Starting phenix.real_space_refine on Fri Apr 5 16:55:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtz_36657/04_2024/8jtz_36657_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtz_36657/04_2024/8jtz_36657.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.27 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtz_36657/04_2024/8jtz_36657.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtz_36657/04_2024/8jtz_36657.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtz_36657/04_2024/8jtz_36657_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8jtz_36657/04_2024/8jtz_36657_updated.pdb" } resolution = 3.27 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= 0.001 sd= 0.086 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 34 5.16 5 C 2620 2.51 5 N 650 2.21 5 O 695 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 68": "OE1" <-> "OE2" Residue "A TYR 127": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 168": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 244": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 279": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 336": "OD1" <-> "OD2" Residue "A PHE 348": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3999 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3970 Number of conformers: 1 Conformer: "" Number of residues, atoms: 530, 3970 Classifications: {'peptide': 530} Incomplete info: {'truncation_to_alanine': 38} Link IDs: {'PTRANS': 27, 'TRANS': 502} Unresolved non-hydrogen bonds: 146 Unresolved non-hydrogen angles: 190 Unresolved non-hydrogen dihedrals: 123 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 2, 'HIS:plan': 2, 'TYR:plan': 1, 'ASN:plan1': 1, 'TRP:plan': 2, 'ASP:plan': 5, 'GLU:plan': 4, 'ARG:plan': 3} Unresolved non-hydrogen planarities: 92 Chain: "A" Number of atoms: 29 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 29 Unusual residues: {'SNL': 1} Classifications: {'undetermined': 1} Time building chain proxies: 2.80, per 1000 atoms: 0.70 Number of scatterers: 3999 At special positions: 0 Unit cell: (111.498, 55.2075, 66.0325, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 34 16.00 O 695 8.00 N 650 7.00 C 2620 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=3, symmetry=0 Simple disulfide: pdb=" SG CYS A 50 " - pdb=" SG CYS A 121 " distance=2.03 Simple disulfide: pdb=" SG CYS A 62 " - pdb=" SG CYS A 102 " distance=2.03 Simple disulfide: pdb=" SG CYS A 88 " - pdb=" SG CYS A 142 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.75 Conformation dependent library (CDL) restraints added in 762.7 milliseconds 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 974 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 21 helices and 1 sheets defined 66.2% alpha, 0.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.84 Creating SS restraints... Processing helix chain 'A' and resid 4 through 11 Processing helix chain 'A' and resid 16 through 30 removed outlier: 4.391A pdb=" N LEU A 28 " --> pdb=" O ILE A 24 " (cutoff:3.500A) removed outlier: 4.067A pdb=" N SER A 29 " --> pdb=" O LEU A 25 " (cutoff:3.500A) Processing helix chain 'A' and resid 33 through 42 removed outlier: 5.769A pdb=" N ILE A 39 " --> pdb=" O ILE A 35 " (cutoff:3.500A) removed outlier: 6.697A pdb=" N VAL A 40 " --> pdb=" O CYS A 36 " (cutoff:3.500A) removed outlier: 4.772A pdb=" N PHE A 41 " --> pdb=" O VAL A 37 " (cutoff:3.500A) Processing helix chain 'A' and resid 53 through 62 removed outlier: 3.700A pdb=" N GLU A 57 " --> pdb=" O PRO A 53 " (cutoff:3.500A) Processing helix chain 'A' and resid 66 through 73 Processing helix chain 'A' and resid 84 through 87 No H-bonds generated for 'chain 'A' and resid 84 through 87' Processing helix chain 'A' and resid 134 through 138 Processing helix chain 'A' and resid 145 through 193 removed outlier: 3.508A pdb=" N ASP A 149 " --> pdb=" O TRP A 146 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 158 " --> pdb=" O LEU A 155 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N PHE A 161 " --> pdb=" O GLY A 158 " (cutoff:3.500A) removed outlier: 3.574A pdb=" N GLY A 162 " --> pdb=" O PHE A 159 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N GLY A 165 " --> pdb=" O GLY A 162 " (cutoff:3.500A) removed outlier: 3.640A pdb=" N VAL A 166 " --> pdb=" O SER A 163 " (cutoff:3.500A) removed outlier: 4.158A pdb=" N PHE A 173 " --> pdb=" O ALA A 170 " (cutoff:3.500A) removed outlier: 4.290A pdb=" N GLY A 174 " --> pdb=" O ASP A 171 " (cutoff:3.500A) removed outlier: 7.267A pdb=" N ARG A 175 " --> pdb=" O ARG A 172 " (cutoff:3.500A) removed outlier: 5.214A pdb=" N LYS A 176 " --> pdb=" O PHE A 173 " (cutoff:3.500A) removed outlier: 4.227A pdb=" N LEU A 177 " --> pdb=" O GLY A 174 " (cutoff:3.500A) removed outlier: 3.641A pdb=" N THR A 182 " --> pdb=" O LEU A 179 " (cutoff:3.500A) removed outlier: 3.734A pdb=" N LEU A 192 " --> pdb=" O SER A 189 " (cutoff:3.500A) Processing helix chain 'A' and resid 199 through 227 removed outlier: 4.459A pdb=" N LYS A 214 " --> pdb=" O GLY A 210 " (cutoff:3.500A) removed outlier: 4.898A pdb=" N GLY A 215 " --> pdb=" O LEU A 211 " (cutoff:3.500A) Processing helix chain 'A' and resid 233 through 257 removed outlier: 3.696A pdb=" N MET A 239 " --> pdb=" O THR A 235 " (cutoff:3.500A) removed outlier: 4.208A pdb=" N GLN A 241 " --> pdb=" O ALA A 237 " (cutoff:3.500A) removed outlier: 3.733A pdb=" N MET A 242 " --> pdb=" O ILE A 238 " (cutoff:3.500A) removed outlier: 3.704A pdb=" N ALA A 243 " --> pdb=" O MET A 239 " (cutoff:3.500A) removed outlier: 3.872A pdb=" N PHE A 244 " --> pdb=" O TYR A 240 " (cutoff:3.500A) Processing helix chain 'A' and resid 261 through 268 Processing helix chain 'A' and resid 270 through 277 Processing helix chain 'A' and resid 286 through 292 Processing helix chain 'A' and resid 295 through 309 Processing helix chain 'A' and resid 341 through 367 Processing helix chain 'A' and resid 375 through 396 removed outlier: 3.829A pdb=" N VAL A 385 " --> pdb=" O TYR A 381 " (cutoff:3.500A) removed outlier: 4.887A pdb=" N GLU A 386 " --> pdb=" O SER A 382 " (cutoff:3.500A) removed outlier: 4.793A pdb=" N ILE A 387 " --> pdb=" O ALA A 383 " (cutoff:3.500A) Proline residue: A 388 - end of helix Processing helix chain 'A' and resid 404 through 419 Processing helix chain 'A' and resid 428 through 455 removed outlier: 3.686A pdb=" N ALA A 454 " --> pdb=" O CYS A 450 " (cutoff:3.500A) Processing helix chain 'A' and resid 459 through 490 removed outlier: 6.377A pdb=" N ASN A 463 " --> pdb=" O PHE A 460 " (cutoff:3.500A) removed outlier: 3.546A pdb=" N GLY A 465 " --> pdb=" O ARG A 462 " (cutoff:3.500A) removed outlier: 3.616A pdb=" N SER A 470 " --> pdb=" O MET A 467 " (cutoff:3.500A) removed outlier: 4.113A pdb=" N LEU A 472 " --> pdb=" O CYS A 469 " (cutoff:3.500A) removed outlier: 3.633A pdb=" N ASP A 474 " --> pdb=" O SER A 471 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N ILE A 475 " --> pdb=" O LEU A 472 " (cutoff:3.500A) removed outlier: 3.533A pdb=" N ILE A 479 " --> pdb=" O GLY A 476 " (cutoff:3.500A) removed outlier: 4.125A pdb=" N THR A 480 " --> pdb=" O GLY A 477 " (cutoff:3.500A) Proline residue: A 481 - end of helix removed outlier: 3.590A pdb=" N VAL A 484 " --> pdb=" O PRO A 481 " (cutoff:3.500A) removed outlier: 3.520A pdb=" N ARG A 486 " --> pdb=" O ILE A 483 " (cutoff:3.500A) removed outlier: 3.602A pdb=" N LEU A 487 " --> pdb=" O VAL A 484 " (cutoff:3.500A) Processing helix chain 'A' and resid 494 through 512 removed outlier: 4.226A pdb=" N LEU A 511 " --> pdb=" O ALA A 507 " (cutoff:3.500A) removed outlier: 4.779A pdb=" N LEU A 512 " --> pdb=" O GLY A 508 " (cutoff:3.500A) Processing helix chain 'A' and resid 525 through 530 removed outlier: 3.624A pdb=" N GLU A 529 " --> pdb=" O MET A 525 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 48 through 50 removed outlier: 3.723A pdb=" N HIS A 49 " --> pdb=" O VAL A 126 " (cutoff:3.500A) removed outlier: 3.529A pdb=" N VAL A 126 " --> pdb=" O HIS A 49 " (cutoff:3.500A) No H-bonds generated for sheet with id= A 219 hydrogen bonds defined for protein. 513 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: 1.29 Time building geometry restraints manager: 1.85 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.18 - 1.31: 625 1.31 - 1.44: 1085 1.44 - 1.57: 2338 1.57 - 1.69: 2 1.69 - 1.82: 50 Bond restraints: 4100 Sorted by residual: bond pdb=" C15 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 1.332 1.553 -0.221 2.00e-02 2.50e+03 1.22e+02 bond pdb=" C22 SNL A 601 " pdb=" S61 SNL A 601 " ideal model delta sigma weight residual 1.829 1.676 0.153 2.00e-02 2.50e+03 5.86e+01 bond pdb=" C16 SNL A 601 " pdb=" S61 SNL A 601 " ideal model delta sigma weight residual 1.767 1.677 0.090 2.00e-02 2.50e+03 2.02e+01 bond pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 1.443 1.527 -0.084 2.00e-02 2.50e+03 1.75e+01 bond pdb=" C18 SNL A 601 " pdb=" C19 SNL A 601 " ideal model delta sigma weight residual 1.463 1.536 -0.073 2.00e-02 2.50e+03 1.34e+01 ... (remaining 4095 not shown) Histogram of bond angle deviations from ideal: 97.51 - 104.81: 100 104.81 - 112.11: 2010 112.11 - 119.42: 1384 119.42 - 126.72: 2033 126.72 - 134.02: 76 Bond angle restraints: 5603 Sorted by residual: angle pdb=" C13 SNL A 601 " pdb=" C9 SNL A 601 " pdb=" C5 SNL A 601 " ideal model delta sigma weight residual 116.85 133.07 -16.22 3.00e+00 1.11e-01 2.92e+01 angle pdb=" C8 SNL A 601 " pdb=" C9 SNL A 601 " pdb=" O58 SNL A 601 " ideal model delta sigma weight residual 111.01 97.51 13.50 3.00e+00 1.11e-01 2.03e+01 angle pdb=" N CYS A 26 " pdb=" CA CYS A 26 " pdb=" C CYS A 26 " ideal model delta sigma weight residual 113.01 108.27 4.74 1.20e+00 6.94e-01 1.56e+01 angle pdb=" N GLU A 529 " pdb=" CA GLU A 529 " pdb=" C GLU A 529 " ideal model delta sigma weight residual 112.54 107.82 4.72 1.22e+00 6.72e-01 1.50e+01 angle pdb=" CB MET A 448 " pdb=" CG MET A 448 " pdb=" SD MET A 448 " ideal model delta sigma weight residual 112.70 123.89 -11.19 3.00e+00 1.11e-01 1.39e+01 ... (remaining 5598 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.28: 2152 17.28 - 34.57: 229 34.57 - 51.85: 66 51.85 - 69.13: 13 69.13 - 86.42: 2 Dihedral angle restraints: 2462 sinusoidal: 944 harmonic: 1518 Sorted by residual: dihedral pdb=" CB CYS A 50 " pdb=" SG CYS A 50 " pdb=" SG CYS A 121 " pdb=" CB CYS A 121 " ideal model delta sinusoidal sigma weight residual -86.00 -137.58 51.58 1 1.00e+01 1.00e-02 3.63e+01 dihedral pdb=" CA VAL A 461 " pdb=" C VAL A 461 " pdb=" N ARG A 462 " pdb=" CA ARG A 462 " ideal model delta harmonic sigma weight residual -180.00 -158.37 -21.63 0 5.00e+00 4.00e-02 1.87e+01 dihedral pdb=" CB CYS A 88 " pdb=" SG CYS A 88 " pdb=" SG CYS A 142 " pdb=" CB CYS A 142 " ideal model delta sinusoidal sigma weight residual 93.00 126.86 -33.86 1 1.00e+01 1.00e-02 1.63e+01 ... (remaining 2459 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.140: 650 0.140 - 0.280: 7 0.280 - 0.420: 0 0.420 - 0.560: 0 0.560 - 0.700: 2 Chirality restraints: 659 Sorted by residual: chirality pdb=" C9 SNL A 601 " pdb=" C13 SNL A 601 " pdb=" C5 SNL A 601 " pdb=" C8 SNL A 601 " both_signs ideal model delta sigma weight residual False -2.67 -1.97 -0.70 2.00e-01 2.50e+01 1.22e+01 chirality pdb=" C2 SNL A 601 " pdb=" C1 SNL A 601 " pdb=" C20 SNL A 601 " pdb=" C24 SNL A 601 " both_signs ideal model delta sigma weight residual False -2.82 -2.22 -0.59 2.00e-01 2.50e+01 8.84e+00 chirality pdb=" CG LEU A 192 " pdb=" CB LEU A 192 " pdb=" CD1 LEU A 192 " pdb=" CD2 LEU A 192 " both_signs ideal model delta sigma weight residual False -2.59 -2.35 -0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 656 not shown) Planarity restraints: 699 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 340 " -0.035 5.00e-02 4.00e+02 5.25e-02 4.41e+00 pdb=" N PRO A 341 " 0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 341 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 341 " -0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 279 " -0.008 2.00e-02 2.50e+03 1.37e-02 3.76e+00 pdb=" CG TYR A 279 " 0.033 2.00e-02 2.50e+03 pdb=" CD1 TYR A 279 " -0.013 2.00e-02 2.50e+03 pdb=" CD2 TYR A 279 " -0.014 2.00e-02 2.50e+03 pdb=" CE1 TYR A 279 " 0.000 2.00e-02 2.50e+03 pdb=" CE2 TYR A 279 " 0.002 2.00e-02 2.50e+03 pdb=" CZ TYR A 279 " -0.000 2.00e-02 2.50e+03 pdb=" OH TYR A 279 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA A 393 " 0.009 2.00e-02 2.50e+03 1.76e-02 3.09e+00 pdb=" C ALA A 393 " -0.030 2.00e-02 2.50e+03 pdb=" O ALA A 393 " 0.011 2.00e-02 2.50e+03 pdb=" N LEU A 394 " 0.010 2.00e-02 2.50e+03 ... (remaining 696 not shown) Histogram of nonbonded interaction distances: 2.24 - 2.77: 784 2.77 - 3.30: 3876 3.30 - 3.84: 6905 3.84 - 4.37: 7541 4.37 - 4.90: 13239 Nonbonded interactions: 32345 Sorted by model distance: nonbonded pdb=" O GLY A 476 " pdb=" OG1 THR A 480 " model vdw 2.239 2.440 nonbonded pdb=" NH1 ARG A 486 " pdb=" OE1 GLU A 489 " model vdw 2.356 2.520 nonbonded pdb=" O THR A 516 " pdb=" OG1 THR A 516 " model vdw 2.378 2.440 nonbonded pdb=" OD1 ASN A 186 " pdb=" OG SER A 213 " model vdw 2.384 2.440 nonbonded pdb=" NH2 ARG A 233 " pdb=" O VAL A 519 " model vdw 2.412 2.520 ... (remaining 32340 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. 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: 0.350 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: 0.000 Extract box with map and model: 1.960 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 16.240 Find NCS groups from input model: 0.100 Set up NCS constraints: 0.030 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:2.990 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.760 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7086 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 : 0.006 0.221 4100 Z= 0.425 Angle : 0.904 16.225 5603 Z= 0.433 Chirality : 0.057 0.700 659 Planarity : 0.005 0.052 699 Dihedral : 15.420 86.417 1479 Min Nonbonded Distance : 2.239 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.25 % Allowed : 22.17 % Favored : 77.59 % 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: -1.05 (0.34), residues: 528 helix: -0.20 (0.25), residues: 374 sheet: None (None), residues: 0 loop : -1.69 (0.47), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 354 HIS 0.003 0.001 HIS A 48 PHE 0.009 0.001 PHE A 44 TYR 0.033 0.002 TYR A 279 ARG 0.004 0.001 ARG A 339 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 68 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.425 Fit side-chains REVERT: A 173 PHE cc_start: 0.8210 (m-80) cc_final: 0.7963 (m-80) REVERT: A 368 MET cc_start: 0.7095 (tpp) cc_final: 0.6661 (tpp) outliers start: 1 outliers final: 1 residues processed: 68 average time/residue: 0.1728 time to fit residues: 14.6917 Evaluate side-chains 63 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 62 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 227 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 21 optimal weight: 0.6980 chunk 41 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 25 optimal weight: 1.9990 chunk 30 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 453 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7219 moved from start: 0.1270 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4100 Z= 0.215 Angle : 0.534 5.812 5603 Z= 0.268 Chirality : 0.036 0.119 659 Planarity : 0.005 0.043 699 Dihedral : 4.875 57.702 638 Min Nonbonded Distance : 2.310 Molprobity Statistics. All-atom Clashscore : 7.53 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 2.96 % Allowed : 20.69 % Favored : 76.35 % 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: -0.24 (0.37), residues: 528 helix: 0.36 (0.27), residues: 373 sheet: None (None), residues: 0 loop : -1.24 (0.52), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 146 HIS 0.003 0.001 HIS A 48 PHE 0.011 0.001 PHE A 159 TYR 0.007 0.001 TYR A 279 ARG 0.002 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 77 time to evaluate : 0.450 Fit side-chains REVERT: A 368 MET cc_start: 0.7102 (tpp) cc_final: 0.6642 (tpp) REVERT: A 408 MET cc_start: 0.3726 (OUTLIER) cc_final: 0.3194 (ttt) outliers start: 12 outliers final: 5 residues processed: 85 average time/residue: 0.1474 time to fit residues: 15.9939 Evaluate side-chains 78 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 72 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 26 optimal weight: 2.9990 chunk 14 optimal weight: 0.3980 chunk 40 optimal weight: 1.9990 chunk 32 optimal weight: 6.9990 chunk 13 optimal weight: 0.5980 chunk 48 optimal weight: 2.9990 chunk 52 optimal weight: 2.9990 chunk 42 optimal weight: 0.6980 chunk 47 optimal weight: 3.9990 chunk 16 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7242 moved from start: 0.1693 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 4100 Z= 0.193 Angle : 0.519 5.695 5603 Z= 0.255 Chirality : 0.036 0.135 659 Planarity : 0.005 0.044 699 Dihedral : 4.144 36.194 636 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 2.96 % Allowed : 22.17 % Favored : 74.88 % 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: 0.04 (0.38), residues: 528 helix: 0.61 (0.28), residues: 375 sheet: None (None), residues: 0 loop : -1.27 (0.52), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 261 HIS 0.002 0.001 HIS A 48 PHE 0.010 0.001 PHE A 227 TYR 0.011 0.001 TYR A 168 ARG 0.002 0.000 ARG A 61 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 70 time to evaluate : 0.416 Fit side-chains REVERT: A 368 MET cc_start: 0.7066 (tpp) cc_final: 0.6629 (tpp) outliers start: 12 outliers final: 6 residues processed: 76 average time/residue: 0.1536 time to fit residues: 14.8652 Evaluate side-chains 72 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 66 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 47 optimal weight: 2.9990 chunk 36 optimal weight: 0.8980 chunk 25 optimal weight: 2.9990 chunk 5 optimal weight: 9.9990 chunk 23 optimal weight: 3.9990 chunk 32 optimal weight: 4.9990 chunk 48 optimal weight: 0.5980 chunk 51 optimal weight: 1.9990 chunk 45 optimal weight: 0.9990 chunk 13 optimal weight: 0.9980 chunk 42 optimal weight: 1.9990 overall best weight: 1.0984 ------------------------------------------------------------------------------- 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: 0.7300 moved from start: 0.2157 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 4100 Z= 0.265 Angle : 0.546 5.828 5603 Z= 0.269 Chirality : 0.037 0.125 659 Planarity : 0.004 0.040 699 Dihedral : 4.161 35.821 636 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 9.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 4.19 % Allowed : 21.18 % Favored : 74.63 % 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 (0.38), residues: 528 helix: 0.57 (0.28), residues: 376 sheet: None (None), residues: 0 loop : -1.23 (0.53), residues: 152 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 261 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 151 TYR 0.008 0.001 TYR A 352 ARG 0.002 0.000 ARG A 462 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.442 Fit side-chains REVERT: A 239 MET cc_start: 0.8113 (ttp) cc_final: 0.7728 (ttp) REVERT: A 368 MET cc_start: 0.7129 (tpp) cc_final: 0.6694 (tpp) REVERT: A 381 TYR cc_start: 0.7385 (m-10) cc_final: 0.7177 (m-10) outliers start: 17 outliers final: 12 residues processed: 79 average time/residue: 0.1427 time to fit residues: 14.6000 Evaluate side-chains 79 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 67 time to evaluate : 0.448 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 277 LEU Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 1.9990 chunk 0 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 21 optimal weight: 0.6980 chunk 43 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 26 optimal weight: 1.9990 chunk 45 optimal weight: 2.9990 chunk 12 optimal weight: 0.3980 chunk 17 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 overall best weight: 0.7384 ------------------------------------------------------------------------------- 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: 0.7278 moved from start: 0.2191 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4100 Z= 0.194 Angle : 0.509 5.828 5603 Z= 0.247 Chirality : 0.036 0.121 659 Planarity : 0.004 0.040 699 Dihedral : 4.031 33.286 636 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.93 % Allowed : 20.94 % Favored : 74.14 % 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: 0.18 (0.39), residues: 528 helix: 0.68 (0.29), residues: 375 sheet: None (None), residues: 0 loop : -1.14 (0.53), residues: 153 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 125 HIS 0.002 0.001 HIS A 49 PHE 0.006 0.001 PHE A 151 TYR 0.007 0.001 TYR A 352 ARG 0.001 0.000 ARG A 175 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.464 Fit side-chains REVERT: A 175 ARG cc_start: 0.7498 (OUTLIER) cc_final: 0.7057 (mpt180) REVERT: A 234 ARG cc_start: 0.8359 (OUTLIER) cc_final: 0.8060 (ttp-170) REVERT: A 368 MET cc_start: 0.7220 (tpp) cc_final: 0.6855 (tpp) REVERT: A 381 TYR cc_start: 0.7384 (m-10) cc_final: 0.7170 (m-10) outliers start: 20 outliers final: 11 residues processed: 82 average time/residue: 0.1736 time to fit residues: 17.6789 Evaluate side-chains 78 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 65 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 531 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 10 optimal weight: 2.9990 chunk 30 optimal weight: 6.9990 chunk 12 optimal weight: 0.9980 chunk 51 optimal weight: 0.0270 chunk 42 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 4 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 5 optimal weight: 9.9990 overall best weight: 0.8040 ------------------------------------------------------------------------------- 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: 0.7286 moved from start: 0.2328 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4100 Z= 0.209 Angle : 0.516 6.080 5603 Z= 0.252 Chirality : 0.036 0.122 659 Planarity : 0.004 0.040 699 Dihedral : 4.035 33.080 636 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 8.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 4.43 % Allowed : 21.92 % Favored : 73.65 % 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: 0.19 (0.39), residues: 528 helix: 0.71 (0.29), residues: 374 sheet: None (None), residues: 0 loop : -1.18 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.002 0.001 HIS A 49 PHE 0.010 0.001 PHE A 227 TYR 0.007 0.001 TYR A 352 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 68 time to evaluate : 0.448 Fit side-chains REVERT: A 175 ARG cc_start: 0.7552 (OUTLIER) cc_final: 0.7036 (mpt180) REVERT: A 192 LEU cc_start: 0.8692 (OUTLIER) cc_final: 0.8404 (mt) REVERT: A 234 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8052 (ttp-170) REVERT: A 368 MET cc_start: 0.7142 (tpp) cc_final: 0.6893 (tpp) outliers start: 18 outliers final: 14 residues processed: 83 average time/residue: 0.1628 time to fit residues: 16.8534 Evaluate side-chains 85 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 68 time to evaluate : 0.389 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 531 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 29 optimal weight: 0.8980 chunk 37 optimal weight: 1.9990 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 1.9990 chunk 51 optimal weight: 2.9990 chunk 31 optimal weight: 0.6980 chunk 23 optimal weight: 2.9990 chunk 20 optimal weight: 1.9990 chunk 30 optimal weight: 0.9980 chunk 15 optimal weight: 0.8980 chunk 10 optimal weight: 8.9990 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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: 0.7290 moved from start: 0.2436 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 4100 Z= 0.221 Angle : 0.520 6.240 5603 Z= 0.255 Chirality : 0.037 0.124 659 Planarity : 0.004 0.040 699 Dihedral : 4.053 32.380 636 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 8.66 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.36 % Favored : 95.64 % Rotamer: Outliers : 4.93 % Allowed : 22.91 % Favored : 72.17 % 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: 0.21 (0.39), residues: 528 helix: 0.72 (0.28), residues: 374 sheet: None (None), residues: 0 loop : -1.18 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.002 0.001 HIS A 49 PHE 0.008 0.001 PHE A 275 TYR 0.011 0.001 TYR A 279 ARG 0.001 0.000 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.406 Fit side-chains REVERT: A 175 ARG cc_start: 0.7612 (OUTLIER) cc_final: 0.7086 (mpt180) REVERT: A 192 LEU cc_start: 0.8725 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 234 ARG cc_start: 0.8367 (OUTLIER) cc_final: 0.8047 (ttp-170) REVERT: A 368 MET cc_start: 0.7150 (tpp) cc_final: 0.6887 (tpp) outliers start: 20 outliers final: 14 residues processed: 82 average time/residue: 0.1618 time to fit residues: 16.5815 Evaluate side-chains 83 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 66 time to evaluate : 0.435 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 531 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 9 optimal weight: 0.4980 chunk 32 optimal weight: 5.9990 chunk 34 optimal weight: 0.5980 chunk 25 optimal weight: 0.6980 chunk 4 optimal weight: 3.9990 chunk 40 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 44 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7182 ------------------------------------------------------------------------------- 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: 0.7281 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 4100 Z= 0.196 Angle : 0.523 7.419 5603 Z= 0.252 Chirality : 0.036 0.122 659 Planarity : 0.004 0.040 699 Dihedral : 3.998 31.466 636 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.17 % Favored : 95.83 % Rotamer: Outliers : 4.93 % Allowed : 22.91 % Favored : 72.17 % 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 (0.39), residues: 528 helix: 0.77 (0.29), residues: 373 sheet: None (None), residues: 0 loop : -1.16 (0.53), residues: 155 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 125 HIS 0.002 0.001 HIS A 49 PHE 0.007 0.001 PHE A 275 TYR 0.006 0.001 TYR A 352 ARG 0.002 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.531 Fit side-chains REVERT: A 171 ASP cc_start: 0.7824 (t70) cc_final: 0.7584 (t70) REVERT: A 175 ARG cc_start: 0.7565 (OUTLIER) cc_final: 0.7080 (mpt180) REVERT: A 192 LEU cc_start: 0.8717 (OUTLIER) cc_final: 0.8434 (mt) REVERT: A 234 ARG cc_start: 0.8369 (OUTLIER) cc_final: 0.8096 (ttp-170) REVERT: A 368 MET cc_start: 0.7161 (tpp) cc_final: 0.6892 (tpp) REVERT: A 467 MET cc_start: 0.7435 (mmp) cc_final: 0.7164 (mmp) outliers start: 20 outliers final: 15 residues processed: 83 average time/residue: 0.1570 time to fit residues: 16.2993 Evaluate side-chains 87 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 69 time to evaluate : 0.375 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 340 THR Chi-restraints excluded: chain A residue 346 ARG Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 366 LEU Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL Chi-restraints excluded: chain A residue 531 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.6980 chunk 14 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 45 optimal weight: 0.1980 chunk 47 optimal weight: 0.0050 chunk 31 optimal weight: 1.9990 chunk 50 optimal weight: 0.6980 chunk 30 optimal weight: 0.9980 chunk 23 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 463 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7252 moved from start: 0.2443 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.039 4100 Z= 0.163 Angle : 0.513 7.906 5603 Z= 0.244 Chirality : 0.035 0.118 659 Planarity : 0.004 0.042 699 Dihedral : 3.909 29.814 636 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 7.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.98 % Favored : 96.02 % Rotamer: Outliers : 3.69 % Allowed : 24.14 % Favored : 72.17 % 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: 0.33 (0.39), residues: 528 helix: 0.80 (0.29), residues: 374 sheet: None (None), residues: 0 loop : -1.09 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 16 HIS 0.002 0.001 HIS A 49 PHE 0.007 0.001 PHE A 275 TYR 0.008 0.001 TYR A 279 ARG 0.001 0.000 ARG A 439 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.351 Fit side-chains REVERT: A 27 LEU cc_start: 0.7887 (tt) cc_final: 0.7599 (tp) REVERT: A 171 ASP cc_start: 0.7829 (t70) cc_final: 0.7582 (t70) REVERT: A 175 ARG cc_start: 0.7489 (OUTLIER) cc_final: 0.7116 (mpt180) REVERT: A 192 LEU cc_start: 0.8681 (OUTLIER) cc_final: 0.8428 (mt) REVERT: A 234 ARG cc_start: 0.8381 (OUTLIER) cc_final: 0.7780 (ttp-110) REVERT: A 351 MET cc_start: 0.8395 (OUTLIER) cc_final: 0.8151 (ttp) REVERT: A 368 MET cc_start: 0.7183 (tpp) cc_final: 0.6914 (tpp) outliers start: 15 outliers final: 9 residues processed: 75 average time/residue: 0.1633 time to fit residues: 15.4454 Evaluate side-chains 77 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 64 time to evaluate : 0.455 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 52 optimal weight: 0.8980 chunk 48 optimal weight: 0.5980 chunk 42 optimal weight: 0.5980 chunk 4 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 25 optimal weight: 0.0570 chunk 33 optimal weight: 3.9990 chunk 44 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.4980 chunk 6 optimal weight: 5.9990 overall best weight: 0.4698 ------------------------------------------------------------------------------- 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: 0.7247 moved from start: 0.2456 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.037 4100 Z= 0.165 Angle : 0.517 8.371 5603 Z= 0.245 Chirality : 0.035 0.121 659 Planarity : 0.004 0.042 699 Dihedral : 3.860 29.638 636 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.79 % Favored : 96.21 % Rotamer: Outliers : 3.45 % Allowed : 23.89 % Favored : 72.66 % 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: 0.41 (0.39), residues: 528 helix: 0.86 (0.29), residues: 374 sheet: None (None), residues: 0 loop : -1.07 (0.53), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.002 0.001 HIS A 49 PHE 0.007 0.001 PHE A 275 TYR 0.007 0.001 TYR A 279 ARG 0.001 0.000 ARG A 439 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1056 Ramachandran restraints generated. 528 Oldfield, 0 Emsley, 528 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.441 Fit side-chains REVERT: A 175 ARG cc_start: 0.7460 (OUTLIER) cc_final: 0.7135 (mpt180) REVERT: A 192 LEU cc_start: 0.8613 (OUTLIER) cc_final: 0.8364 (mt) REVERT: A 234 ARG cc_start: 0.8371 (OUTLIER) cc_final: 0.7755 (ttp-110) REVERT: A 239 MET cc_start: 0.7736 (ttp) cc_final: 0.7333 (ttp) REVERT: A 339 ARG cc_start: 0.8269 (ttm-80) cc_final: 0.8037 (ttm-80) REVERT: A 351 MET cc_start: 0.8370 (OUTLIER) cc_final: 0.8143 (ttp) REVERT: A 368 MET cc_start: 0.7191 (tpp) cc_final: 0.6920 (tpp) outliers start: 14 outliers final: 10 residues processed: 74 average time/residue: 0.1675 time to fit residues: 15.6784 Evaluate side-chains 78 residues out of total 444 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 64 time to evaluate : 0.458 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 159 PHE Chi-restraints excluded: chain A residue 175 ARG Chi-restraints excluded: chain A residue 192 LEU Chi-restraints excluded: chain A residue 225 THR Chi-restraints excluded: chain A residue 234 ARG Chi-restraints excluded: chain A residue 351 MET Chi-restraints excluded: chain A residue 365 ILE Chi-restraints excluded: chain A residue 408 MET Chi-restraints excluded: chain A residue 419 VAL Chi-restraints excluded: chain A residue 421 ILE Chi-restraints excluded: chain A residue 442 ILE Chi-restraints excluded: chain A residue 450 CYS Chi-restraints excluded: chain A residue 504 LEU Chi-restraints excluded: chain A residue 509 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 53 random chunks: chunk 11 optimal weight: 7.9990 chunk 42 optimal weight: 0.0970 chunk 17 optimal weight: 0.6980 chunk 43 optimal weight: 3.9990 chunk 5 optimal weight: 8.9990 chunk 7 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 2 optimal weight: 0.5980 chunk 30 optimal weight: 0.9990 chunk 48 optimal weight: 4.9990 chunk 28 optimal weight: 0.7980 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.159904 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3544 r_free = 0.3544 target = 0.125221 restraints weight = 4611.470| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 2.58 r_work: 0.3386 rms_B_bonded: 3.25 restraints_weight: 0.5000 r_work (final): 0.3386 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7212 moved from start: 0.2524 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 4100 Z= 0.182 Angle : 0.521 8.247 5603 Z= 0.249 Chirality : 0.036 0.121 659 Planarity : 0.004 0.041 699 Dihedral : 3.864 29.721 636 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 8.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 3.45 % Allowed : 24.14 % Favored : 72.41 % 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: 0.46 (0.39), residues: 528 helix: 0.90 (0.29), residues: 371 sheet: None (None), residues: 0 loop : -0.99 (0.52), residues: 157 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 16 HIS 0.002 0.001 HIS A 49 PHE 0.009 0.001 PHE A 275 TYR 0.006 0.001 TYR A 279 ARG 0.001 0.000 ARG A 439 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1306.63 seconds wall clock time: 24 minutes 17.17 seconds (1457.17 seconds total)