5 67.61 - 84.51: 6 Dihedral angle restraints: 2703 sinusoidal: 1053 harmonic: 1650 Sorted by residual: dihedral pdb=" CD ARG B 457 " pdb=" NE ARG B 457 " pdb=" CZ ARG B 457 " pdb=" NH1 ARG B 457 " ideal model delta sinusoidal sigma weight residual 0.00 -35.01 35.01 1 1.00e+01 1.00e-02 1.74e+01 dihedral pdb=" CG ARG B 403 " pdb=" CD ARG B 403 " pdb=" NE ARG B 403 " pdb=" CZ ARG B 403 " ideal model delta sinusoidal sigma weight residual 90.00 134.71 -44.71 2 1.50e+01 4.44e-03 1.06e+01 dihedral pdb=" CD ARG A 408 " pdb=" NE ARG A 408 " pdb=" CZ ARG A 408 " pdb=" NH1 ARG A 408 " ideal model delta sinusoidal sigma weight residual 0.00 -26.31 26.31 1 1.00e+01 1.00e-02 9.95e+00 ... (remaining 2700 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 365 0.031 - 0.062: 175 0.062 - 0.093: 71 0.093 - 0.124: 33 0.124 - 0.155: 15 Chirality restraints: 659 Sorted by residual: chirality pdb=" CA ILE L 48 " pdb=" N ILE L 48 " pdb=" C ILE L 48 " pdb=" CB ILE L 48 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.99e-01 chirality pdb=" CA ILE H 37 " pdb=" N ILE H 37 " pdb=" C ILE H 37 " pdb=" CB ILE H 37 " both_signs ideal model delta sigma weight residual False 2.43 2.59 -0.15 2.00e-01 2.50e+01 5.93e-01 chirality pdb=" CA ILE B 402 " pdb=" N ILE B 402 " pdb=" C ILE B 402 " pdb=" CB ILE B 402 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.73e-01 ... (remaining 656 not shown) Planarity restraints: 820 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG B 457 " 0.479 9.50e-02 1.11e+02 2.16e-01 3.63e+01 pdb=" NE ARG B 457 " -0.046 2.00e-02 2.50e+03 pdb=" CZ ARG B 457 " 0.044 2.00e-02 2.50e+03 pdb=" NH1 ARG B 457 " -0.019 2.00e-02 2.50e+03 pdb=" NH2 ARG B 457 " 0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG A 408 " 0.369 9.50e-02 1.11e+02 1.67e-01 2.15e+01 pdb=" NE ARG A 408 " -0.035 2.00e-02 2.50e+03 pdb=" CZ ARG A 408 " 0.033 2.00e-02 2.50e+03 pdb=" NH1 ARG A 408 " -0.015 2.00e-02 2.50e+03 pdb=" NH2 ARG A 408 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CD ARG B 355 " 0.191 9.50e-02 1.11e+02 8.65e-02 6.00e+00 pdb=" NE ARG B 355 " -0.018 2.00e-02 2.50e+03 pdb=" CZ ARG B 355 " 0.019 2.00e-02 2.50e+03 pdb=" NH1 ARG B 355 " -0.009 2.00e-02 2.50e+03 pdb=" NH2 ARG B 355 " -0.000 2.00e-02 2.50e+03 ... (remaining 817 not shown) Histogram of nonbonded interaction distances: 2.31 - 2.83: 1466 2.83 - 3.35: 3712 3.35 - 3.87: 6515 3.87 - 4.38: 7635 4.38 - 4.90: 13939 Nonbonded interactions: 33267 Sorted by model distance: nonbonded pdb=" NH2 ARG B 355 " pdb=" OD1 ASP B 398 " model vdw 2.313 3.120 nonbonded pdb=" NH1 ARG A 357 " pdb=" O ILE A 358 " model vdw 2.315 3.120 nonbonded pdb=" N LYS A 462 " pdb=" OE2 GLU A 465 " model vdw 2.333 3.120 nonbonded pdb=" OE1 GLU A 406 " pdb=" NE2 GLN A 409 " model vdw 2.350 3.120 nonbonded pdb=" OG SER A 349 " pdb=" O LEU A 452 " model vdw 2.359 3.040 ... (remaining 33262 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' and (resid 338 through 358 or resid 366 through 380 or resid 394 thro \ ugh 515)) selection = (chain 'B' and (resid 338 through 358 or resid 366 through 458 or (resid 459 and \ (name N or name CA or name C or name O or name CB )) or resid 460 through 515)) \ } 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: 5.300 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: 0.190 Check model and map are aligned: 0.040 Set scattering table: 0.050 Process input model: 18.380 Find NCS groups from input model: 0.120 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:11.390 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.500 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7920 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 : 0.003 0.047 4665 Z= 0.163 Angle : 0.674 7.352 6341 Z= 0.366 Chirality : 0.048 0.155 659 Planarity : 0.012 0.216 820 Dihedral : 12.207 84.510 1641 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 0.00 % Allowed : 1.22 % Favored : 98.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -1.40 (0.33), residues: 555 helix: -3.86 (0.58), residues: 32 sheet: 0.20 (0.41), residues: 170 loop : -1.27 (0.29), residues: 353 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP A 353 HIS 0.003 0.001 HIS H 77 PHE 0.016 0.002 PHE A 377 TYR 0.021 0.003 TYR L 49 ARG 0.049 0.004 ARG B 457 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 130 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.549 Fit side-chains REVERT: B 444 LYS cc_start: 0.6749 (ttmm) cc_final: 0.6480 (tppt) REVERT: L 45 LYS cc_start: 0.8337 (ptmm) cc_final: 0.7931 (pttt) outliers start: 0 outliers final: 1 residues processed: 130 average time/residue: 0.9561 time to fit residues: 129.6990 Evaluate side-chains 81 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 80 time to evaluate : 0.557 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 45 optimal weight: 0.0170 chunk 40 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 13 optimal weight: 0.2980 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.2980 chunk 42 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 25 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 49 optimal weight: 4.9990 overall best weight: 0.3218 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 6 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8074 moved from start: 0.2530 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4665 Z= 0.174 Angle : 0.588 11.876 6341 Z= 0.306 Chirality : 0.046 0.164 659 Planarity : 0.004 0.035 820 Dihedral : 4.220 31.153 637 Min Nonbonded Distance : 2.496 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.63 % Allowed : 12.42 % Favored : 85.95 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.94 (0.33), residues: 555 helix: -3.51 (0.64), residues: 33 sheet: 0.66 (0.41), residues: 170 loop : -1.02 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.000 HIS H 101 PHE 0.011 0.001 PHE A 377 TYR 0.011 0.001 TYR A 369 ARG 0.010 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 0.555 Fit side-chains REVERT: A 466 ARG cc_start: 0.7503 (ttp-110) cc_final: 0.7175 (ttm110) REVERT: A 506 GLN cc_start: 0.8913 (OUTLIER) cc_final: 0.8699 (mp10) REVERT: B 444 LYS cc_start: 0.7061 (ttmm) cc_final: 0.6740 (tppt) REVERT: L 4 MET cc_start: 0.7261 (mpp) cc_final: 0.7018 (mtm) REVERT: L 45 LYS cc_start: 0.8537 (ptmm) cc_final: 0.8171 (pttt) outliers start: 8 outliers final: 3 residues processed: 100 average time/residue: 1.2861 time to fit residues: 133.2273 Evaluate side-chains 85 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 81 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain H residue 78 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 4.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 0.0470 chunk 49 optimal weight: 0.8980 chunk 53 optimal weight: 0.5980 chunk 43 optimal weight: 0.0980 chunk 48 optimal weight: 0.0170 chunk 16 optimal weight: 1.9990 chunk 39 optimal weight: 6.9990 overall best weight: 0.3316 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 440 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8135 moved from start: 0.3142 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.064 4665 Z= 0.162 Angle : 0.538 10.490 6341 Z= 0.282 Chirality : 0.044 0.158 659 Planarity : 0.004 0.032 820 Dihedral : 4.051 30.920 637 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 1.83 % Allowed : 14.87 % Favored : 83.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.68 (0.33), residues: 555 helix: -3.16 (0.69), residues: 33 sheet: 0.92 (0.41), residues: 167 loop : -0.90 (0.29), residues: 355 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 436 HIS 0.001 0.001 HIS H 77 PHE 0.010 0.001 PHE B 377 TYR 0.011 0.001 TYR A 369 ARG 0.004 0.001 ARG A 457 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 83 time to evaluate : 0.547 Fit side-chains REVERT: A 408 ARG cc_start: 0.8634 (OUTLIER) cc_final: 0.8029 (ttm-80) REVERT: A 466 ARG cc_start: 0.7606 (ttp-110) cc_final: 0.7278 (ttm110) REVERT: A 506 GLN cc_start: 0.8908 (OUTLIER) cc_final: 0.8212 (mt0) REVERT: B 444 LYS cc_start: 0.7019 (ttmm) cc_final: 0.6708 (ttmt) REVERT: B 498 GLN cc_start: 0.8414 (OUTLIER) cc_final: 0.7892 (mt0) REVERT: L 4 MET cc_start: 0.7347 (mpp) cc_final: 0.6963 (mtm) REVERT: L 45 LYS cc_start: 0.8615 (ptmm) cc_final: 0.8295 (pttt) outliers start: 9 outliers final: 4 residues processed: 91 average time/residue: 1.3297 time to fit residues: 125.4033 Evaluate side-chains 87 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 80 time to evaluate : 0.545 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 48 optimal weight: 2.9990 chunk 36 optimal weight: 0.5980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 0.9990 chunk 23 optimal weight: 0.0670 chunk 32 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 52 optimal weight: 0.8980 chunk 46 optimal weight: 0.9980 chunk 14 optimal weight: 0.0010 chunk 43 optimal weight: 0.5980 overall best weight: 0.4324 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8183 moved from start: 0.3633 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.066 4665 Z= 0.177 Angle : 0.549 12.136 6341 Z= 0.290 Chirality : 0.045 0.163 659 Planarity : 0.004 0.052 820 Dihedral : 4.008 18.207 635 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 3.26 % Allowed : 15.07 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.63 (0.33), residues: 555 helix: -3.05 (0.73), residues: 33 sheet: 0.97 (0.41), residues: 170 loop : -0.90 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.001 HIS H 77 PHE 0.014 0.001 PHE B 377 TYR 0.014 0.001 TYR A 489 ARG 0.007 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.598 Fit side-chains REVERT: A 403 ARG cc_start: 0.8425 (ttp-170) cc_final: 0.8063 (ttp-170) REVERT: A 408 ARG cc_start: 0.8716 (OUTLIER) cc_final: 0.7974 (ttm-80) REVERT: A 466 ARG cc_start: 0.7626 (ttp-110) cc_final: 0.7395 (ttm110) REVERT: A 506 GLN cc_start: 0.9017 (OUTLIER) cc_final: 0.8388 (mt0) REVERT: B 444 LYS cc_start: 0.7060 (ttmm) cc_final: 0.6748 (ttmt) REVERT: B 498 GLN cc_start: 0.8424 (OUTLIER) cc_final: 0.7917 (mt0) REVERT: B 512 VAL cc_start: 0.9047 (OUTLIER) cc_final: 0.8782 (t) REVERT: L 4 MET cc_start: 0.7293 (mpp) cc_final: 0.7025 (mtm) REVERT: L 45 LYS cc_start: 0.8717 (ptmm) cc_final: 0.8465 (pttt) outliers start: 16 outliers final: 6 residues processed: 97 average time/residue: 1.2625 time to fit residues: 126.8874 Evaluate side-chains 93 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 83 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 506 GLN Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.0470 chunk 0 optimal weight: 2.9990 chunk 38 optimal weight: 0.0060 chunk 21 optimal weight: 0.9980 chunk 44 optimal weight: 0.7980 chunk 36 optimal weight: 0.0870 chunk 26 optimal weight: 0.1980 chunk 46 optimal weight: 0.8980 chunk 13 optimal weight: 0.0060 chunk 17 optimal weight: 1.9990 chunk 47 optimal weight: 0.9980 overall best weight: 0.0688 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 474 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8083 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.050 4665 Z= 0.124 Angle : 0.474 9.386 6341 Z= 0.250 Chirality : 0.043 0.157 659 Planarity : 0.004 0.037 820 Dihedral : 3.574 19.051 635 Min Nonbonded Distance : 2.464 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.98 % Favored : 98.02 % Rotamer: Outliers : 1.63 % Allowed : 16.70 % Favored : 81.67 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.49 (0.33), residues: 555 helix: -3.08 (0.70), residues: 34 sheet: 1.01 (0.41), residues: 171 loop : -0.74 (0.29), residues: 350 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 436 HIS 0.002 0.001 HIS H 77 PHE 0.013 0.001 PHE A 400 TYR 0.009 0.001 TYR A 369 ARG 0.008 0.000 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.544 Fit side-chains REVERT: A 403 ARG cc_start: 0.8208 (ttp-170) cc_final: 0.7959 (ttp-170) REVERT: A 466 ARG cc_start: 0.7556 (ttp-110) cc_final: 0.7317 (ttm110) REVERT: B 378 LYS cc_start: 0.7574 (ptmt) cc_final: 0.7253 (pttt) REVERT: B 444 LYS cc_start: 0.7065 (ttmm) cc_final: 0.6758 (ttmt) REVERT: L 4 MET cc_start: 0.7254 (mpp) cc_final: 0.6895 (mtm) REVERT: L 45 LYS cc_start: 0.8591 (ptmm) cc_final: 0.8347 (pttt) outliers start: 8 outliers final: 4 residues processed: 92 average time/residue: 1.2112 time to fit residues: 115.4546 Evaluate side-chains 83 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 79 time to evaluate : 0.485 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain L residue 103 LYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 10 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.0020 chunk 52 optimal weight: 1.9990 chunk 43 optimal weight: 0.6980 chunk 24 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 50 optimal weight: 3.9990 chunk 5 optimal weight: 1.9990 overall best weight: 0.8990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 414 GLN B 474 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8258 moved from start: 0.4185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.083 4665 Z= 0.277 Angle : 0.641 13.235 6341 Z= 0.340 Chirality : 0.047 0.195 659 Planarity : 0.005 0.037 820 Dihedral : 4.475 19.046 635 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.67 % Allowed : 17.11 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.54 (0.34), residues: 555 helix: -3.32 (0.67), residues: 33 sheet: 1.16 (0.42), residues: 175 loop : -0.90 (0.29), residues: 347 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.002 0.001 HIS H 40 PHE 0.020 0.002 PHE B 338 TYR 0.018 0.002 TYR A 489 ARG 0.005 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 84 time to evaluate : 0.554 Fit side-chains REVERT: A 403 ARG cc_start: 0.8559 (ttp-170) cc_final: 0.8338 (ttp-170) REVERT: A 408 ARG cc_start: 0.8701 (OUTLIER) cc_final: 0.7927 (ttm-80) REVERT: B 444 LYS cc_start: 0.7133 (ttmm) cc_final: 0.6839 (ttmt) REVERT: B 498 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7904 (mt0) REVERT: B 512 VAL cc_start: 0.9061 (OUTLIER) cc_final: 0.8841 (t) REVERT: L 4 MET cc_start: 0.7530 (mpp) cc_final: 0.7318 (mtm) outliers start: 18 outliers final: 9 residues processed: 95 average time/residue: 1.3109 time to fit residues: 128.9344 Evaluate side-chains 92 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.535 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain L residue 103 LYS Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 29 optimal weight: 0.8980 chunk 38 optimal weight: 0.9990 chunk 43 optimal weight: 2.9990 chunk 52 optimal weight: 0.9990 chunk 32 optimal weight: 0.6980 chunk 31 optimal weight: 0.1980 chunk 24 optimal weight: 0.6980 chunk 20 optimal weight: 0.0970 chunk 15 optimal weight: 0.7980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 0.0470 overall best weight: 0.3276 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8199 moved from start: 0.4274 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.064 4665 Z= 0.159 Angle : 0.531 10.924 6341 Z= 0.282 Chirality : 0.044 0.157 659 Planarity : 0.004 0.037 820 Dihedral : 4.066 19.665 635 Min Nonbonded Distance : 2.493 Molprobity Statistics. All-atom Clashscore : 2.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.88 % Favored : 97.12 % Rotamer: Outliers : 3.05 % Allowed : 17.72 % Favored : 79.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.49 (0.34), residues: 555 helix: -3.29 (0.67), residues: 34 sheet: 1.16 (0.42), residues: 170 loop : -0.81 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP H 47 HIS 0.001 0.000 HIS H 101 PHE 0.009 0.001 PHE B 377 TYR 0.014 0.001 TYR A 489 ARG 0.009 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 98 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 83 time to evaluate : 0.533 Fit side-chains revert: symmetry clash REVERT: A 403 ARG cc_start: 0.8465 (ttp-170) cc_final: 0.8034 (ttp-170) REVERT: A 408 ARG cc_start: 0.8678 (OUTLIER) cc_final: 0.7931 (ttm-80) REVERT: B 378 LYS cc_start: 0.7808 (OUTLIER) cc_final: 0.7520 (ttpt) REVERT: B 444 LYS cc_start: 0.7166 (ttmm) cc_final: 0.6890 (ttmt) REVERT: B 498 GLN cc_start: 0.8399 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: H 81 LYS cc_start: 0.8805 (OUTLIER) cc_final: 0.8433 (mppt) REVERT: L 3 GLN cc_start: 0.7471 (mm110) cc_final: 0.7218 (mm110) REVERT: L 4 MET cc_start: 0.7421 (mpp) cc_final: 0.7127 (mtm) outliers start: 15 outliers final: 7 residues processed: 92 average time/residue: 1.2120 time to fit residues: 115.6448 Evaluate side-chains 91 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.546 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 81 LYS Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 35 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 4 optimal weight: 2.9990 chunk 40 optimal weight: 2.9990 chunk 47 optimal weight: 0.3980 chunk 49 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.9980 chunk 29 optimal weight: 5.9990 chunk 21 optimal weight: 0.6980 chunk 38 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4432 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.072 4665 Z= 0.229 Angle : 0.598 12.029 6341 Z= 0.317 Chirality : 0.046 0.167 659 Planarity : 0.005 0.040 820 Dihedral : 4.357 19.982 635 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 2.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.05 % Allowed : 18.53 % Favored : 78.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.46 (0.34), residues: 555 helix: -3.48 (0.75), residues: 28 sheet: 1.21 (0.42), residues: 175 loop : -0.87 (0.29), residues: 352 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.001 HIS H 40 PHE 0.015 0.002 PHE B 338 TYR 0.015 0.001 TYR A 489 ARG 0.008 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 84 time to evaluate : 0.542 Fit side-chains REVERT: A 403 ARG cc_start: 0.8543 (ttp-170) cc_final: 0.8301 (ttp-170) REVERT: A 408 ARG cc_start: 0.8707 (OUTLIER) cc_final: 0.7938 (ttm-80) REVERT: B 378 LYS cc_start: 0.7797 (OUTLIER) cc_final: 0.7533 (ttpt) REVERT: B 444 LYS cc_start: 0.7130 (ttmm) cc_final: 0.6881 (tppt) REVERT: B 498 GLN cc_start: 0.8410 (OUTLIER) cc_final: 0.7922 (mt0) REVERT: B 512 VAL cc_start: 0.9049 (OUTLIER) cc_final: 0.8800 (t) REVERT: L 4 MET cc_start: 0.7507 (mpp) cc_final: 0.7300 (mtm) outliers start: 15 outliers final: 8 residues processed: 93 average time/residue: 1.2540 time to fit residues: 120.7868 Evaluate side-chains 95 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 83 time to evaluate : 0.495 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 340 GLU Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain L residue 100 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 14 optimal weight: 0.7980 chunk 43 optimal weight: 2.9990 chunk 45 optimal weight: 3.9990 chunk 48 optimal weight: 0.7980 chunk 31 optimal weight: 0.2980 chunk 51 optimal weight: 0.9990 chunk 24 optimal weight: 0.0770 chunk 35 optimal weight: 3.9990 chunk 53 optimal weight: 0.9980 chunk 49 optimal weight: 2.9990 chunk 42 optimal weight: 0.5980 overall best weight: 0.5138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8232 moved from start: 0.4471 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.067 4665 Z= 0.191 Angle : 0.564 11.284 6341 Z= 0.299 Chirality : 0.044 0.162 659 Planarity : 0.004 0.040 820 Dihedral : 4.228 20.617 635 Min Nonbonded Distance : 2.513 Molprobity Statistics. All-atom Clashscore : 3.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.05 % Allowed : 18.74 % Favored : 78.21 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.50 (0.34), residues: 555 helix: -3.38 (0.65), residues: 34 sheet: 1.07 (0.41), residues: 180 loop : -0.82 (0.29), residues: 341 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP H 47 HIS 0.001 0.001 HIS H 101 PHE 0.011 0.001 PHE B 377 TYR 0.016 0.001 TYR A 489 ARG 0.007 0.001 ARG L 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 82 time to evaluate : 0.497 Fit side-chains REVERT: A 408 ARG cc_start: 0.8676 (OUTLIER) cc_final: 0.7918 (ttm-80) REVERT: B 378 LYS cc_start: 0.7753 (OUTLIER) cc_final: 0.7488 (ttpt) REVERT: B 444 LYS cc_start: 0.7144 (ttmm) cc_final: 0.6901 (tppt) REVERT: B 498 GLN cc_start: 0.8426 (OUTLIER) cc_final: 0.7924 (mt0) REVERT: H 81 LYS cc_start: 0.8788 (OUTLIER) cc_final: 0.8417 (mppt) REVERT: L 4 MET cc_start: 0.7477 (mpp) cc_final: 0.7212 (mtm) outliers start: 15 outliers final: 7 residues processed: 91 average time/residue: 1.2535 time to fit residues: 118.2474 Evaluate side-chains 91 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 80 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 81 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 4 optimal weight: 4.9990 chunk 33 optimal weight: 0.5980 chunk 26 optimal weight: 0.0370 chunk 34 optimal weight: 0.9980 chunk 45 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 6 optimal weight: 1.9990 chunk 11 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 chunk 17 optimal weight: 0.5980 overall best weight: 0.6458 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8252 moved from start: 0.4548 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.070 4665 Z= 0.220 Angle : 0.597 11.637 6341 Z= 0.316 Chirality : 0.045 0.162 659 Planarity : 0.005 0.041 820 Dihedral : 4.341 20.781 635 Min Nonbonded Distance : 2.519 Molprobity Statistics. All-atom Clashscore : 3.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.78 % Favored : 96.22 % Rotamer: Outliers : 3.26 % Allowed : 19.76 % Favored : 76.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.50 (0.34), residues: 555 helix: -3.42 (0.65), residues: 34 sheet: 1.13 (0.41), residues: 181 loop : -0.86 (0.29), residues: 340 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP H 47 HIS 0.001 0.001 HIS H 101 PHE 0.013 0.001 PHE B 338 TYR 0.019 0.001 TYR A 489 ARG 0.008 0.001 ARG B 346 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1110 Ramachandran restraints generated. 555 Oldfield, 0 Emsley, 555 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.536 Fit side-chains REVERT: A 408 ARG cc_start: 0.8704 (OUTLIER) cc_final: 0.7942 (ttm-80) REVERT: B 378 LYS cc_start: 0.7756 (OUTLIER) cc_final: 0.7489 (ttpt) REVERT: B 444 LYS cc_start: 0.7145 (ttmm) cc_final: 0.6882 (tppt) REVERT: B 498 GLN cc_start: 0.8415 (OUTLIER) cc_final: 0.7911 (mt0) REVERT: B 512 VAL cc_start: 0.9023 (OUTLIER) cc_final: 0.8749 (t) REVERT: L 4 MET cc_start: 0.7532 (mpp) cc_final: 0.7314 (mtm) outliers start: 16 outliers final: 9 residues processed: 91 average time/residue: 1.2256 time to fit residues: 115.7578 Evaluate side-chains 92 residues out of total 493 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 79 time to evaluate : 0.468 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 382 VAL Chi-restraints excluded: chain A residue 401 VAL Chi-restraints excluded: chain A residue 408 ARG Chi-restraints excluded: chain A residue 465 GLU Chi-restraints excluded: chain A residue 510 VAL Chi-restraints excluded: chain B residue 345 THR Chi-restraints excluded: chain B residue 378 LYS Chi-restraints excluded: chain B residue 427 ASP Chi-restraints excluded: chain B residue 498 GLN Chi-restraints excluded: chain B residue 512 VAL Chi-restraints excluded: chain H residue 65 ASN Chi-restraints excluded: chain H residue 78 LEU Chi-restraints excluded: chain L residue 103 LYS Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 54 random chunks: chunk 44 optimal weight: 0.3980 chunk 5 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 37 optimal weight: 0.1980 chunk 2 optimal weight: 0.8980 chunk 30 optimal weight: 1.9990 chunk 49 optimal weight: 2.9990 chunk 28 optimal weight: 0.0270 chunk 36 optimal weight: 0.0170 chunk 1 optimal weight: 0.8980 chunk 34 optimal weight: 3.9990 overall best weight: 0.3076 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 3 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.133697 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 51)----------------| | r_work = 0.3387 r_free = 0.3387 target = 0.111643 restraints weight = 6355.182| |-----------------------------------------------------------------------------| r_work (start): 0.3387 rms_B_bonded: 1.96 r_work: 0.3263 rms_B_bonded: 2.56 restraints_weight: 0.5000 r_work: 0.3137 rms_B_bonded: 4.21 restraints_weight: 0.2500 r_work (final): 0.3137 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.4563 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.059 4665 Z= 0.156 Angle : 0.532 10.063 6341 Z= 0.282 Chirality : 0.043 0.159 659 Planarity : 0.004 0.037 820 Dihedral : 4.059 20.684 635 Min Nonbonded Distance : 2.515 Molprobity Statistics. All-atom Clashscore : 3.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.70 % Favored : 97.30 % Rotamer: Outliers : 3.05 % Allowed : 19.35 % Favored : 77.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 3.70 % 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: -0.43 (0.34), residues: 555 helix: -3.42 (0.65), residues: 34 sheet: 1.30 (0.43), residues: 170 loop : -0.80 (0.29), residues: 351 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP H 47 HIS 0.001 0.000 HIS H 101 PHE 0.009 0.001 PHE A 400 TYR 0.018 0.001 TYR A 489 ARG 0.008 0.001 ARG B 346 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2773.27 seconds wall clock time: 48 minutes 49.14 seconds (2929.14 seconds total)