Starting phenix.real_space_refine on Fri Dec 27 19:48:24 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gzz_34406/12_2024/8gzz_34406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzz_34406/12_2024/8gzz_34406.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.52 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/cci-nas-00/data/ceres_data/8gzz_34406/12_2024/8gzz_34406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzz_34406/12_2024/8gzz_34406.map" model { file = "/net/cci-nas-00/data/ceres_data/8gzz_34406/12_2024/8gzz_34406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzz_34406/12_2024/8gzz_34406.cif" } resolution = 3.52 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= -0.003 sd= 0.027 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 36 5.16 5 C 4186 2.51 5 N 1084 2.21 5 O 1262 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 6 residue(s): 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5532/modules/chem_data/mon_lib" Total number of atoms: 6568 Number of models: 1 Model: "" Number of chains: 6 Chain: "A" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "B" Number of atoms: 1558 Number of conformers: 1 Conformer: "" Number of residues, atoms: 194, 1558 Classifications: {'peptide': 194} Link IDs: {'PTRANS': 12, 'TRANS': 181} Chain: "D" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "E" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Chain: "F" Number of atoms: 824 Number of conformers: 1 Conformer: "" Number of residues, atoms: 111, 824 Classifications: {'peptide': 111} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 104} Chain: "G" Number of atoms: 902 Number of conformers: 1 Conformer: "" Number of residues, atoms: 122, 902 Classifications: {'peptide': 122} Link IDs: {'PTRANS': 4, 'TRANS': 117} Time building chain proxies: 6.60, per 1000 atoms: 1.00 Number of scatterers: 6568 At special positions: 0 Unit cell: (87.36, 130.624, 79.04, 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 36 16.00 O 1262 8.00 N 1084 7.00 C 4186 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=14, symmetry=0 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.03 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.04 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS B 336 " - pdb=" SG CYS B 361 " distance=2.03 Simple disulfide: pdb=" SG CYS B 379 " - pdb=" SG CYS B 432 " distance=2.04 Simple disulfide: pdb=" SG CYS B 391 " - pdb=" SG CYS B 525 " distance=2.03 Simple disulfide: pdb=" SG CYS B 480 " - pdb=" SG CYS B 488 " distance=2.03 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS E 21 " - pdb=" SG CYS E 96 " distance=2.03 Simple disulfide: pdb=" SG CYS E 35 " - pdb=" SG CYS E 50 " distance=2.03 Simple disulfide: pdb=" SG CYS F 23 " - pdb=" SG CYS F 88 " distance=2.04 Simple disulfide: pdb=" SG CYS G 21 " - pdb=" SG CYS G 96 " distance=2.03 Simple disulfide: pdb=" SG CYS G 35 " - pdb=" SG CYS G 50 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.64 Conformation dependent library (CDL) restraints added in 1.0 seconds 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1556 Finding SS restraints... Secondary structure from input PDB file: 15 helices and 17 sheets defined 9.6% alpha, 27.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.91 Creating SS restraints... Processing helix chain 'A' and resid 337 through 343 removed outlier: 3.523A pdb=" N VAL A 341 " --> pdb=" O PRO A 337 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 368 removed outlier: 3.914A pdb=" N VAL A 367 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 384 through 388 removed outlier: 4.056A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.508A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 4.203A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'B' and resid 337 through 343 removed outlier: 3.868A pdb=" N VAL B 341 " --> pdb=" O PRO B 337 " (cutoff:3.500A) Processing helix chain 'B' and resid 383 through 387 Processing helix chain 'B' and resid 406 through 410 Processing helix chain 'B' and resid 416 through 422 Processing helix chain 'B' and resid 502 through 505 Processing helix chain 'E' and resid 63 through 66 Processing helix chain 'E' and resid 87 through 91 removed outlier: 4.092A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing helix chain 'G' and resid 63 through 66 Processing helix chain 'G' and resid 87 through 91 removed outlier: 3.981A pdb=" N THR G 91 " --> pdb=" O ALA G 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'A' and resid 356 through 358 removed outlier: 3.572A pdb=" N VAL A 395 " --> pdb=" O ILE A 358 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.805A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'A' and resid 473 through 474 Processing sheet with id=AA5, first strand: chain 'B' and resid 356 through 358 removed outlier: 3.575A pdb=" N VAL B 395 " --> pdb=" O ILE B 358 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 361 through 362 removed outlier: 6.741A pdb=" N CYS B 361 " --> pdb=" O CYS B 525 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'B' and resid 452 through 454 Processing sheet with id=AA8, first strand: chain 'B' and resid 473 through 474 Processing sheet with id=AA9, first strand: chain 'D' and resid 4 through 7 Processing sheet with id=AB1, first strand: chain 'D' and resid 10 through 13 removed outlier: 3.609A pdb=" N GLU D 13 " --> pdb=" O VAL D 108 " (cutoff:3.500A) removed outlier: 6.493A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) Processing sheet with id=AB2, first strand: chain 'E' and resid 5 through 6 removed outlier: 3.717A pdb=" N THR E 20 " --> pdb=" O SER E 6 " (cutoff:3.500A) Processing sheet with id=AB3, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.576A pdb=" N CYS E 50 " --> pdb=" O TYR E 60 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) removed outlier: 3.928A pdb=" N LEU E 111 " --> pdb=" O ARG E 98 " (cutoff:3.500A) Processing sheet with id=AB4, first strand: chain 'E' and resid 60 through 61 removed outlier: 3.576A pdb=" N CYS E 50 " --> pdb=" O TYR E 60 " (cutoff:3.500A) removed outlier: 6.682A pdb=" N TRP E 36 " --> pdb=" O ILE E 48 " (cutoff:3.500A) removed outlier: 4.562A pdb=" N CYS E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.866A pdb=" N MET E 34 " --> pdb=" O CYS E 50 " (cutoff:3.500A) removed outlier: 4.372A pdb=" N ASP E 33 " --> pdb=" O ASP E 99 " (cutoff:3.500A) Processing sheet with id=AB5, first strand: chain 'F' and resid 4 through 7 Processing sheet with id=AB6, first strand: chain 'F' and resid 10 through 13 removed outlier: 3.668A pdb=" N GLU F 13 " --> pdb=" O VAL F 108 " (cutoff:3.500A) removed outlier: 6.483A pdb=" N TRP F 35 " --> pdb=" O LEU F 47 " (cutoff:3.500A) Processing sheet with id=AB7, first strand: chain 'G' and resid 5 through 6 removed outlier: 3.738A pdb=" N THR G 20 " --> pdb=" O SER G 6 " (cutoff:3.500A) Processing sheet with id=AB8, first strand: chain 'G' and resid 60 through 61 removed outlier: 6.646A pdb=" N TRP G 36 " --> pdb=" O ILE G 48 " (cutoff:3.500A) removed outlier: 4.458A pdb=" N CYS G 50 " --> pdb=" O MET G 34 " (cutoff:3.500A) removed outlier: 6.781A pdb=" N MET G 34 " --> pdb=" O CYS G 50 " (cutoff:3.500A) 197 hydrogen bonds defined for protein. 459 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: 1.83 Time building geometry restraints manager: 1.87 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 2082 1.34 - 1.47: 1820 1.47 - 1.59: 2798 1.59 - 1.71: 0 1.71 - 1.83: 42 Bond restraints: 6742 Sorted by residual: bond pdb=" C LYS A 356 " pdb=" N ARG A 357 " ideal model delta sigma weight residual 1.330 1.372 -0.042 1.32e-02 5.74e+03 1.02e+01 bond pdb=" C GLN F 24 " pdb=" N ALA F 25 " ideal model delta sigma weight residual 1.329 1.285 0.044 1.44e-02 4.82e+03 9.46e+00 bond pdb=" C CYS F 23 " pdb=" N GLN F 24 " ideal model delta sigma weight residual 1.330 1.291 0.039 1.44e-02 4.82e+03 7.41e+00 bond pdb=" N GLN F 24 " pdb=" CA GLN F 24 " ideal model delta sigma weight residual 1.455 1.488 -0.032 1.23e-02 6.61e+03 6.89e+00 bond pdb=" N TYR A 449 " pdb=" CA TYR A 449 " ideal model delta sigma weight residual 1.458 1.486 -0.028 1.08e-02 8.57e+03 6.79e+00 ... (remaining 6737 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.15: 8628 1.15 - 2.31: 435 2.31 - 3.46: 91 3.46 - 4.62: 24 4.62 - 5.77: 6 Bond angle restraints: 9184 Sorted by residual: angle pdb=" C TYR F 49 " pdb=" CA TYR F 49 " pdb=" CB TYR F 49 " ideal model delta sigma weight residual 109.80 115.57 -5.77 1.65e+00 3.67e-01 1.22e+01 angle pdb=" C LYS A 356 " pdb=" N ARG A 357 " pdb=" CA ARG A 357 " ideal model delta sigma weight residual 123.00 118.33 4.67 1.38e+00 5.25e-01 1.15e+01 angle pdb=" CA GLN A 414 " pdb=" C GLN A 414 " pdb=" O GLN A 414 " ideal model delta sigma weight residual 121.56 118.05 3.51 1.09e+00 8.42e-01 1.04e+01 angle pdb=" N TYR F 49 " pdb=" CA TYR F 49 " pdb=" C TYR F 49 " ideal model delta sigma weight residual 110.42 105.78 4.64 1.55e+00 4.16e-01 8.96e+00 angle pdb=" N PHE A 377 " pdb=" CA PHE A 377 " pdb=" C PHE A 377 " ideal model delta sigma weight residual 112.72 109.48 3.24 1.14e+00 7.69e-01 8.09e+00 ... (remaining 9179 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.80: 3617 17.80 - 35.61: 289 35.61 - 53.41: 29 53.41 - 71.22: 7 71.22 - 89.02: 4 Dihedral angle restraints: 3946 sinusoidal: 1490 harmonic: 2456 Sorted by residual: dihedral pdb=" CB CYS A 379 " pdb=" SG CYS A 379 " pdb=" SG CYS A 432 " pdb=" CB CYS A 432 " ideal model delta sinusoidal sigma weight residual 93.00 24.54 68.46 1 1.00e+01 1.00e-02 6.08e+01 dihedral pdb=" CB CYS B 379 " pdb=" SG CYS B 379 " pdb=" SG CYS B 432 " pdb=" CB CYS B 432 " ideal model delta sinusoidal sigma weight residual 93.00 26.66 66.34 1 1.00e+01 1.00e-02 5.75e+01 dihedral pdb=" CA CYS A 379 " pdb=" C CYS A 379 " pdb=" N TYR A 380 " pdb=" CA TYR A 380 " ideal model delta harmonic sigma weight residual -180.00 -161.72 -18.28 0 5.00e+00 4.00e-02 1.34e+01 ... (remaining 3943 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.030: 529 0.030 - 0.059: 314 0.059 - 0.089: 88 0.089 - 0.118: 57 0.118 - 0.148: 12 Chirality restraints: 1000 Sorted by residual: chirality pdb=" CA ILE F 21 " pdb=" N ILE F 21 " pdb=" C ILE F 21 " pdb=" CB ILE F 21 " both_signs ideal model delta sigma weight residual False 2.43 2.58 -0.15 2.00e-01 2.50e+01 5.48e-01 chirality pdb=" CA GLN F 24 " pdb=" N GLN F 24 " pdb=" C GLN F 24 " pdb=" CB GLN F 24 " both_signs ideal model delta sigma weight residual False 2.51 2.65 -0.14 2.00e-01 2.50e+01 4.77e-01 chirality pdb=" CA GLU B 465 " pdb=" N GLU B 465 " pdb=" C GLU B 465 " pdb=" CB GLU B 465 " both_signs ideal model delta sigma weight residual False 2.51 2.64 -0.13 2.00e-01 2.50e+01 4.29e-01 ... (remaining 997 not shown) Planarity restraints: 1184 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE F 48 " -0.007 2.00e-02 2.50e+03 1.54e-02 2.36e+00 pdb=" C ILE F 48 " 0.027 2.00e-02 2.50e+03 pdb=" O ILE F 48 " -0.010 2.00e-02 2.50e+03 pdb=" N TYR F 49 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA GLN F 24 " -0.007 2.00e-02 2.50e+03 1.48e-02 2.21e+00 pdb=" C GLN F 24 " 0.026 2.00e-02 2.50e+03 pdb=" O GLN F 24 " -0.009 2.00e-02 2.50e+03 pdb=" N ALA F 25 " -0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR D 49 " -0.012 2.00e-02 2.50e+03 9.52e-03 1.81e+00 pdb=" CG TYR D 49 " 0.023 2.00e-02 2.50e+03 pdb=" CD1 TYR D 49 " -0.003 2.00e-02 2.50e+03 pdb=" CD2 TYR D 49 " -0.003 2.00e-02 2.50e+03 pdb=" CE1 TYR D 49 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR D 49 " -0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 49 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR D 49 " -0.001 2.00e-02 2.50e+03 ... (remaining 1181 not shown) Histogram of nonbonded interaction distances: 2.25 - 2.78: 1441 2.78 - 3.31: 5887 3.31 - 3.84: 10276 3.84 - 4.37: 12188 4.37 - 4.90: 21752 Nonbonded interactions: 51544 Sorted by model distance: nonbonded pdb=" OD1 ASP B 442 " pdb=" OH TYR G 103 " model vdw 2.248 3.040 nonbonded pdb=" O SER E 29 " pdb=" OG1 THR E 53 " model vdw 2.299 3.040 nonbonded pdb=" O SER G 29 " pdb=" OG1 THR G 53 " model vdw 2.334 3.040 nonbonded pdb=" NE2 GLN F 90 " pdb=" O SER F 93 " model vdw 2.337 3.120 nonbonded pdb=" OD2 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.340 3.040 ... (remaining 51539 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Time spend for trying shortcut: 0.00 Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' } ncs_group { reference = chain 'D' selection = chain 'F' } ncs_group { reference = chain 'E' selection = chain 'G' } 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: 9.250 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.290 Check model and map are aligned: 0.040 Set scattering table: 0.070 Process input model: 21.190 Find NCS groups from input model: 0.180 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8363 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 : 0.004 0.044 6742 Z= 0.281 Angle : 0.620 5.770 9184 Z= 0.361 Chirality : 0.044 0.148 1000 Planarity : 0.003 0.028 1184 Dihedral : 12.188 89.023 2348 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 8.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 0.00 % Allowed : 0.56 % Favored : 99.44 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.99 (0.28), residues: 842 helix: -3.59 (0.49), residues: 54 sheet: 0.41 (0.33), residues: 264 loop : -0.90 (0.26), residues: 524 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.002 0.001 HIS A 505 PHE 0.021 0.002 PHE A 347 TYR 0.023 0.001 TYR D 49 ARG 0.002 0.000 ARG B 466 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 113 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 113 time to evaluate : 0.814 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2090 time to fit residues: 30.8724 Evaluate side-chains 93 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 0 poor density : 93 time to evaluate : 0.818 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 70 optimal weight: 0.2980 chunk 63 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 0.9990 chunk 42 optimal weight: 0.9980 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 0.0050 chunk 25 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 1.9990 chunk 76 optimal weight: 0.6980 overall best weight: 0.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 360 ASN D 31 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1136 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 6742 Z= 0.198 Angle : 0.537 4.999 9184 Z= 0.289 Chirality : 0.043 0.145 1000 Planarity : 0.004 0.040 1184 Dihedral : 4.186 16.306 932 Min Nonbonded Distance : 2.541 Molprobity Statistics. All-atom Clashscore : 6.07 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 0.85 % Allowed : 7.89 % Favored : 91.27 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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 (0.29), residues: 842 helix: -3.92 (0.42), residues: 54 sheet: 0.24 (0.32), residues: 292 loop : -0.89 (0.27), residues: 496 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.045 0.001 PHE B 374 TYR 0.011 0.001 TYR A 380 ARG 0.005 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 6 poor density : 100 time to evaluate : 0.758 Fit side-chains revert: symmetry clash REVERT: D 82 ASP cc_start: 0.7503 (m-30) cc_final: 0.7103 (m-30) REVERT: D 96 ASP cc_start: 0.7965 (p0) cc_final: 0.7050 (p0) outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 0.2151 time to fit residues: 28.8794 Evaluate side-chains 96 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 4 poor density : 92 time to evaluate : 0.742 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.0870 chunk 23 optimal weight: 0.9980 chunk 63 optimal weight: 1.9990 chunk 51 optimal weight: 0.5980 chunk 21 optimal weight: 3.9990 chunk 76 optimal weight: 0.8980 chunk 82 optimal weight: 0.0020 chunk 68 optimal weight: 0.9980 chunk 75 optimal weight: 0.8980 chunk 26 optimal weight: 3.9990 chunk 61 optimal weight: 0.6980 overall best weight: 0.4566 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8354 moved from start: 0.1425 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6742 Z= 0.165 Angle : 0.495 4.676 9184 Z= 0.264 Chirality : 0.042 0.139 1000 Planarity : 0.004 0.034 1184 Dihedral : 4.039 15.240 932 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 6.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.44 % Favored : 96.56 % Rotamer: Outliers : 1.41 % Allowed : 10.00 % Favored : 88.59 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.99 (0.29), residues: 842 helix: -4.05 (0.41), residues: 54 sheet: 0.34 (0.32), residues: 282 loop : -0.84 (0.27), residues: 506 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.009 0.001 PHE A 347 TYR 0.013 0.001 TYR A 380 ARG 0.003 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 98 time to evaluate : 0.768 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.8739 (m) cc_final: 0.8182 (p) REVERT: D 82 ASP cc_start: 0.7409 (m-30) cc_final: 0.7089 (m-30) REVERT: D 96 ASP cc_start: 0.7966 (p0) cc_final: 0.7026 (p0) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.1941 time to fit residues: 26.9352 Evaluate side-chains 99 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 92 time to evaluate : 0.782 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 3.9990 chunk 57 optimal weight: 3.9990 chunk 39 optimal weight: 0.0870 chunk 8 optimal weight: 0.7980 chunk 36 optimal weight: 0.6980 chunk 51 optimal weight: 1.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 72 optimal weight: 0.8980 chunk 21 optimal weight: 0.7980 overall best weight: 0.6558 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6742 Z= 0.197 Angle : 0.495 6.223 9184 Z= 0.266 Chirality : 0.042 0.137 1000 Planarity : 0.004 0.034 1184 Dihedral : 4.014 16.303 932 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 5.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.55 % Allowed : 12.68 % Favored : 85.77 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -0.95 (0.29), residues: 842 helix: -4.04 (0.41), residues: 54 sheet: 0.37 (0.32), residues: 280 loop : -0.81 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.009 0.001 PHE E 95 TYR 0.011 0.001 TYR A 380 ARG 0.002 0.000 ARG A 357 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 95 time to evaluate : 0.789 Fit side-chains revert: symmetry clash REVERT: D 96 ASP cc_start: 0.8006 (p0) cc_final: 0.7098 (p0) outliers start: 11 outliers final: 8 residues processed: 100 average time/residue: 0.1847 time to fit residues: 24.7961 Evaluate side-chains 101 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 8 poor density : 93 time to evaluate : 0.744 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 67 optimal weight: 1.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 4.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 0.6980 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8472 moved from start: 0.1798 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.041 6742 Z= 0.474 Angle : 0.613 5.484 9184 Z= 0.331 Chirality : 0.046 0.138 1000 Planarity : 0.004 0.036 1184 Dihedral : 4.688 16.778 932 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 7.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.82 % Favored : 94.18 % Rotamer: Outliers : 2.11 % Allowed : 13.38 % Favored : 84.51 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.34 (0.29), residues: 842 helix: -3.94 (0.46), residues: 54 sheet: -0.13 (0.33), residues: 266 loop : -0.95 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP B 436 HIS 0.002 0.001 HIS A 505 PHE 0.017 0.002 PHE E 95 TYR 0.014 0.002 TYR E 103 ARG 0.005 0.001 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 111 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 96 time to evaluate : 0.780 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.9078 (m) cc_final: 0.8518 (p) REVERT: D 96 ASP cc_start: 0.8078 (p0) cc_final: 0.7168 (p0) outliers start: 15 outliers final: 12 residues processed: 105 average time/residue: 0.1669 time to fit residues: 24.2742 Evaluate side-chains 100 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 88 time to evaluate : 0.854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 27 optimal weight: 1.9990 chunk 73 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 47 optimal weight: 0.7980 chunk 20 optimal weight: 0.8980 chunk 81 optimal weight: 0.8980 chunk 67 optimal weight: 2.9990 chunk 37 optimal weight: 0.8980 chunk 6 optimal weight: 0.0970 chunk 26 optimal weight: 0.9980 chunk 42 optimal weight: 0.0570 overall best weight: 0.5496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8407 moved from start: 0.1908 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 6742 Z= 0.189 Angle : 0.522 6.057 9184 Z= 0.281 Chirality : 0.042 0.138 1000 Planarity : 0.004 0.036 1184 Dihedral : 4.308 16.266 932 Min Nonbonded Distance : 2.495 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 1.97 % Allowed : 14.08 % Favored : 83.94 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.43 (0.28), residues: 842 helix: -4.09 (0.41), residues: 54 sheet: -0.22 (0.32), residues: 280 loop : -1.01 (0.27), residues: 508 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.052 0.001 PHE B 374 TYR 0.009 0.001 TYR D 49 ARG 0.003 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 115 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 101 time to evaluate : 0.776 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.8882 (m) cc_final: 0.8231 (p) REVERT: B 474 GLN cc_start: 0.8280 (tm-30) cc_final: 0.8049 (tm-30) REVERT: D 96 ASP cc_start: 0.8007 (p0) cc_final: 0.7111 (p0) outliers start: 14 outliers final: 10 residues processed: 109 average time/residue: 0.1810 time to fit residues: 26.7384 Evaluate side-chains 104 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 94 time to evaluate : 0.732 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 78 optimal weight: 0.6980 chunk 9 optimal weight: 2.9990 chunk 46 optimal weight: 0.7980 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.9980 chunk 68 optimal weight: 3.9990 chunk 80 optimal weight: 0.7980 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 4.9990 chunk 32 optimal weight: 4.9990 overall best weight: 1.0582 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8434 moved from start: 0.2015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 6742 Z= 0.286 Angle : 0.554 6.993 9184 Z= 0.295 Chirality : 0.043 0.134 1000 Planarity : 0.004 0.038 1184 Dihedral : 4.353 17.186 932 Min Nonbonded Distance : 2.492 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 2.25 % Allowed : 14.79 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.54 (0.28), residues: 842 helix: -4.04 (0.43), residues: 54 sheet: -0.28 (0.32), residues: 278 loop : -1.09 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.000 HIS A 505 PHE 0.011 0.001 PHE E 95 TYR 0.009 0.001 TYR D 49 ARG 0.003 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 93 time to evaluate : 0.790 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8135 (pt0) cc_final: 0.7915 (pt0) REVERT: B 376 THR cc_start: 0.8937 (m) cc_final: 0.8410 (p) REVERT: D 96 ASP cc_start: 0.8061 (p0) cc_final: 0.7186 (p0) outliers start: 16 outliers final: 11 residues processed: 104 average time/residue: 0.1813 time to fit residues: 25.4675 Evaluate side-chains 102 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 91 time to evaluate : 0.981 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.9980 chunk 24 optimal weight: 3.9990 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 0.0040 chunk 55 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 2.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 0.0770 chunk 77 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 overall best weight: 0.5550 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.2165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6742 Z= 0.184 Angle : 0.539 12.709 9184 Z= 0.280 Chirality : 0.042 0.134 1000 Planarity : 0.004 0.038 1184 Dihedral : 4.133 15.836 932 Min Nonbonded Distance : 2.466 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 2.39 % Allowed : 14.65 % Favored : 82.96 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.48 (0.28), residues: 842 helix: -4.11 (0.41), residues: 54 sheet: -0.13 (0.33), residues: 256 loop : -1.08 (0.26), residues: 532 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.008 0.001 PHE E 95 TYR 0.010 0.001 TYR A 380 ARG 0.002 0.000 ARG D 61 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 116 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 17 poor density : 99 time to evaluate : 0.719 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8150 (pt0) cc_final: 0.7927 (pt0) REVERT: B 376 THR cc_start: 0.8826 (m) cc_final: 0.8250 (p) REVERT: B 394 ASN cc_start: 0.7537 (OUTLIER) cc_final: 0.6939 (p0) REVERT: B 420 ASP cc_start: 0.8707 (t0) cc_final: 0.8106 (t0) REVERT: D 42 GLN cc_start: 0.8601 (OUTLIER) cc_final: 0.8112 (mp10) REVERT: D 96 ASP cc_start: 0.8024 (p0) cc_final: 0.7145 (p0) outliers start: 17 outliers final: 10 residues processed: 110 average time/residue: 0.1805 time to fit residues: 26.6981 Evaluate side-chains 104 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 12 poor density : 92 time to evaluate : 0.733 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 394 ASN Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 0.9980 chunk 45 optimal weight: 0.8980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 0.0170 chunk 23 optimal weight: 3.9990 chunk 68 optimal weight: 1.9990 chunk 71 optimal weight: 1.9990 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 overall best weight: 0.7418 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8406 moved from start: 0.2259 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6742 Z= 0.218 Angle : 0.535 7.433 9184 Z= 0.283 Chirality : 0.042 0.133 1000 Planarity : 0.004 0.039 1184 Dihedral : 4.120 15.612 932 Min Nonbonded Distance : 2.428 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.11 % Allowed : 15.77 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.43 (0.28), residues: 842 helix: -4.09 (0.42), residues: 54 sheet: -0.11 (0.33), residues: 266 loop : -1.05 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.013 0.001 PHE B 486 TYR 0.017 0.001 TYR F 36 ARG 0.002 0.000 ARG B 454 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 92 time to evaluate : 0.749 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8165 (pt0) cc_final: 0.7946 (pt0) REVERT: B 376 THR cc_start: 0.8808 (m) cc_final: 0.8385 (p) REVERT: D 42 GLN cc_start: 0.8598 (OUTLIER) cc_final: 0.8108 (mp10) REVERT: D 96 ASP cc_start: 0.8044 (p0) cc_final: 0.7183 (p0) outliers start: 15 outliers final: 13 residues processed: 101 average time/residue: 0.1792 time to fit residues: 24.3449 Evaluate side-chains 104 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 90 time to evaluate : 0.714 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 91 THR Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 37 optimal weight: 1.9990 chunk 55 optimal weight: 0.0670 chunk 83 optimal weight: 0.9990 chunk 77 optimal weight: 0.0470 chunk 66 optimal weight: 0.7980 chunk 6 optimal weight: 0.7980 chunk 51 optimal weight: 0.9980 chunk 40 optimal weight: 1.9990 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 3.9990 chunk 20 optimal weight: 2.9990 overall best weight: 0.5416 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** B 394 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8388 moved from start: 0.2312 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 6742 Z= 0.178 Angle : 0.523 6.760 9184 Z= 0.276 Chirality : 0.042 0.133 1000 Planarity : 0.004 0.039 1184 Dihedral : 4.019 16.239 932 Min Nonbonded Distance : 2.424 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.80 % Favored : 96.20 % Rotamer: Outliers : 2.11 % Allowed : 15.77 % Favored : 82.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % 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: -1.38 (0.28), residues: 842 helix: -4.05 (0.42), residues: 54 sheet: -0.00 (0.33), residues: 252 loop : -1.04 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.001 PHE B 486 TYR 0.010 0.001 TYR A 380 ARG 0.001 0.000 ARG B 454 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1684 Ramachandran restraints generated. 842 Oldfield, 0 Emsley, 842 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 109 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 15 poor density : 94 time to evaluate : 0.881 Fit side-chains revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8172 (pt0) cc_final: 0.7949 (pt0) REVERT: B 376 THR cc_start: 0.8790 (m) cc_final: 0.8445 (p) REVERT: D 42 GLN cc_start: 0.8559 (OUTLIER) cc_final: 0.8078 (mp10) REVERT: D 96 ASP cc_start: 0.8005 (p0) cc_final: 0.7138 (p0) outliers start: 15 outliers final: 12 residues processed: 102 average time/residue: 0.1842 time to fit residues: 25.5793 Evaluate side-chains 106 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 93 time to evaluate : 0.811 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain D residue 42 GLN Chi-restraints excluded: chain D residue 90 GLN Chi-restraints excluded: chain E residue 37 VAL Chi-restraints excluded: chain E residue 58 ASN Chi-restraints excluded: chain G residue 37 VAL Chi-restraints excluded: chain G residue 59 ILE Chi-restraints excluded: chain G residue 79 VAL Chi-restraints excluded: chain G residue 117 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 61 optimal weight: 3.9990 chunk 9 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 66 optimal weight: 0.9990 chunk 27 optimal weight: 3.9990 chunk 68 optimal weight: 3.9990 chunk 8 optimal weight: 0.5980 chunk 12 optimal weight: 0.5980 chunk 58 optimal weight: 0.9990 chunk 3 optimal weight: 3.9990 chunk 48 optimal weight: 1.9990 overall best weight: 0.8386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 394 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3301 r_free = 0.3301 target = 0.080888 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3018 r_free = 0.3018 target = 0.066626 restraints weight = 16757.525| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 27)----------------| | r_work = 0.3070 r_free = 0.3070 target = 0.069193 restraints weight = 8089.240| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3104 r_free = 0.3104 target = 0.070870 restraints weight = 5166.500| |-----------------------------------------------------------------------------| r_work (final): 0.3101 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8396 moved from start: 0.2340 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 6742 Z= 0.237 Angle : 0.541 6.226 9184 Z= 0.286 Chirality : 0.043 0.135 1000 Planarity : 0.004 0.040 1184 Dihedral : 4.092 16.519 932 Min Nonbonded Distance : 2.398 Molprobity Statistics. All-atom Clashscore : 6.54 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.11 % Allowed : 16.20 % Favored : 81.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.55 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.41 (0.28), residues: 842 helix: -3.98 (0.43), residues: 54 sheet: -0.13 (0.33), residues: 266 loop : -1.03 (0.27), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.010 0.001 PHE B 486 TYR 0.014 0.001 TYR F 36 ARG 0.002 0.000 ARG B 454 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1975.59 seconds wall clock time: 36 minutes 58.36 seconds (2218.36 seconds total)