Starting phenix.real_space_refine on Tue Feb 13 19:06:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.57 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7f3x_31442/02_2024/7f3x_31442_updated.pdb" } resolution = 3.57 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.005 sd= 0.061 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 46 5.16 5 C 4968 2.51 5 N 1148 2.21 5 O 1244 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 149": "OE1" <-> "OE2" Residue "A TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 232": "OD1" <-> "OD2" Residue "A GLU 277": "OE1" <-> "OE2" Residue "A ASP 417": "OD1" <-> "OD2" Residue "A PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 459": "OD1" <-> "OD2" Residue "B PHE 104": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 152": "OD1" <-> "OD2" Residue "B TYR 208": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 229": "OE1" <-> "OE2" Residue "B PHE 241": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 267": "OE1" <-> "OE2" Residue "B PHE 344": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 445": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 456": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B ASP 459": "OD1" <-> "OD2" Residue "B PHE 477": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.03s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 7408 Number of models: 1 Model: "" Number of chains: 4 Chain: "A" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3675 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain: "B" Number of atoms: 3675 Number of conformers: 1 Conformer: "" Number of residues, atoms: 449, 3675 Classifications: {'peptide': 449} Link IDs: {'PTRANS': 17, 'TRANS': 431} Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'LAP': 1} Classifications: {'undetermined': 1} Chain: "B" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'LAP': 1} Classifications: {'undetermined': 1} Time building chain proxies: 4.35, per 1000 atoms: 0.59 Number of scatterers: 7408 At special positions: 0 Unit cell: (111.8, 117.82, 77.4, 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 46 16.00 P 2 15.00 O 1244 8.00 N 1148 7.00 C 4968 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 3.22 Conformation dependent library (CDL) restraints added in 1.4 seconds 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1680 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 39 helices and 0 sheets defined 61.8% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.43 Creating SS restraints... Processing helix chain 'A' and resid 43 through 49 Processing helix chain 'A' and resid 53 through 74 removed outlier: 3.946A pdb=" N GLY A 65 " --> pdb=" O SER A 61 " (cutoff:3.500A) removed outlier: 4.791A pdb=" N TYR A 66 " --> pdb=" O ILE A 62 " (cutoff:3.500A) Proline residue: A 67 - end of helix removed outlier: 3.548A pdb=" N TYR A 74 " --> pdb=" O LEU A 70 " (cutoff:3.500A) Processing helix chain 'A' and resid 81 through 99 Processing helix chain 'A' and resid 104 through 119 removed outlier: 3.621A pdb=" N LEU A 112 " --> pdb=" O LEU A 108 " (cutoff:3.500A) Processing helix chain 'A' and resid 125 through 146 Processing helix chain 'A' and resid 156 through 176 Processing helix chain 'A' and resid 185 through 189 Processing helix chain 'A' and resid 198 through 205 Processing helix chain 'A' and resid 220 through 227 Processing helix chain 'A' and resid 241 through 261 removed outlier: 3.813A pdb=" N LYS A 246 " --> pdb=" O VAL A 242 " (cutoff:3.500A) removed outlier: 3.501A pdb=" N ARG A 247 " --> pdb=" O PRO A 243 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 289 Processing helix chain 'A' and resid 294 through 310 removed outlier: 3.873A pdb=" N VAL A 299 " --> pdb=" O TYR A 296 " (cutoff:3.500A) removed outlier: 4.576A pdb=" N THR A 300 " --> pdb=" O LYS A 297 " (cutoff:3.500A) removed outlier: 3.989A pdb=" N ILE A 310 " --> pdb=" O GLY A 307 " (cutoff:3.500A) Processing helix chain 'A' and resid 345 through 347 No H-bonds generated for 'chain 'A' and resid 345 through 347' Processing helix chain 'A' and resid 354 through 362 Processing helix chain 'A' and resid 364 through 366 No H-bonds generated for 'chain 'A' and resid 364 through 366' Processing helix chain 'A' and resid 375 through 387 removed outlier: 3.918A pdb=" N LEU A 381 " --> pdb=" O GLN A 377 " (cutoff:3.500A) Processing helix chain 'A' and resid 393 through 414 Processing helix chain 'A' and resid 421 through 426 removed outlier: 3.713A pdb=" N SER A 426 " --> pdb=" O SER A 422 " (cutoff:3.500A) Processing helix chain 'A' and resid 432 through 454 removed outlier: 3.985A pdb=" N SER A 449 " --> pdb=" O PHE A 445 " (cutoff:3.500A) Proline residue: A 452 - end of helix Processing helix chain 'A' and resid 460 through 468 removed outlier: 4.248A pdb=" N SER A 467 " --> pdb=" O LYS A 463 " (cutoff:3.500A) removed outlier: 4.759A pdb=" N ILE A 468 " --> pdb=" O VAL A 464 " (cutoff:3.500A) Processing helix chain 'A' and resid 471 through 489 Proline residue: A 484 - end of helix Processing helix chain 'B' and resid 43 through 49 Processing helix chain 'B' and resid 53 through 74 removed outlier: 3.886A pdb=" N GLY B 65 " --> pdb=" O SER B 61 " (cutoff:3.500A) removed outlier: 4.815A pdb=" N TYR B 66 " --> pdb=" O ILE B 62 " (cutoff:3.500A) Proline residue: B 67 - end of helix removed outlier: 3.510A pdb=" N TYR B 74 " --> pdb=" O LEU B 70 " (cutoff:3.500A) Processing helix chain 'B' and resid 81 through 99 Processing helix chain 'B' and resid 103 through 119 removed outlier: 4.926A pdb=" N LEU B 112 " --> pdb=" O LEU B 109 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N ILE B 113 " --> pdb=" O CYS B 110 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N GLN B 114 " --> pdb=" O VAL B 111 " (cutoff:3.500A) removed outlier: 3.646A pdb=" N LEU B 118 " --> pdb=" O PHE B 115 " (cutoff:3.500A) Processing helix chain 'B' and resid 125 through 146 removed outlier: 3.564A pdb=" N PHE B 129 " --> pdb=" O VAL B 125 " (cutoff:3.500A) Processing helix chain 'B' and resid 156 through 176 Processing helix chain 'B' and resid 185 through 190 Processing helix chain 'B' and resid 198 through 205 Processing helix chain 'B' and resid 220 through 226 Processing helix chain 'B' and resid 241 through 261 removed outlier: 4.204A pdb=" N LYS B 246 " --> pdb=" O VAL B 242 " (cutoff:3.500A) removed outlier: 3.996A pdb=" N ARG B 247 " --> pdb=" O PRO B 243 " (cutoff:3.500A) Processing helix chain 'B' and resid 280 through 289 Processing helix chain 'B' and resid 294 through 310 removed outlier: 3.817A pdb=" N VAL B 299 " --> pdb=" O TYR B 296 " (cutoff:3.500A) removed outlier: 4.590A pdb=" N THR B 300 " --> pdb=" O LYS B 297 " (cutoff:3.500A) removed outlier: 3.860A pdb=" N ILE B 310 " --> pdb=" O GLY B 307 " (cutoff:3.500A) Processing helix chain 'B' and resid 355 through 362 Processing helix chain 'B' and resid 375 through 387 removed outlier: 4.109A pdb=" N LEU B 381 " --> pdb=" O GLN B 377 " (cutoff:3.500A) removed outlier: 4.268A pdb=" N PHE B 382 " --> pdb=" O ALA B 378 " (cutoff:3.500A) Processing helix chain 'B' and resid 393 through 414 Processing helix chain 'B' and resid 433 through 454 removed outlier: 4.019A pdb=" N SER B 449 " --> pdb=" O PHE B 445 " (cutoff:3.500A) Proline residue: B 452 - end of helix Processing helix chain 'B' and resid 458 through 468 removed outlier: 3.845A pdb=" N MET B 462 " --> pdb=" O TRP B 458 " (cutoff:3.500A) removed outlier: 4.221A pdb=" N SER B 467 " --> pdb=" O LYS B 463 " (cutoff:3.500A) removed outlier: 4.890A pdb=" N ILE B 468 " --> pdb=" O VAL B 464 " (cutoff:3.500A) Processing helix chain 'B' and resid 471 through 489 Proline residue: B 484 - end of helix 353 hydrogen bonds defined for protein. 963 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: 1.73 Time building geometry restraints manager: 3.41 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.31: 1068 1.31 - 1.44: 2330 1.44 - 1.56: 4154 1.56 - 1.69: 4 1.69 - 1.81: 76 Bond restraints: 7632 Sorted by residual: bond pdb=" C17 LAP B 601 " pdb=" N8 LAP B 601 " ideal model delta sigma weight residual 1.452 1.500 -0.048 2.00e-02 2.50e+03 5.71e+00 bond pdb=" C17 LAP A 601 " pdb=" N8 LAP A 601 " ideal model delta sigma weight residual 1.452 1.500 -0.048 2.00e-02 2.50e+03 5.64e+00 bond pdb=" C16 LAP A 601 " pdb=" C17 LAP A 601 " ideal model delta sigma weight residual 1.527 1.560 -0.033 2.00e-02 2.50e+03 2.75e+00 bond pdb=" C16 LAP B 601 " pdb=" C17 LAP B 601 " ideal model delta sigma weight residual 1.527 1.560 -0.033 2.00e-02 2.50e+03 2.65e+00 bond pdb=" C18 LAP A 601 " pdb=" N8 LAP A 601 " ideal model delta sigma weight residual 1.451 1.483 -0.032 2.00e-02 2.50e+03 2.58e+00 ... (remaining 7627 not shown) Histogram of bond angle deviations from ideal: 99.60 - 106.49: 200 106.49 - 113.38: 4009 113.38 - 120.28: 2987 120.28 - 127.17: 3083 127.17 - 134.06: 97 Bond angle restraints: 10376 Sorted by residual: angle pdb=" C SER B 272 " pdb=" N ASP B 273 " pdb=" CA ASP B 273 " ideal model delta sigma weight residual 121.54 128.14 -6.60 1.91e+00 2.74e-01 1.19e+01 angle pdb=" C ASN A 372 " pdb=" N LYS A 373 " pdb=" CA LYS A 373 " ideal model delta sigma weight residual 121.54 128.06 -6.52 1.91e+00 2.74e-01 1.16e+01 angle pdb=" C LYS A 154 " pdb=" N TRP A 155 " pdb=" CA TRP A 155 " ideal model delta sigma weight residual 120.63 125.89 -5.26 1.61e+00 3.86e-01 1.07e+01 angle pdb=" C17 LAP B 601 " pdb=" N8 LAP B 601 " pdb=" C18 LAP B 601 " ideal model delta sigma weight residual 109.47 119.17 -9.70 3.00e+00 1.11e-01 1.05e+01 angle pdb=" C17 LAP A 601 " pdb=" N8 LAP A 601 " pdb=" C18 LAP A 601 " ideal model delta sigma weight residual 109.47 119.14 -9.67 3.00e+00 1.11e-01 1.04e+01 ... (remaining 10371 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.14: 3665 14.14 - 28.29: 470 28.29 - 42.43: 180 42.43 - 56.57: 42 56.57 - 70.72: 9 Dihedral angle restraints: 4366 sinusoidal: 1730 harmonic: 2636 Sorted by residual: dihedral pdb=" CA TRP B 155 " pdb=" C TRP B 155 " pdb=" N THR B 156 " pdb=" CA THR B 156 " ideal model delta harmonic sigma weight residual 180.00 -162.04 -17.96 0 5.00e+00 4.00e-02 1.29e+01 dihedral pdb=" CA GLN B 431 " pdb=" C GLN B 431 " pdb=" N PRO B 432 " pdb=" CA PRO B 432 " ideal model delta harmonic sigma weight residual 180.00 162.10 17.90 0 5.00e+00 4.00e-02 1.28e+01 dihedral pdb=" CA TRP A 155 " pdb=" C TRP A 155 " pdb=" N THR A 156 " pdb=" CA THR A 156 " ideal model delta harmonic sigma weight residual -180.00 -162.61 -17.39 0 5.00e+00 4.00e-02 1.21e+01 ... (remaining 4363 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.040: 823 0.040 - 0.079: 265 0.079 - 0.119: 58 0.119 - 0.159: 4 0.159 - 0.199: 4 Chirality restraints: 1154 Sorted by residual: chirality pdb=" CB THR A 341 " pdb=" CA THR A 341 " pdb=" OG1 THR A 341 " pdb=" CG2 THR A 341 " both_signs ideal model delta sigma weight residual False 2.55 2.35 0.20 2.00e-01 2.50e+01 9.86e-01 chirality pdb=" CB THR B 341 " pdb=" CA THR B 341 " pdb=" OG1 THR B 341 " pdb=" CG2 THR B 341 " both_signs ideal model delta sigma weight residual False 2.55 2.37 0.18 2.00e-01 2.50e+01 8.53e-01 chirality pdb=" CA MET B 157 " pdb=" N MET B 157 " pdb=" C MET B 157 " pdb=" CB MET B 157 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.61e-01 ... (remaining 1151 not shown) Planarity restraints: 1250 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C VAL A 233 " 0.029 5.00e-02 4.00e+02 4.47e-02 3.19e+00 pdb=" N PRO A 234 " -0.077 5.00e-02 4.00e+02 pdb=" CA PRO A 234 " 0.023 5.00e-02 4.00e+02 pdb=" CD PRO A 234 " 0.025 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TRP B 302 " 0.008 2.00e-02 2.50e+03 1.61e-02 2.60e+00 pdb=" C TRP B 302 " -0.028 2.00e-02 2.50e+03 pdb=" O TRP B 302 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU B 303 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA TRP A 302 " 0.008 2.00e-02 2.50e+03 1.58e-02 2.50e+00 pdb=" C TRP A 302 " -0.027 2.00e-02 2.50e+03 pdb=" O TRP A 302 " 0.010 2.00e-02 2.50e+03 pdb=" N LEU A 303 " 0.009 2.00e-02 2.50e+03 ... (remaining 1247 not shown) Histogram of nonbonded interaction distances: 2.12 - 2.67: 77 2.67 - 3.23: 7390 3.23 - 3.79: 10759 3.79 - 4.34: 13788 4.34 - 4.90: 22287 Nonbonded interactions: 54301 Sorted by model distance: nonbonded pdb=" OG1 THR B 197 " pdb=" OE1 GLU B 200 " model vdw 2.117 2.440 nonbonded pdb=" OG1 THR A 197 " pdb=" OE1 GLU A 200 " model vdw 2.188 2.440 nonbonded pdb=" OH TYR B 448 " pdb=" OH TYR B 465 " model vdw 2.202 2.440 nonbonded pdb=" OH TYR A 448 " pdb=" OH TYR A 465 " model vdw 2.202 2.440 nonbonded pdb=" OE1 GLN A 135 " pdb=" OG1 THR A 163 " model vdw 2.252 2.440 ... (remaining 54296 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.770 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: 4.470 Check model and map are aligned: 0.110 Set scattering table: 0.070 Process input model: 23.660 Find NCS groups from input model: 0.360 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.730 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.220 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8060 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 0.048 7632 Z= 0.202 Angle : 0.669 9.698 10376 Z= 0.355 Chirality : 0.040 0.199 1154 Planarity : 0.004 0.045 1250 Dihedral : 15.049 70.717 2686 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 6.43 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.16 % Favored : 92.62 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.61 (0.30), residues: 894 helix: 0.66 (0.22), residues: 596 sheet: None (None), residues: 0 loop : -2.67 (0.36), residues: 298 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.001 TRP B 461 HIS 0.005 0.001 HIS A 106 PHE 0.012 0.001 PHE A 105 TYR 0.013 0.001 TYR B 82 ARG 0.002 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 162 time to evaluate : 0.783 Fit side-chains REVERT: A 124 THR cc_start: 0.8776 (t) cc_final: 0.8510 (p) REVERT: A 338 TYR cc_start: 0.8316 (t80) cc_final: 0.7976 (t80) REVERT: B 102 MET cc_start: 0.6755 (tpt) cc_final: 0.6301 (tpp) REVERT: B 338 TYR cc_start: 0.8313 (t80) cc_final: 0.8040 (t80) outliers start: 0 outliers final: 0 residues processed: 162 average time/residue: 0.1623 time to fit residues: 36.5905 Evaluate side-chains 127 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.812 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 74 optimal weight: 1.9990 chunk 66 optimal weight: 2.9990 chunk 37 optimal weight: 0.0870 chunk 22 optimal weight: 4.9990 chunk 44 optimal weight: 10.0000 chunk 35 optimal weight: 0.7980 chunk 68 optimal weight: 2.9990 chunk 26 optimal weight: 0.5980 chunk 41 optimal weight: 0.0570 chunk 51 optimal weight: 1.9990 chunk 79 optimal weight: 1.9990 overall best weight: 0.7078 ------------------------------------------------------------------------------- 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: 0.8103 moved from start: 0.0905 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7632 Z= 0.169 Angle : 0.611 9.180 10376 Z= 0.307 Chirality : 0.040 0.177 1154 Planarity : 0.004 0.045 1250 Dihedral : 7.071 52.179 1022 Min Nonbonded Distance : 2.095 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.49 % Favored : 92.28 % Rotamer: Outliers : 0.63 % Allowed : 10.98 % Favored : 88.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.13 (0.30), residues: 894 helix: 1.06 (0.22), residues: 610 sheet: None (None), residues: 0 loop : -2.73 (0.37), residues: 284 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 461 HIS 0.003 0.001 HIS B 388 PHE 0.016 0.001 PHE A 369 TYR 0.014 0.001 TYR A 174 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 145 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 140 time to evaluate : 0.867 Fit side-chains REVERT: B 102 MET cc_start: 0.6746 (tpt) cc_final: 0.6495 (tpp) REVERT: B 137 THR cc_start: 0.9150 (p) cc_final: 0.8942 (t) outliers start: 5 outliers final: 3 residues processed: 142 average time/residue: 0.1526 time to fit residues: 31.7749 Evaluate side-chains 131 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 128 time to evaluate : 0.823 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 248 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 44 optimal weight: 10.0000 chunk 24 optimal weight: 0.6980 chunk 66 optimal weight: 2.9990 chunk 54 optimal weight: 0.9980 chunk 22 optimal weight: 4.9990 chunk 80 optimal weight: 0.8980 chunk 86 optimal weight: 1.9990 chunk 71 optimal weight: 8.9990 chunk 79 optimal weight: 1.9990 chunk 27 optimal weight: 3.9990 chunk 64 optimal weight: 4.9990 overall best weight: 1.3184 ------------------------------------------------------------------------------- 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: 0.8185 moved from start: 0.1386 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7632 Z= 0.214 Angle : 0.607 6.922 10376 Z= 0.307 Chirality : 0.041 0.274 1154 Planarity : 0.004 0.045 1250 Dihedral : 6.464 54.547 1022 Min Nonbonded Distance : 2.093 Molprobity Statistics. All-atom Clashscore : 8.18 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.83 % Favored : 91.95 % Rotamer: Outliers : 1.39 % Allowed : 15.15 % Favored : 83.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.10 (0.30), residues: 894 helix: 1.08 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -2.73 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 461 HIS 0.004 0.001 HIS A 442 PHE 0.032 0.001 PHE B 105 TYR 0.013 0.001 TYR A 174 ARG 0.002 0.000 ARG A 193 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 152 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 141 time to evaluate : 0.901 Fit side-chains REVERT: B 102 MET cc_start: 0.7049 (tpt) cc_final: 0.6641 (tpp) outliers start: 11 outliers final: 9 residues processed: 148 average time/residue: 0.1512 time to fit residues: 32.0728 Evaluate side-chains 138 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 129 time to evaluate : 0.862 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 308 VAL Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 386 ILE Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 41 optimal weight: 1.9990 chunk 8 optimal weight: 0.9980 chunk 38 optimal weight: 7.9990 chunk 53 optimal weight: 0.9990 chunk 80 optimal weight: 0.8980 chunk 85 optimal weight: 0.3980 chunk 76 optimal weight: 1.9990 chunk 22 optimal weight: 2.9990 chunk 70 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.1576 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 7632 Z= 0.166 Angle : 0.580 7.203 10376 Z= 0.294 Chirality : 0.041 0.273 1154 Planarity : 0.004 0.044 1250 Dihedral : 6.317 53.288 1022 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.31 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.05 % Favored : 92.73 % Rotamer: Outliers : 1.89 % Allowed : 16.41 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.02 (0.30), residues: 894 helix: 1.14 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -2.70 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP B 461 HIS 0.002 0.001 HIS A 388 PHE 0.021 0.001 PHE B 105 TYR 0.012 0.001 TYR B 82 ARG 0.001 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 145 time to evaluate : 0.890 Fit side-chains REVERT: A 164 LEU cc_start: 0.8497 (OUTLIER) cc_final: 0.8246 (tt) REVERT: A 403 LEU cc_start: 0.9013 (tp) cc_final: 0.8746 (tp) REVERT: B 102 MET cc_start: 0.6964 (tpt) cc_final: 0.6650 (tpp) REVERT: B 164 LEU cc_start: 0.8616 (OUTLIER) cc_final: 0.8402 (tt) outliers start: 15 outliers final: 10 residues processed: 155 average time/residue: 0.1398 time to fit residues: 32.0406 Evaluate side-chains 152 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 140 time to evaluate : 0.668 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 164 LEU Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 TRP Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 48 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 63 optimal weight: 6.9990 chunk 35 optimal weight: 0.6980 chunk 72 optimal weight: 0.9990 chunk 58 optimal weight: 1.9990 chunk 0 optimal weight: 5.9990 chunk 43 optimal weight: 3.9990 chunk 76 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 28 optimal weight: 0.3980 overall best weight: 0.7582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8150 moved from start: 0.1739 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 7632 Z= 0.161 Angle : 0.588 10.798 10376 Z= 0.294 Chirality : 0.041 0.208 1154 Planarity : 0.004 0.043 1250 Dihedral : 6.230 53.155 1022 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.38 % Favored : 92.39 % Rotamer: Outliers : 1.89 % Allowed : 18.31 % Favored : 79.80 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.06 (0.30), residues: 894 helix: 1.23 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -2.74 (0.37), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP A 443 HIS 0.002 0.001 HIS B 388 PHE 0.029 0.001 PHE B 105 TYR 0.012 0.001 TYR B 82 ARG 0.001 0.000 ARG A 409 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 149 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.850 Fit side-chains REVERT: A 403 LEU cc_start: 0.8964 (tp) cc_final: 0.8738 (tp) REVERT: B 102 MET cc_start: 0.7010 (tpt) cc_final: 0.6792 (tpp) REVERT: B 164 LEU cc_start: 0.8595 (OUTLIER) cc_final: 0.8333 (tt) outliers start: 15 outliers final: 11 residues processed: 141 average time/residue: 0.1424 time to fit residues: 29.5074 Evaluate side-chains 145 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 133 time to evaluate : 0.855 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 386 ILE Chi-restraints excluded: chain B residue 461 TRP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 76 optimal weight: 3.9990 chunk 16 optimal weight: 3.9990 chunk 49 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 85 optimal weight: 0.0070 chunk 70 optimal weight: 0.8980 chunk 39 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 10.0000 chunk 82 optimal weight: 0.7980 overall best weight: 0.7200 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8144 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.024 7632 Z= 0.155 Angle : 0.580 9.167 10376 Z= 0.290 Chirality : 0.040 0.179 1154 Planarity : 0.004 0.043 1250 Dihedral : 6.164 53.563 1022 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 7.64 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.61 % Favored : 92.17 % Rotamer: Outliers : 2.40 % Allowed : 19.95 % Favored : 77.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.17 (0.30), residues: 894 helix: 1.31 (0.22), residues: 612 sheet: None (None), residues: 0 loop : -2.70 (0.36), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 461 HIS 0.002 0.001 HIS A 388 PHE 0.027 0.001 PHE B 105 TYR 0.012 0.001 TYR A 82 ARG 0.001 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 162 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 143 time to evaluate : 0.858 Fit side-chains REVERT: B 102 MET cc_start: 0.7013 (tpt) cc_final: 0.6791 (tpt) REVERT: B 164 LEU cc_start: 0.8579 (OUTLIER) cc_final: 0.8325 (tt) REVERT: B 465 TYR cc_start: 0.8690 (OUTLIER) cc_final: 0.8428 (t80) REVERT: B 466 LYS cc_start: 0.8932 (ttpp) cc_final: 0.8721 (tttt) outliers start: 19 outliers final: 11 residues processed: 155 average time/residue: 0.1462 time to fit residues: 33.0148 Evaluate side-chains 150 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 137 time to evaluate : 0.781 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 TRP Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 9 optimal weight: 0.9980 chunk 48 optimal weight: 0.8980 chunk 62 optimal weight: 2.9990 chunk 71 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 84 optimal weight: 4.9990 chunk 53 optimal weight: 0.9990 chunk 51 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 52 optimal weight: 0.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.9786 ------------------------------------------------------------------------------- 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: 0.8163 moved from start: 0.1955 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7632 Z= 0.180 Angle : 0.611 8.635 10376 Z= 0.300 Chirality : 0.041 0.189 1154 Planarity : 0.004 0.043 1250 Dihedral : 6.183 54.541 1022 Min Nonbonded Distance : 2.103 Molprobity Statistics. All-atom Clashscore : 8.04 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.05 % Favored : 91.72 % Rotamer: Outliers : 2.27 % Allowed : 20.58 % Favored : 77.15 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.27 (0.30), residues: 894 helix: 1.38 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.54 (0.36), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 461 HIS 0.002 0.001 HIS B 442 PHE 0.025 0.001 PHE B 105 TYR 0.012 0.001 TYR A 82 ARG 0.001 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 160 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 142 time to evaluate : 0.894 Fit side-chains REVERT: A 465 TYR cc_start: 0.8803 (OUTLIER) cc_final: 0.8432 (t80) REVERT: B 102 MET cc_start: 0.7035 (tpt) cc_final: 0.6823 (tpt) REVERT: B 106 HIS cc_start: 0.7860 (OUTLIER) cc_final: 0.7371 (t-90) REVERT: B 164 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8347 (tt) REVERT: B 465 TYR cc_start: 0.8745 (OUTLIER) cc_final: 0.8514 (t80) REVERT: B 466 LYS cc_start: 0.8941 (ttpp) cc_final: 0.8726 (tttt) outliers start: 18 outliers final: 12 residues processed: 153 average time/residue: 0.1474 time to fit residues: 33.0017 Evaluate side-chains 151 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 135 time to evaluate : 0.898 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 221 ASP Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 TRP Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 50 optimal weight: 0.9990 chunk 25 optimal weight: 1.9990 chunk 16 optimal weight: 3.9990 chunk 53 optimal weight: 0.8980 chunk 57 optimal weight: 4.9990 chunk 41 optimal weight: 0.7980 chunk 7 optimal weight: 0.9990 chunk 66 optimal weight: 0.0020 chunk 77 optimal weight: 6.9990 chunk 81 optimal weight: 6.9990 chunk 74 optimal weight: 2.9990 overall best weight: 0.7392 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 99 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8146 moved from start: 0.2048 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 7632 Z= 0.161 Angle : 0.609 11.299 10376 Z= 0.297 Chirality : 0.040 0.188 1154 Planarity : 0.004 0.043 1250 Dihedral : 6.160 54.651 1022 Min Nonbonded Distance : 2.110 Molprobity Statistics. All-atom Clashscore : 8.24 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.38 % Favored : 92.39 % Rotamer: Outliers : 2.40 % Allowed : 21.34 % Favored : 76.26 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 894 helix: 1.39 (0.22), residues: 604 sheet: None (None), residues: 0 loop : -2.50 (0.37), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 443 HIS 0.002 0.001 HIS A 388 PHE 0.027 0.001 PHE B 105 TYR 0.012 0.001 TYR B 82 ARG 0.001 0.000 ARG B 237 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 161 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 142 time to evaluate : 0.839 Fit side-chains REVERT: A 465 TYR cc_start: 0.8819 (OUTLIER) cc_final: 0.8509 (t80) REVERT: A 466 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8689 (tttt) REVERT: B 102 MET cc_start: 0.7109 (tpt) cc_final: 0.6903 (tpt) REVERT: B 106 HIS cc_start: 0.7837 (OUTLIER) cc_final: 0.7346 (t-90) REVERT: B 164 LEU cc_start: 0.8594 (OUTLIER) cc_final: 0.8340 (tt) REVERT: B 465 TYR cc_start: 0.8748 (OUTLIER) cc_final: 0.8471 (t80) outliers start: 19 outliers final: 11 residues processed: 154 average time/residue: 0.1610 time to fit residues: 35.7126 Evaluate side-chains 149 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 134 time to evaluate : 0.841 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 TRP Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 79 optimal weight: 0.3980 chunk 81 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 34 optimal weight: 3.9990 chunk 62 optimal weight: 5.9990 chunk 24 optimal weight: 1.9990 chunk 71 optimal weight: 3.9990 chunk 74 optimal weight: 0.3980 chunk 78 optimal weight: 0.4980 chunk 51 optimal weight: 0.8980 chunk 83 optimal weight: 2.9990 overall best weight: 0.8382 ------------------------------------------------------------------------------- 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: 0.8156 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 7632 Z= 0.172 Angle : 0.627 10.990 10376 Z= 0.308 Chirality : 0.042 0.285 1154 Planarity : 0.004 0.043 1250 Dihedral : 6.162 55.215 1022 Min Nonbonded Distance : 2.106 Molprobity Statistics. All-atom Clashscore : 8.58 Ramachandran Plot: Outliers : 0.22 % Allowed : 8.17 % Favored : 91.61 % Rotamer: Outliers : 2.15 % Allowed : 21.97 % Favored : 75.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.26 (0.30), residues: 894 helix: 1.30 (0.22), residues: 616 sheet: None (None), residues: 0 loop : -2.51 (0.38), residues: 278 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 461 HIS 0.002 0.001 HIS B 442 PHE 0.026 0.001 PHE B 105 TYR 0.011 0.001 TYR B 82 ARG 0.001 0.000 ARG A 188 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 155 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 138 time to evaluate : 1.060 Fit side-chains REVERT: A 465 TYR cc_start: 0.8838 (OUTLIER) cc_final: 0.8502 (t80) REVERT: A 466 LYS cc_start: 0.8927 (ttpp) cc_final: 0.8707 (tttt) REVERT: B 102 MET cc_start: 0.7124 (tpt) cc_final: 0.6906 (tpt) REVERT: B 106 HIS cc_start: 0.7885 (OUTLIER) cc_final: 0.7436 (t-90) REVERT: B 164 LEU cc_start: 0.8600 (OUTLIER) cc_final: 0.8333 (tt) REVERT: B 465 TYR cc_start: 0.8789 (OUTLIER) cc_final: 0.8555 (t80) outliers start: 17 outliers final: 12 residues processed: 148 average time/residue: 0.1623 time to fit residues: 34.9754 Evaluate side-chains 153 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 137 time to evaluate : 0.830 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 221 ASP Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 164 LEU Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 266 SER Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 310 ILE Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 TRP Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 51 optimal weight: 0.9980 chunk 39 optimal weight: 0.3980 chunk 58 optimal weight: 0.9990 chunk 87 optimal weight: 0.8980 chunk 80 optimal weight: 0.8980 chunk 69 optimal weight: 1.9990 chunk 7 optimal weight: 1.9990 chunk 53 optimal weight: 0.6980 chunk 42 optimal weight: 2.9990 chunk 55 optimal weight: 0.0980 chunk 74 optimal weight: 0.0270 overall best weight: 0.4238 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 439 GLN B 99 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8105 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 7632 Z= 0.144 Angle : 0.617 11.285 10376 Z= 0.300 Chirality : 0.040 0.235 1154 Planarity : 0.004 0.043 1250 Dihedral : 6.079 54.969 1022 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 8.65 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.27 % Favored : 92.51 % Rotamer: Outliers : 2.27 % Allowed : 21.72 % Favored : 76.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.29 (0.30), residues: 894 helix: 1.32 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -2.49 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 443 HIS 0.002 0.000 HIS A 106 PHE 0.025 0.001 PHE B 105 TYR 0.011 0.001 TYR A 82 ARG 0.001 0.000 ARG A 188 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1788 Ramachandran restraints generated. 894 Oldfield, 0 Emsley, 894 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 169 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 151 time to evaluate : 0.932 Fit side-chains REVERT: A 172 ASP cc_start: 0.8038 (t70) cc_final: 0.7739 (t0) REVERT: A 465 TYR cc_start: 0.8810 (OUTLIER) cc_final: 0.8562 (t80) REVERT: A 466 LYS cc_start: 0.8924 (ttpp) cc_final: 0.8701 (tttt) REVERT: B 106 HIS cc_start: 0.7915 (OUTLIER) cc_final: 0.7470 (t-90) REVERT: B 172 ASP cc_start: 0.7854 (t70) cc_final: 0.7532 (t0) REVERT: B 173 TYR cc_start: 0.7697 (t80) cc_final: 0.7417 (t80) REVERT: B 465 TYR cc_start: 0.8780 (OUTLIER) cc_final: 0.8550 (t80) outliers start: 18 outliers final: 10 residues processed: 161 average time/residue: 0.1453 time to fit residues: 34.2963 Evaluate side-chains 161 residues out of total 792 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 148 time to evaluate : 0.814 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 153 ILE Chi-restraints excluded: chain A residue 155 TRP Chi-restraints excluded: chain A residue 195 VAL Chi-restraints excluded: chain A residue 256 VAL Chi-restraints excluded: chain A residue 309 CYS Chi-restraints excluded: chain A residue 461 TRP Chi-restraints excluded: chain A residue 465 TYR Chi-restraints excluded: chain B residue 106 HIS Chi-restraints excluded: chain B residue 248 LEU Chi-restraints excluded: chain B residue 308 VAL Chi-restraints excluded: chain B residue 370 LEU Chi-restraints excluded: chain B residue 461 TRP Chi-restraints excluded: chain B residue 465 TYR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 88 random chunks: chunk 21 optimal weight: 0.9980 chunk 64 optimal weight: 0.0980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 2.9990 chunk 69 optimal weight: 0.5980 chunk 29 optimal weight: 0.0670 chunk 71 optimal weight: 6.9990 chunk 8 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 61 optimal weight: 2.9990 chunk 3 optimal weight: 4.9990 overall best weight: 0.5518 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 216 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3737 r_free = 0.3737 target = 0.135956 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 47)----------------| | r_work = 0.3273 r_free = 0.3273 target = 0.101497 restraints weight = 12531.270| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 37)----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.105461 restraints weight = 6909.623| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 40)----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.108168 restraints weight = 4918.914| |-----------------------------------------------------------------------------| r_work (final): 0.3364 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7800 moved from start: 0.2255 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 7632 Z= 0.161 Angle : 0.640 11.306 10376 Z= 0.311 Chirality : 0.041 0.228 1154 Planarity : 0.004 0.043 1250 Dihedral : 6.050 55.823 1022 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.22 % Allowed : 7.49 % Favored : 92.28 % Rotamer: Outliers : 1.64 % Allowed : 22.98 % Favored : 75.38 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.35 (0.30), residues: 894 helix: 1.38 (0.22), residues: 614 sheet: None (None), residues: 0 loop : -2.48 (0.37), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP B 443 HIS 0.002 0.001 HIS A 106 PHE 0.025 0.001 PHE B 105 TYR 0.011 0.001 TYR B 82 ARG 0.001 0.000 ARG A 188 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1670.01 seconds wall clock time: 31 minutes 30.27 seconds (1890.27 seconds total)