Starting phenix.real_space_refine on Sun Nov 17 06:52:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/11_2024/8fyf_29572.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/11_2024/8fyf_29572.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/11_2024/8fyf_29572.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/11_2024/8fyf_29572.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/11_2024/8fyf_29572.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8fyf_29572/11_2024/8fyf_29572.cif" } resolution = 3.4 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= 0.003 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 38 5.16 5 C 4244 2.51 5 N 1086 2.21 5 O 1080 1.98 5 H 6754 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 25 residue(s): 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5513/modules/chem_data/mon_lib" Total number of atoms: 13202 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "B" Number of atoms: 6163 Number of conformers: 1 Conformer: "" Number of residues, atoms: 387, 6163 Classifications: {'peptide': 387} Link IDs: {'PTRANS': 16, 'TRANS': 370} Chain breaks: 1 Chain: "C" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Chain: "D" Number of atoms: 438 Number of conformers: 1 Conformer: "" Number of residues, atoms: 28, 438 Classifications: {'peptide': 28} Link IDs: {'PTRANS': 1, 'TRANS': 26} Time building chain proxies: 7.26, per 1000 atoms: 0.55 Number of scatterers: 13202 At special positions: 0 Unit cell: (105.25, 73.254, 82.516, 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 38 16.00 O 1080 8.00 N 1086 7.00 C 4244 6.00 H 6754 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.48 Conformation dependent library (CDL) restraints added in 907.4 milliseconds 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1576 Finding SS restraints... Secondary structure from input PDB file: 46 helices and 4 sheets defined 89.4% alpha, 1.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.87 Creating SS restraints... Processing helix chain 'A' and resid 33 through 50 Processing helix chain 'A' and resid 51 through 57 removed outlier: 4.354A pdb=" N VAL A 55 " --> pdb=" O MET A 51 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 102 removed outlier: 5.521A pdb=" N ARG A 72 " --> pdb=" O ARG A 68 " (cutoff:3.500A) removed outlier: 4.201A pdb=" N LEU A 73 " --> pdb=" O SER A 69 " (cutoff:3.500A) Processing helix chain 'A' and resid 106 through 121 Processing helix chain 'A' and resid 122 through 133 Processing helix chain 'A' and resid 136 through 164 removed outlier: 4.447A pdb=" N ILE A 140 " --> pdb=" O VAL A 136 " (cutoff:3.500A) Processing helix chain 'A' and resid 165 through 168 Processing helix chain 'A' and resid 169 through 175 Processing helix chain 'A' and resid 177 through 190 removed outlier: 3.882A pdb=" N ARG A 183 " --> pdb=" O ALA A 179 " (cutoff:3.500A) removed outlier: 4.118A pdb=" N LEU A 186 " --> pdb=" O ARG A 182 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 274 Processing helix chain 'A' and resid 274 through 284 removed outlier: 3.977A pdb=" N LEU A 278 " --> pdb=" O THR A 274 " (cutoff:3.500A) removed outlier: 4.376A pdb=" N ASP A 279 " --> pdb=" O LEU A 275 " (cutoff:3.500A) removed outlier: 3.976A pdb=" N ILE A 280 " --> pdb=" O LEU A 276 " (cutoff:3.500A) Processing helix chain 'A' and resid 287 through 294 Processing helix chain 'A' and resid 298 through 305 Processing helix chain 'A' and resid 306 through 332 removed outlier: 3.701A pdb=" N PHE A 310 " --> pdb=" O THR A 306 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 353 Processing helix chain 'A' and resid 354 through 364 Processing helix chain 'A' and resid 368 through 399 removed outlier: 3.881A pdb=" N GLU A 372 " --> pdb=" O GLN A 368 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE A 389 " --> pdb=" O LEU A 385 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N GLN A 390 " --> pdb=" O ALA A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 400 through 405 Processing helix chain 'A' and resid 406 through 410 Processing helix chain 'A' and resid 415 through 440 removed outlier: 4.910A pdb=" N TYR A 426 " --> pdb=" O LYS A 422 " (cutoff:3.500A) Proline residue: A 427 - end of helix removed outlier: 3.566A pdb=" N THR A 437 " --> pdb=" O ALA A 433 " (cutoff:3.500A) removed outlier: 3.890A pdb=" N CYS A 438 " --> pdb=" O PHE A 434 " (cutoff:3.500A) Processing helix chain 'A' and resid 443 through 461 Proline residue: A 456 - end of helix Processing helix chain 'A' and resid 461 through 474 Processing helix chain 'B' and resid 33 through 50 Processing helix chain 'B' and resid 51 through 57 removed outlier: 4.354A pdb=" N VAL B 55 " --> pdb=" O MET B 51 " (cutoff:3.500A) Processing helix chain 'B' and resid 66 through 102 removed outlier: 5.521A pdb=" N ARG B 72 " --> pdb=" O ARG B 68 " (cutoff:3.500A) removed outlier: 4.200A pdb=" N LEU B 73 " --> pdb=" O SER B 69 " (cutoff:3.500A) Processing helix chain 'B' and resid 106 through 121 removed outlier: 3.500A pdb=" N LEU B 111 " --> pdb=" O ASP B 107 " (cutoff:3.500A) Processing helix chain 'B' and resid 122 through 133 Processing helix chain 'B' and resid 136 through 164 removed outlier: 4.447A pdb=" N ILE B 140 " --> pdb=" O VAL B 136 " (cutoff:3.500A) Processing helix chain 'B' and resid 165 through 168 Processing helix chain 'B' and resid 169 through 175 Processing helix chain 'B' and resid 177 through 190 removed outlier: 3.886A pdb=" N ARG B 183 " --> pdb=" O ALA B 179 " (cutoff:3.500A) removed outlier: 4.115A pdb=" N LEU B 186 " --> pdb=" O ARG B 182 " (cutoff:3.500A) Processing helix chain 'B' and resid 257 through 274 Processing helix chain 'B' and resid 274 through 284 removed outlier: 3.977A pdb=" N LEU B 278 " --> pdb=" O THR B 274 " (cutoff:3.500A) removed outlier: 4.375A pdb=" N ASP B 279 " --> pdb=" O LEU B 275 " (cutoff:3.500A) removed outlier: 3.977A pdb=" N ILE B 280 " --> pdb=" O LEU B 276 " (cutoff:3.500A) Processing helix chain 'B' and resid 287 through 294 Processing helix chain 'B' and resid 298 through 305 Processing helix chain 'B' and resid 306 through 332 removed outlier: 3.699A pdb=" N PHE B 310 " --> pdb=" O THR B 306 " (cutoff:3.500A) Processing helix chain 'B' and resid 339 through 353 Processing helix chain 'B' and resid 354 through 364 Processing helix chain 'B' and resid 368 through 399 removed outlier: 3.856A pdb=" N GLU B 372 " --> pdb=" O GLN B 368 " (cutoff:3.500A) removed outlier: 3.887A pdb=" N PHE B 389 " --> pdb=" O LEU B 385 " (cutoff:3.500A) removed outlier: 4.082A pdb=" N GLN B 390 " --> pdb=" O ALA B 386 " (cutoff:3.500A) Processing helix chain 'B' and resid 400 through 405 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 415 through 440 removed outlier: 4.911A pdb=" N TYR B 426 " --> pdb=" O LYS B 422 " (cutoff:3.500A) Proline residue: B 427 - end of helix removed outlier: 3.567A pdb=" N THR B 437 " --> pdb=" O ALA B 433 " (cutoff:3.500A) removed outlier: 3.889A pdb=" N CYS B 438 " --> pdb=" O PHE B 434 " (cutoff:3.500A) Processing helix chain 'B' and resid 443 through 461 Proline residue: B 456 - end of helix Processing helix chain 'B' and resid 461 through 474 Processing helix chain 'C' and resid 384 through 410 Processing helix chain 'D' and resid 384 through 410 Processing sheet with id=AA1, first strand: chain 'A' and resid 31 through 32 Processing sheet with id=AA2, first strand: chain 'A' and resid 255 through 256 removed outlier: 4.266A pdb=" N ALA A 337 " --> pdb=" O LEU A 256 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 31 through 32 Processing sheet with id=AA4, first strand: chain 'B' and resid 255 through 256 removed outlier: 4.287A pdb=" N ALA B 337 " --> pdb=" O LEU B 256 " (cutoff:3.500A) 523 hydrogen bonds defined for protein. 1545 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: 5.06 Time building geometry restraints manager: 4.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.84 - 1.03: 6736 1.03 - 1.23: 20 1.23 - 1.42: 2680 1.42 - 1.61: 3852 1.61 - 1.81: 58 Bond restraints: 13346 Sorted by residual: bond pdb=" C THR B 306 " pdb=" N GLY B 307 " ideal model delta sigma weight residual 1.340 1.328 0.012 6.60e-03 2.30e+04 3.27e+00 bond pdb=" C THR A 306 " pdb=" N GLY A 307 " ideal model delta sigma weight residual 1.340 1.328 0.012 6.60e-03 2.30e+04 3.12e+00 bond pdb=" N LEU C 383 " pdb=" CA LEU C 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.08e+00 bond pdb=" N LEU D 383 " pdb=" CA LEU D 383 " ideal model delta sigma weight residual 1.458 1.491 -0.033 1.90e-02 2.77e+03 3.05e+00 bond pdb=" N ILE A 30 " pdb=" CA ILE A 30 " ideal model delta sigma weight residual 1.458 1.489 -0.031 1.90e-02 2.77e+03 2.68e+00 ... (remaining 13341 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.34: 23336 1.34 - 2.68: 794 2.68 - 4.02: 58 4.02 - 5.36: 12 5.36 - 6.71: 2 Bond angle restraints: 24202 Sorted by residual: angle pdb=" N GLU A 403 " pdb=" CA GLU A 403 " pdb=" C GLU A 403 " ideal model delta sigma weight residual 114.56 111.34 3.22 1.27e+00 6.20e-01 6.45e+00 angle pdb=" N GLU B 403 " pdb=" CA GLU B 403 " pdb=" C GLU B 403 " ideal model delta sigma weight residual 114.56 111.36 3.20 1.27e+00 6.20e-01 6.35e+00 angle pdb=" C ILE A 60 " pdb=" N SER A 61 " pdb=" CA SER A 61 " ideal model delta sigma weight residual 122.00 119.39 2.61 1.08e+00 8.57e-01 5.86e+00 angle pdb=" N SER B 61 " pdb=" CA SER B 61 " pdb=" C SER B 61 " ideal model delta sigma weight residual 108.55 112.86 -4.31 1.79e+00 3.12e-01 5.81e+00 angle pdb=" C ILE B 60 " pdb=" N SER B 61 " pdb=" CA SER B 61 " ideal model delta sigma weight residual 122.00 119.43 2.57 1.08e+00 8.57e-01 5.66e+00 ... (remaining 24197 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.62: 5611 17.62 - 35.23: 459 35.23 - 52.85: 127 52.85 - 70.47: 43 70.47 - 88.09: 8 Dihedral angle restraints: 6248 sinusoidal: 3352 harmonic: 2896 Sorted by residual: dihedral pdb=" CA GLU A 59 " pdb=" C GLU A 59 " pdb=" N ILE A 60 " pdb=" CA ILE A 60 " ideal model delta harmonic sigma weight residual -180.00 -159.95 -20.05 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA GLU B 59 " pdb=" C GLU B 59 " pdb=" N ILE B 60 " pdb=" CA ILE B 60 " ideal model delta harmonic sigma weight residual 180.00 -159.96 -20.04 0 5.00e+00 4.00e-02 1.61e+01 dihedral pdb=" CA LEU A 276 " pdb=" C LEU A 276 " pdb=" N ILE A 277 " pdb=" CA ILE A 277 " ideal model delta harmonic sigma weight residual 180.00 160.05 19.95 0 5.00e+00 4.00e-02 1.59e+01 ... (remaining 6245 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 716 0.028 - 0.055: 235 0.055 - 0.083: 109 0.083 - 0.111: 36 0.111 - 0.138: 10 Chirality restraints: 1106 Sorted by residual: chirality pdb=" CA ILE A 30 " pdb=" N ILE A 30 " pdb=" C ILE A 30 " pdb=" CB ILE A 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.79e-01 chirality pdb=" CA ILE B 30 " pdb=" N ILE B 30 " pdb=" C ILE B 30 " pdb=" CB ILE B 30 " both_signs ideal model delta sigma weight residual False 2.43 2.57 -0.14 2.00e-01 2.50e+01 4.75e-01 chirality pdb=" CA VAL B 136 " pdb=" N VAL B 136 " pdb=" C VAL B 136 " pdb=" CB VAL B 136 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.12 2.00e-01 2.50e+01 3.88e-01 ... (remaining 1103 not shown) Planarity restraints: 1888 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU B 254 " -0.023 5.00e-02 4.00e+02 3.41e-02 1.87e+00 pdb=" N PRO B 255 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 255 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 255 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP B 287 " -0.022 5.00e-02 4.00e+02 3.39e-02 1.84e+00 pdb=" N PRO B 288 " 0.059 5.00e-02 4.00e+02 pdb=" CA PRO B 288 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO B 288 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C ASP A 287 " -0.022 5.00e-02 4.00e+02 3.37e-02 1.82e+00 pdb=" N PRO A 288 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 288 " -0.017 5.00e-02 4.00e+02 pdb=" CD PRO A 288 " -0.019 5.00e-02 4.00e+02 ... (remaining 1885 not shown) Histogram of nonbonded interaction distances: 1.45 - 2.08: 203 2.08 - 2.71: 21938 2.71 - 3.34: 39930 3.34 - 3.97: 47602 3.97 - 4.60: 76240 Nonbonded interactions: 185913 Sorted by model distance: nonbonded pdb=" OE1 GLU A 259 " pdb=" H GLU A 259 " model vdw 1.451 2.450 nonbonded pdb=" OE1 GLU B 259 " pdb=" H GLU B 259 " model vdw 1.452 2.450 nonbonded pdb=" OE1 GLN A 171 " pdb=" H GLN A 171 " model vdw 1.633 2.450 nonbonded pdb=" OE1 GLN B 171 " pdb=" H GLN B 171 " model vdw 1.637 2.450 nonbonded pdb=" HE2 HIS A 95 " pdb=" OD1 ASN A 113 " model vdw 1.666 2.450 ... (remaining 185908 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = 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: 1.170 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: 0.240 Extract box with map and model: 0.510 Check model and map are aligned: 0.100 Set scattering table: 0.150 Process input model: 31.080 Find NCS groups from input model: 0.470 Set up NCS constraints: 0.060 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.010 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.820 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 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 0.033 6592 Z= 0.188 Angle : 0.582 6.706 8974 Z= 0.331 Chirality : 0.036 0.138 1106 Planarity : 0.004 0.034 1098 Dihedral : 14.089 88.087 2318 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 5.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Rotamer: Outliers : 0.14 % Allowed : 10.34 % Favored : 89.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.89 (0.30), residues: 818 helix: 2.32 (0.20), residues: 686 sheet: None (None), residues: 0 loop : -0.24 (0.63), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 324 HIS 0.003 0.001 HIS B 328 PHE 0.011 0.001 PHE B 314 TYR 0.008 0.001 TYR A 313 ARG 0.002 0.000 ARG B 335 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 74 time to evaluate : 1.086 Fit side-chains REVERT: B 426 TYR cc_start: 0.9087 (OUTLIER) cc_final: 0.7217 (t80) outliers start: 1 outliers final: 0 residues processed: 75 average time/residue: 0.4106 time to fit residues: 43.0766 Evaluate side-chains 72 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 1 poor density : 71 time to evaluate : 1.094 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 67 optimal weight: 2.9990 chunk 60 optimal weight: 4.9990 chunk 33 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 40 optimal weight: 0.4980 chunk 32 optimal weight: 0.7980 chunk 62 optimal weight: 4.9990 chunk 24 optimal weight: 0.9990 chunk 38 optimal weight: 2.9990 chunk 46 optimal weight: 4.9990 chunk 72 optimal weight: 5.9990 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.0562 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 6592 Z= 0.216 Angle : 0.551 5.030 8974 Z= 0.299 Chirality : 0.037 0.112 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.900 49.401 892 Min Nonbonded Distance : 2.486 Molprobity Statistics. All-atom Clashscore : 4.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 0.86 % Allowed : 10.92 % Favored : 88.22 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.87 (0.30), residues: 818 helix: 2.29 (0.20), residues: 700 sheet: None (None), residues: 0 loop : -0.49 (0.68), residues: 118 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS A 449 PHE 0.009 0.001 PHE B 99 TYR 0.009 0.001 TYR A 160 ARG 0.001 0.000 ARG B 375 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 75 time to evaluate : 1.134 Fit side-chains REVERT: A 65 GLN cc_start: 0.3339 (OUTLIER) cc_final: 0.2718 (tm-30) REVERT: A 293 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7224 (mp0) REVERT: A 426 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.7421 (t80) REVERT: B 65 GLN cc_start: 0.3315 (OUTLIER) cc_final: 0.2695 (tm-30) REVERT: B 293 GLU cc_start: 0.8156 (OUTLIER) cc_final: 0.7220 (mp0) REVERT: B 426 TYR cc_start: 0.9113 (OUTLIER) cc_final: 0.7305 (t80) outliers start: 6 outliers final: 0 residues processed: 81 average time/residue: 0.3875 time to fit residues: 43.4240 Evaluate side-chains 77 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 71 time to evaluate : 1.084 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 40 optimal weight: 0.5980 chunk 22 optimal weight: 3.9990 chunk 60 optimal weight: 4.9990 chunk 49 optimal weight: 3.9990 chunk 20 optimal weight: 5.9990 chunk 72 optimal weight: 6.9990 chunk 78 optimal weight: 1.9990 chunk 64 optimal weight: 1.9990 chunk 24 optimal weight: 3.9990 chunk 58 optimal weight: 7.9990 chunk 71 optimal weight: 2.9990 overall best weight: 2.3188 ------------------------------------------------------------------------------- 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: 0.8414 moved from start: 0.0808 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 6592 Z= 0.264 Angle : 0.553 5.043 8974 Z= 0.298 Chirality : 0.037 0.110 1106 Planarity : 0.004 0.032 1098 Dihedral : 4.917 49.777 892 Min Nonbonded Distance : 2.474 Molprobity Statistics. All-atom Clashscore : 4.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.44 % Allowed : 10.49 % Favored : 88.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.84 (0.30), residues: 818 helix: 2.31 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.60 (0.66), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS B 328 PHE 0.011 0.001 PHE A 264 TYR 0.010 0.001 TYR A 313 ARG 0.001 0.000 ARG B 260 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 78 time to evaluate : 1.079 Fit side-chains REVERT: A 65 GLN cc_start: 0.3312 (OUTLIER) cc_final: 0.2707 (tm-30) REVERT: A 293 GLU cc_start: 0.8215 (OUTLIER) cc_final: 0.7273 (mp0) REVERT: A 426 TYR cc_start: 0.9169 (OUTLIER) cc_final: 0.7359 (t80) REVERT: B 65 GLN cc_start: 0.3296 (OUTLIER) cc_final: 0.2693 (tm-30) REVERT: B 293 GLU cc_start: 0.8227 (OUTLIER) cc_final: 0.7280 (mp0) REVERT: B 426 TYR cc_start: 0.9168 (OUTLIER) cc_final: 0.7212 (t80) outliers start: 10 outliers final: 2 residues processed: 86 average time/residue: 0.3571 time to fit residues: 42.8714 Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 75 time to evaluate : 1.161 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 54 optimal weight: 6.9990 chunk 37 optimal weight: 3.9990 chunk 8 optimal weight: 4.9990 chunk 34 optimal weight: 5.9990 chunk 48 optimal weight: 1.9990 chunk 73 optimal weight: 5.9990 chunk 77 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 69 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 64 optimal weight: 3.9990 overall best weight: 1.9186 ------------------------------------------------------------------------------- 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: 0.8403 moved from start: 0.0974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6592 Z= 0.229 Angle : 0.533 5.003 8974 Z= 0.286 Chirality : 0.036 0.111 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.880 50.349 892 Min Nonbonded Distance : 2.481 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.58 % Allowed : 10.78 % Favored : 87.64 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.96 (0.30), residues: 818 helix: 2.42 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.68 (0.65), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.004 0.001 HIS B 328 PHE 0.010 0.001 PHE A 99 TYR 0.010 0.001 TYR A 313 ARG 0.002 0.000 ARG B 309 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 77 time to evaluate : 0.985 Fit side-chains REVERT: A 65 GLN cc_start: 0.3284 (OUTLIER) cc_final: 0.2704 (tm-30) REVERT: A 293 GLU cc_start: 0.8162 (OUTLIER) cc_final: 0.7218 (mp0) REVERT: A 426 TYR cc_start: 0.9164 (OUTLIER) cc_final: 0.7290 (t80) REVERT: B 65 GLN cc_start: 0.3267 (OUTLIER) cc_final: 0.2692 (tm-30) REVERT: B 293 GLU cc_start: 0.8168 (OUTLIER) cc_final: 0.7227 (mp0) REVERT: B 426 TYR cc_start: 0.9157 (OUTLIER) cc_final: 0.7298 (t80) outliers start: 11 outliers final: 3 residues processed: 87 average time/residue: 0.3425 time to fit residues: 41.7805 Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.071 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 43 optimal weight: 0.6980 chunk 1 optimal weight: 1.9990 chunk 57 optimal weight: 0.0370 chunk 31 optimal weight: 4.9990 chunk 65 optimal weight: 5.9990 chunk 53 optimal weight: 4.9990 chunk 0 optimal weight: 4.9990 chunk 39 optimal weight: 0.6980 chunk 69 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 overall best weight: 1.0862 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6592 Z= 0.171 Angle : 0.513 4.952 8974 Z= 0.272 Chirality : 0.036 0.111 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.768 50.804 892 Min Nonbonded Distance : 2.479 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.18 % Favored : 96.82 % Rotamer: Outliers : 1.58 % Allowed : 11.35 % Favored : 87.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.21 (0.30), residues: 818 helix: 2.60 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.66 (0.64), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 324 HIS 0.003 0.001 HIS B 327 PHE 0.009 0.001 PHE A 99 TYR 0.009 0.001 TYR B 313 ARG 0.002 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 72 time to evaluate : 1.078 Fit side-chains REVERT: A 65 GLN cc_start: 0.3463 (OUTLIER) cc_final: 0.2898 (tm-30) REVERT: A 293 GLU cc_start: 0.8144 (OUTLIER) cc_final: 0.7146 (mp0) REVERT: A 426 TYR cc_start: 0.9111 (OUTLIER) cc_final: 0.7395 (t80) REVERT: B 65 GLN cc_start: 0.3399 (OUTLIER) cc_final: 0.2892 (tm-30) REVERT: B 293 GLU cc_start: 0.8154 (OUTLIER) cc_final: 0.7159 (mp0) REVERT: B 426 TYR cc_start: 0.9115 (OUTLIER) cc_final: 0.7279 (t80) outliers start: 11 outliers final: 5 residues processed: 82 average time/residue: 0.3639 time to fit residues: 41.7134 Evaluate side-chains 84 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 73 time to evaluate : 1.117 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 69 optimal weight: 4.9990 chunk 15 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 19 optimal weight: 2.9990 chunk 77 optimal weight: 6.9990 chunk 64 optimal weight: 1.9990 chunk 35 optimal weight: 4.9990 chunk 6 optimal weight: 3.9990 chunk 25 optimal weight: 4.9990 chunk 40 optimal weight: 0.6980 chunk 74 optimal weight: 1.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 177 HIS B 177 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8408 moved from start: 0.1251 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 6592 Z= 0.269 Angle : 0.541 4.963 8974 Z= 0.294 Chirality : 0.037 0.112 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.843 50.489 892 Min Nonbonded Distance : 2.471 Molprobity Statistics. All-atom Clashscore : 5.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.42 % Favored : 96.58 % Rotamer: Outliers : 2.30 % Allowed : 10.92 % Favored : 86.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.02 (0.30), residues: 818 helix: 2.48 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.85 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 324 HIS 0.027 0.002 HIS A 177 PHE 0.011 0.001 PHE A 99 TYR 0.008 0.001 TYR A 313 ARG 0.003 0.000 ARG A 178 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 74 time to evaluate : 1.022 Fit side-chains REVERT: A 65 GLN cc_start: 0.3289 (OUTLIER) cc_final: 0.2721 (tm-30) REVERT: A 293 GLU cc_start: 0.8077 (OUTLIER) cc_final: 0.7152 (mp0) REVERT: A 426 TYR cc_start: 0.9174 (OUTLIER) cc_final: 0.7323 (t80) REVERT: B 65 GLN cc_start: 0.3273 (OUTLIER) cc_final: 0.2707 (tm-30) REVERT: B 293 GLU cc_start: 0.8101 (OUTLIER) cc_final: 0.7180 (mp0) REVERT: B 426 TYR cc_start: 0.9167 (OUTLIER) cc_final: 0.7283 (t80) outliers start: 16 outliers final: 5 residues processed: 84 average time/residue: 0.4322 time to fit residues: 48.3759 Evaluate side-chains 85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 74 time to evaluate : 1.110 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 177 HIS Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 177 HIS Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 8 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 chunk 56 optimal weight: 1.9990 chunk 43 optimal weight: 0.7980 chunk 65 optimal weight: 7.9990 chunk 77 optimal weight: 6.9990 chunk 48 optimal weight: 0.8980 chunk 47 optimal weight: 0.9980 chunk 35 optimal weight: 6.9990 chunk 30 optimal weight: 2.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.5384 ------------------------------------------------------------------------------- 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: 0.8400 moved from start: 0.1339 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6592 Z= 0.202 Angle : 0.522 4.923 8974 Z= 0.281 Chirality : 0.036 0.112 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.751 50.780 892 Min Nonbonded Distance : 2.463 Molprobity Statistics. All-atom Clashscore : 4.32 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.06 % Favored : 96.94 % Rotamer: Outliers : 1.44 % Allowed : 11.06 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.15 (0.30), residues: 818 helix: 2.58 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.84 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.010 0.001 HIS A 177 PHE 0.009 0.001 PHE A 99 TYR 0.009 0.001 TYR B 313 ARG 0.003 0.000 ARG B 178 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 73 time to evaluate : 0.945 Fit side-chains REVERT: A 65 GLN cc_start: 0.3287 (OUTLIER) cc_final: 0.2696 (tm-30) REVERT: A 293 GLU cc_start: 0.8075 (OUTLIER) cc_final: 0.7145 (mp0) REVERT: A 426 TYR cc_start: 0.9162 (OUTLIER) cc_final: 0.7350 (t80) REVERT: B 65 GLN cc_start: 0.3293 (OUTLIER) cc_final: 0.2692 (tm-30) REVERT: B 293 GLU cc_start: 0.8086 (OUTLIER) cc_final: 0.7156 (mp0) REVERT: B 426 TYR cc_start: 0.9147 (OUTLIER) cc_final: 0.7260 (t80) outliers start: 10 outliers final: 3 residues processed: 81 average time/residue: 0.3609 time to fit residues: 40.6216 Evaluate side-chains 83 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 9 poor density : 74 time to evaluate : 1.050 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 23 optimal weight: 2.9990 chunk 15 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 49 optimal weight: 3.9990 chunk 52 optimal weight: 0.9980 chunk 38 optimal weight: 2.9990 chunk 7 optimal weight: 3.9990 chunk 60 optimal weight: 3.9990 chunk 70 optimal weight: 4.9990 chunk 73 optimal weight: 6.9990 chunk 67 optimal weight: 1.9990 overall best weight: 2.3988 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.1421 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 6592 Z= 0.274 Angle : 0.542 4.981 8974 Z= 0.291 Chirality : 0.037 0.113 1106 Planarity : 0.004 0.034 1098 Dihedral : 4.804 50.527 892 Min Nonbonded Distance : 2.427 Molprobity Statistics. All-atom Clashscore : 4.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 1.72 % Allowed : 10.78 % Favored : 87.50 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.94 (0.30), residues: 818 helix: 2.45 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -0.97 (0.63), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 324 HIS 0.005 0.001 HIS B 328 PHE 0.011 0.002 PHE A 99 TYR 0.008 0.001 TYR B 313 ARG 0.002 0.000 ARG B 294 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 73 time to evaluate : 1.124 Fit side-chains REVERT: A 65 GLN cc_start: 0.3381 (OUTLIER) cc_final: 0.2658 (tm-30) REVERT: A 293 GLU cc_start: 0.8089 (OUTLIER) cc_final: 0.7133 (mp0) REVERT: B 65 GLN cc_start: 0.3365 (OUTLIER) cc_final: 0.2644 (tm-30) REVERT: B 293 GLU cc_start: 0.8099 (OUTLIER) cc_final: 0.7144 (mp0) outliers start: 12 outliers final: 6 residues processed: 81 average time/residue: 0.3922 time to fit residues: 44.9818 Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.240 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 71 optimal weight: 3.9990 chunk 73 optimal weight: 2.9990 chunk 43 optimal weight: 0.9990 chunk 31 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 64 optimal weight: 1.9990 chunk 67 optimal weight: 0.9980 chunk 47 optimal weight: 0.4980 chunk 75 optimal weight: 0.9990 chunk 46 optimal weight: 2.9990 overall best weight: 1.0986 ------------------------------------------------------------------------------- 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: 0.8384 moved from start: 0.1491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 6592 Z= 0.167 Angle : 0.510 5.327 8974 Z= 0.269 Chirality : 0.036 0.110 1106 Planarity : 0.004 0.033 1098 Dihedral : 4.672 51.419 892 Min Nonbonded Distance : 2.447 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.32 % Favored : 97.68 % Rotamer: Outliers : 2.01 % Allowed : 10.63 % Favored : 87.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.32 (0.30), residues: 818 helix: 2.73 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.02 (0.62), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP A 324 HIS 0.002 0.001 HIS B 328 PHE 0.010 0.001 PHE B 314 TYR 0.009 0.001 TYR B 313 ARG 0.001 0.000 ARG A 309 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 76 time to evaluate : 1.167 Fit side-chains REVERT: A 65 GLN cc_start: 0.3427 (OUTLIER) cc_final: 0.2811 (tm-30) REVERT: A 293 GLU cc_start: 0.8058 (OUTLIER) cc_final: 0.7059 (mp0) REVERT: A 426 TYR cc_start: 0.9112 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 65 GLN cc_start: 0.3392 (OUTLIER) cc_final: 0.2696 (tm-30) REVERT: B 293 GLU cc_start: 0.8068 (OUTLIER) cc_final: 0.7071 (mp0) REVERT: B 426 TYR cc_start: 0.9099 (OUTLIER) cc_final: 0.7311 (t80) outliers start: 14 outliers final: 6 residues processed: 84 average time/residue: 0.3819 time to fit residues: 45.8348 Evaluate side-chains 89 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 77 time to evaluate : 1.058 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 30 ILE Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 30 ILE Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 36 optimal weight: 0.9990 chunk 52 optimal weight: 0.4980 chunk 79 optimal weight: 4.9990 chunk 73 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 6 optimal weight: 3.9990 chunk 49 optimal weight: 2.9990 chunk 38 optimal weight: 3.9990 chunk 50 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 19 optimal weight: 4.9990 overall best weight: 1.6386 ------------------------------------------------------------------------------- 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: 0.8400 moved from start: 0.1540 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6592 Z= 0.214 Angle : 0.515 5.117 8974 Z= 0.275 Chirality : 0.036 0.112 1106 Planarity : 0.004 0.032 1098 Dihedral : 4.658 51.012 892 Min Nonbonded Distance : 2.437 Molprobity Statistics. All-atom Clashscore : 4.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.93 % Favored : 97.07 % Rotamer: Outliers : 1.44 % Allowed : 11.64 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.27 (0.30), residues: 818 helix: 2.70 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.07 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 324 HIS 0.003 0.001 HIS A 328 PHE 0.010 0.001 PHE A 99 TYR 0.008 0.001 TYR B 313 ARG 0.001 0.000 ARG A 442 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1636 Ramachandran restraints generated. 818 Oldfield, 0 Emsley, 818 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.112 Fit side-chains REVERT: A 65 GLN cc_start: 0.3278 (OUTLIER) cc_final: 0.2587 (tm-30) REVERT: A 293 GLU cc_start: 0.8074 (OUTLIER) cc_final: 0.7125 (mp0) REVERT: A 426 TYR cc_start: 0.9150 (OUTLIER) cc_final: 0.7330 (t80) REVERT: B 65 GLN cc_start: 0.3258 (OUTLIER) cc_final: 0.2566 (tm-30) REVERT: B 293 GLU cc_start: 0.8088 (OUTLIER) cc_final: 0.7144 (mp0) outliers start: 10 outliers final: 5 residues processed: 80 average time/residue: 0.3645 time to fit residues: 40.6907 Evaluate side-chains 82 residues out of total 696 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 72 time to evaluate : 1.125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 65 GLN Chi-restraints excluded: chain A residue 168 LEU Chi-restraints excluded: chain A residue 293 GLU Chi-restraints excluded: chain A residue 426 TYR Chi-restraints excluded: chain B residue 65 GLN Chi-restraints excluded: chain B residue 168 LEU Chi-restraints excluded: chain B residue 293 GLU Chi-restraints excluded: chain B residue 426 TYR Chi-restraints excluded: chain C residue 386 ILE Chi-restraints excluded: chain D residue 386 ILE Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 80 random chunks: chunk 58 optimal weight: 6.9990 chunk 9 optimal weight: 0.7980 chunk 17 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 65 optimal weight: 0.4980 chunk 8 optimal weight: 0.8980 chunk 11 optimal weight: 3.9990 chunk 55 optimal weight: 3.9990 chunk 3 optimal weight: 0.3980 chunk 45 optimal weight: 4.9990 overall best weight: 1.1182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3647 r_free = 0.3647 target = 0.126528 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3167 r_free = 0.3167 target = 0.095822 restraints weight = 32419.072| |-----------------------------------------------------------------------------| r_work (start): 0.3098 rms_B_bonded: 2.47 r_work: 0.2964 rms_B_bonded: 3.22 restraints_weight: 0.5000 r_work (final): 0.2964 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8536 moved from start: 0.1616 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6592 Z= 0.171 Angle : 0.501 5.909 8974 Z= 0.264 Chirality : 0.036 0.113 1106 Planarity : 0.004 0.032 1098 Dihedral : 4.571 51.303 892 Min Nonbonded Distance : 2.432 Molprobity Statistics. All-atom Clashscore : 4.17 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.20 % Favored : 97.80 % Rotamer: Outliers : 1.29 % Allowed : 11.78 % Favored : 86.93 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.48 (0.30), residues: 818 helix: 2.85 (0.19), residues: 690 sheet: None (None), residues: 0 loop : -1.05 (0.61), residues: 128 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 324 HIS 0.003 0.001 HIS B 328 PHE 0.009 0.001 PHE B 448 TYR 0.008 0.001 TYR B 313 ARG 0.001 0.000 ARG A 260 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 2988.11 seconds wall clock time: 54 minutes 15.66 seconds (3255.66 seconds total)