Starting phenix.real_space_refine on Thu Jul 24 19:00:28 2025 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/cci-nas-00/data/ceres_data/8gzz_34406/07_2025/8gzz_34406.cif Found real_map, /net/cci-nas-00/data/ceres_data/8gzz_34406/07_2025/8gzz_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_34406/07_2025/8gzz_34406.map" default_real_map = "/net/cci-nas-00/data/ceres_data/8gzz_34406/07_2025/8gzz_34406.map" model { file = "/net/cci-nas-00/data/ceres_data/8gzz_34406/07_2025/8gzz_34406.cif" } default_model = "/net/cci-nas-00/data/ceres_data/8gzz_34406/07_2025/8gzz_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-5711/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: 6.99, per 1000 atoms: 1.06 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: 1.48 Conformation dependent library (CDL) restraints added in 871.5 milliseconds 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: 1.02 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: 2.10 Time building geometry restraints manager: 1.79 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: 0.01 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: 9.120 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: 0.250 Check model and map are aligned: 0.050 Set scattering table: 0.060 Process input model: 22.280 Find NCS groups from input model: 0.210 Set up NCS constraints: 0.040 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.820 ------------------------------------------------------------------------------- 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 6756 Z= 0.227 Angle : 0.621 5.770 9212 Z= 0.362 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 Details of bonding type rmsd hydrogen bonds : bond 0.18472 ( 186) hydrogen bonds : angle 8.99483 ( 459) SS BOND : bond 0.00294 ( 14) SS BOND : angle 1.03895 ( 28) covalent geometry : bond 0.00437 ( 6742) covalent geometry : angle 0.61966 ( 9184) *********************** 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 : 0.617 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.1976 time to fit residues: 29.1484 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 : 0.689 ------------------------------------------------------------------------------- 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: 2.9990 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3377 r_free = 0.3377 target = 0.084368 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3101 r_free = 0.3101 target = 0.070281 restraints weight = 16509.755| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3154 r_free = 0.3154 target = 0.072936 restraints weight = 7959.968| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3188 r_free = 0.3188 target = 0.074658 restraints weight = 5083.394| |-----------------------------------------------------------------------------| r_work (final): 0.3180 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8357 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 6756 Z= 0.136 Angle : 0.540 4.998 9212 Z= 0.290 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 Details of bonding type rmsd hydrogen bonds : bond 0.03653 ( 186) hydrogen bonds : angle 6.78567 ( 459) SS BOND : bond 0.00384 ( 14) SS BOND : angle 1.20692 ( 28) covalent geometry : bond 0.00302 ( 6742) covalent geometry : angle 0.53668 ( 9184) *********************** 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 : 0.883 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8592 (m-30) cc_final: 0.8346 (t0) REVERT: D 82 ASP cc_start: 0.7530 (m-30) cc_final: 0.7083 (m-30) REVERT: D 96 ASP cc_start: 0.8083 (p0) cc_final: 0.7178 (p0) outliers start: 6 outliers final: 4 residues processed: 102 average time/residue: 0.3340 time to fit residues: 45.0692 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 : 1.960 ------------------------------------------------------------------------------- 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 18 optimal weight: 4.9990 chunk 66 optimal weight: 0.0570 chunk 14 optimal weight: 0.0370 chunk 52 optimal weight: 3.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 58 optimal weight: 0.9980 chunk 39 optimal weight: 0.9980 chunk 77 optimal weight: 2.9990 chunk 83 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 overall best weight: 0.5376 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3378 r_free = 0.3378 target = 0.084443 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 43)----------------| | r_work = 0.3099 r_free = 0.3099 target = 0.070151 restraints weight = 16603.897| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 36)----------------| | r_work = 0.3152 r_free = 0.3152 target = 0.072832 restraints weight = 8052.389| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3186 r_free = 0.3186 target = 0.074550 restraints weight = 5142.954| |-----------------------------------------------------------------------------| r_work (final): 0.3178 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8352 moved from start: 0.1397 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 6756 Z= 0.122 Angle : 0.499 4.717 9212 Z= 0.267 Chirality : 0.042 0.139 1000 Planarity : 0.004 0.034 1184 Dihedral : 4.071 15.306 932 Min Nonbonded Distance : 2.556 Molprobity Statistics. All-atom Clashscore : 6.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.56 % Favored : 96.44 % Rotamer: Outliers : 1.41 % Allowed : 9.86 % Favored : 88.73 % 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: -1.00 (0.29), residues: 842 helix: -4.04 (0.41), residues: 54 sheet: 0.33 (0.32), residues: 282 loop : -0.85 (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 Details of bonding type rmsd hydrogen bonds : bond 0.03100 ( 186) hydrogen bonds : angle 6.27208 ( 459) SS BOND : bond 0.00575 ( 14) SS BOND : angle 1.08352 ( 28) covalent geometry : bond 0.00274 ( 6742) covalent geometry : angle 0.49628 ( 9184) *********************** 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 107 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 97 time to evaluate : 4.202 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.8673 (m) cc_final: 0.8084 (p) REVERT: B 420 ASP cc_start: 0.8585 (m-30) cc_final: 0.8322 (t0) REVERT: D 96 ASP cc_start: 0.8094 (p0) cc_final: 0.7167 (p0) outliers start: 10 outliers final: 7 residues processed: 103 average time/residue: 0.3385 time to fit residues: 49.5674 Evaluate side-chains 100 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 93 time to evaluate : 1.849 ------------------------------------------------------------------------------- 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 45 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 chunk 70 optimal weight: 3.9990 chunk 9 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 49 optimal weight: 0.9980 chunk 69 optimal weight: 1.9990 chunk 48 optimal weight: 1.9990 chunk 32 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 17 optimal weight: 1.9990 overall best weight: 1.2784 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3328 r_free = 0.3328 target = 0.082003 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.068346 restraints weight = 17029.273| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3111 r_free = 0.3111 target = 0.070903 restraints weight = 8207.349| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3145 r_free = 0.3145 target = 0.072559 restraints weight = 5234.363| |-----------------------------------------------------------------------------| r_work (final): 0.3132 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8417 moved from start: 0.1610 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.039 6756 Z= 0.219 Angle : 0.552 6.180 9212 Z= 0.298 Chirality : 0.044 0.139 1000 Planarity : 0.004 0.036 1184 Dihedral : 4.367 16.775 932 Min Nonbonded Distance : 2.539 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.75 % Favored : 95.25 % Rotamer: Outliers : 1.83 % Allowed : 12.68 % Favored : 85.49 % 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: -1.31 (0.29), residues: 842 helix: -3.98 (0.44), residues: 54 sheet: -0.08 (0.32), residues: 278 loop : -0.95 (0.27), residues: 510 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP B 436 HIS 0.002 0.001 HIS A 505 PHE 0.013 0.001 PHE E 95 TYR 0.010 0.001 TYR D 49 ARG 0.004 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.03127 ( 186) hydrogen bonds : angle 6.35219 ( 459) SS BOND : bond 0.00451 ( 14) SS BOND : angle 1.30113 ( 28) covalent geometry : bond 0.00498 ( 6742) covalent geometry : angle 0.54829 ( 9184) *********************** 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 108 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 95 time to evaluate : 1.648 Fit side-chains revert: symmetry clash REVERT: B 420 ASP cc_start: 0.8549 (OUTLIER) cc_final: 0.8296 (t0) REVERT: D 96 ASP cc_start: 0.8127 (p0) cc_final: 0.7221 (p0) outliers start: 13 outliers final: 9 residues processed: 101 average time/residue: 0.2551 time to fit residues: 35.1153 Evaluate side-chains 100 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 90 time to evaluate : 0.772 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 420 ASP 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=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 7 optimal weight: 1.9990 chunk 42 optimal weight: 0.7980 chunk 15 optimal weight: 0.2980 chunk 48 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 30 optimal weight: 2.9990 chunk 67 optimal weight: 0.6980 chunk 76 optimal weight: 0.0040 chunk 5 optimal weight: 3.9990 chunk 37 optimal weight: 1.9990 chunk 70 optimal weight: 0.9980 overall best weight: 0.5592 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081746 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3040 r_free = 0.3040 target = 0.067679 restraints weight = 16679.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3092 r_free = 0.3092 target = 0.070241 restraints weight = 7952.959| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 41)----------------| | r_work = 0.3125 r_free = 0.3125 target = 0.071925 restraints weight = 5036.149| |-----------------------------------------------------------------------------| r_work (final): 0.3125 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8369 moved from start: 0.1706 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6756 Z= 0.120 Angle : 0.504 5.209 9212 Z= 0.269 Chirality : 0.042 0.138 1000 Planarity : 0.003 0.036 1184 Dihedral : 4.105 15.553 932 Min Nonbonded Distance : 2.543 Molprobity Statistics. All-atom Clashscore : 5.84 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.68 % Favored : 96.32 % Rotamer: Outliers : 1.97 % Allowed : 13.52 % 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: -1.29 (0.29), residues: 842 helix: -4.04 (0.42), residues: 54 sheet: -0.11 (0.32), residues: 278 loop : -0.90 (0.27), residues: 510 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 0.007 0.001 PHE A 347 TYR 0.010 0.001 TYR A 380 ARG 0.003 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.02626 ( 186) hydrogen bonds : angle 6.08047 ( 459) SS BOND : bond 0.00505 ( 14) SS BOND : angle 1.02033 ( 28) covalent geometry : bond 0.00274 ( 6742) covalent geometry : angle 0.50186 ( 9184) *********************** 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 119 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 105 time to evaluate : 0.721 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.8739 (m) cc_final: 0.8130 (p) REVERT: B 420 ASP cc_start: 0.8617 (OUTLIER) cc_final: 0.8324 (t0) REVERT: D 96 ASP cc_start: 0.8157 (p0) cc_final: 0.7277 (p0) outliers start: 14 outliers final: 9 residues processed: 112 average time/residue: 0.1691 time to fit residues: 26.0106 Evaluate side-chains 106 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 10 poor density : 96 time to evaluate : 0.796 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 420 ASP 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=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 15 optimal weight: 0.8980 chunk 63 optimal weight: 4.9990 chunk 11 optimal weight: 2.9990 chunk 68 optimal weight: 0.7980 chunk 50 optimal weight: 0.8980 chunk 66 optimal weight: 0.7980 chunk 81 optimal weight: 2.9990 chunk 43 optimal weight: 3.9990 chunk 10 optimal weight: 0.5980 chunk 3 optimal weight: 4.9990 chunk 70 optimal weight: 0.9990 overall best weight: 0.7980 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3311 r_free = 0.3311 target = 0.081215 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3035 r_free = 0.3035 target = 0.067357 restraints weight = 16768.128| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 41)----------------| | r_work = 0.3088 r_free = 0.3088 target = 0.069913 restraints weight = 7961.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071595 restraints weight = 5019.118| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8382 moved from start: 0.1876 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 6756 Z= 0.154 Angle : 0.528 6.015 9212 Z= 0.284 Chirality : 0.042 0.138 1000 Planarity : 0.004 0.045 1184 Dihedral : 4.199 16.077 932 Min Nonbonded Distance : 2.521 Molprobity Statistics. All-atom Clashscore : 6.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.54 % Allowed : 13.80 % Favored : 83.66 % 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: -4.10 (0.41), residues: 54 sheet: -0.15 (0.32), residues: 278 loop : -0.99 (0.27), residues: 510 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 0.009 0.001 PHE E 95 TYR 0.010 0.001 TYR A 380 ARG 0.002 0.000 ARG D 61 Details of bonding type rmsd hydrogen bonds : bond 0.02767 ( 186) hydrogen bonds : angle 6.09803 ( 459) SS BOND : bond 0.00416 ( 14) SS BOND : angle 1.16413 ( 28) covalent geometry : bond 0.00350 ( 6742) covalent geometry : angle 0.52478 ( 9184) *********************** 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 118 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 18 poor density : 100 time to evaluate : 0.755 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.8741 (m) cc_final: 0.8060 (p) REVERT: B 420 ASP cc_start: 0.8600 (OUTLIER) cc_final: 0.8319 (t0) REVERT: B 474 GLN cc_start: 0.8346 (tm-30) cc_final: 0.8059 (tm-30) REVERT: D 96 ASP cc_start: 0.8194 (p0) cc_final: 0.7306 (p0) outliers start: 18 outliers final: 12 residues processed: 111 average time/residue: 0.1795 time to fit residues: 27.0437 Evaluate side-chains 109 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 13 poor density : 96 time to evaluate : 0.727 ------------------------------------------------------------------------------- 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 420 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS 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=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 60 optimal weight: 2.9990 chunk 75 optimal weight: 2.9990 chunk 69 optimal weight: 2.9990 chunk 26 optimal weight: 0.0570 chunk 57 optimal weight: 4.9990 chunk 66 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 81 optimal weight: 0.8980 chunk 54 optimal weight: 4.9990 chunk 32 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 overall best weight: 0.6900 ------------------------------------------------------------------------------- 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 = 0.3314 r_free = 0.3314 target = 0.081691 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3037 r_free = 0.3037 target = 0.067488 restraints weight = 16743.838| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 33)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070051 restraints weight = 8087.243| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3122 r_free = 0.3122 target = 0.071732 restraints weight = 5166.140| |-----------------------------------------------------------------------------| r_work (final): 0.3118 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.1974 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6756 Z= 0.137 Angle : 0.537 11.646 9212 Z= 0.281 Chirality : 0.042 0.136 1000 Planarity : 0.004 0.045 1184 Dihedral : 4.145 15.802 932 Min Nonbonded Distance : 2.500 Molprobity Statistics. All-atom Clashscore : 6.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.16 % Favored : 95.84 % Rotamer: Outliers : 2.25 % Allowed : 14.51 % Favored : 83.24 % 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: -1.42 (0.28), residues: 842 helix: -4.06 (0.42), residues: 54 sheet: -0.19 (0.32), residues: 278 loop : -1.00 (0.27), residues: 510 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 0.010 0.001 TYR A 380 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.02626 ( 186) hydrogen bonds : angle 6.02170 ( 459) SS BOND : bond 0.00480 ( 14) SS BOND : angle 1.01651 ( 28) covalent geometry : bond 0.00313 ( 6742) covalent geometry : angle 0.53483 ( 9184) *********************** 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 114 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 98 time to evaluate : 0.709 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8298 (pt0) cc_final: 0.8065 (pt0) REVERT: B 376 THR cc_start: 0.8719 (m) cc_final: 0.8167 (p) REVERT: B 420 ASP cc_start: 0.8596 (OUTLIER) cc_final: 0.8304 (t0) REVERT: D 96 ASP cc_start: 0.8173 (p0) cc_final: 0.7302 (p0) outliers start: 16 outliers final: 13 residues processed: 107 average time/residue: 0.1720 time to fit residues: 24.9668 Evaluate side-chains 110 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.684 ------------------------------------------------------------------------------- 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 394 ASN Chi-restraints excluded: chain B residue 420 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 24 optimal weight: 3.9990 chunk 77 optimal weight: 0.4980 chunk 65 optimal weight: 0.9990 chunk 10 optimal weight: 0.9980 chunk 48 optimal weight: 2.9990 chunk 80 optimal weight: 5.9990 chunk 25 optimal weight: 1.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.0670 chunk 83 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 overall best weight: 0.6520 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3317 r_free = 0.3317 target = 0.081497 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 34)----------------| | r_work = 0.3039 r_free = 0.3039 target = 0.067424 restraints weight = 16703.781| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3093 r_free = 0.3093 target = 0.070028 restraints weight = 7958.783| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 26)----------------| | r_work = 0.3126 r_free = 0.3126 target = 0.071700 restraints weight = 5070.431| |-----------------------------------------------------------------------------| r_work (final): 0.3124 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8378 moved from start: 0.2095 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 6756 Z= 0.134 Angle : 0.529 9.921 9212 Z= 0.280 Chirality : 0.042 0.136 1000 Planarity : 0.004 0.045 1184 Dihedral : 4.115 15.588 932 Min Nonbonded Distance : 2.467 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % 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: -1.38 (0.28), residues: 842 helix: -4.07 (0.42), residues: 54 sheet: -0.07 (0.33), residues: 266 loop : -1.02 (0.26), 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 0.012 0.001 PHE B 486 TYR 0.010 0.001 TYR A 380 ARG 0.002 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.02536 ( 186) hydrogen bonds : angle 5.96030 ( 459) SS BOND : bond 0.00411 ( 14) SS BOND : angle 1.01735 ( 28) covalent geometry : bond 0.00303 ( 6742) covalent geometry : angle 0.52724 ( 9184) *********************** 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 112 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 16 poor density : 96 time to evaluate : 0.798 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8308 (pt0) cc_final: 0.8066 (pt0) REVERT: B 376 THR cc_start: 0.8729 (m) cc_final: 0.8099 (p) REVERT: B 420 ASP cc_start: 0.8575 (OUTLIER) cc_final: 0.8294 (t0) REVERT: D 96 ASP cc_start: 0.8195 (p0) cc_final: 0.7336 (p0) outliers start: 16 outliers final: 10 residues processed: 104 average time/residue: 0.1884 time to fit residues: 26.7879 Evaluate side-chains 105 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 11 poor density : 94 time to evaluate : 0.710 ------------------------------------------------------------------------------- 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 420 ASP 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 117 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 3.9990 chunk 59 optimal weight: 0.2980 chunk 38 optimal weight: 3.9990 chunk 2 optimal weight: 2.9990 chunk 1 optimal weight: 1.9990 chunk 5 optimal weight: 0.0570 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 0.9980 chunk 42 optimal weight: 0.9980 chunk 56 optimal weight: 2.9990 overall best weight: 0.5498 ------------------------------------------------------------------------------- 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3324 r_free = 0.3324 target = 0.082138 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3045 r_free = 0.3045 target = 0.067814 restraints weight = 16899.644| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3097 r_free = 0.3097 target = 0.070420 restraints weight = 8115.902| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 37)----------------| | r_work = 0.3130 r_free = 0.3130 target = 0.072099 restraints weight = 5187.116| |-----------------------------------------------------------------------------| r_work (final): 0.3127 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8368 moved from start: 0.2092 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6756 Z= 0.122 Angle : 0.533 8.846 9212 Z= 0.279 Chirality : 0.042 0.135 1000 Planarity : 0.004 0.045 1184 Dihedral : 4.013 15.738 932 Min Nonbonded Distance : 2.455 Molprobity Statistics. All-atom Clashscore : 6.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.97 % Allowed : 15.35 % Favored : 82.68 % 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 (0.28), residues: 842 helix: -3.97 (0.43), residues: 54 sheet: -0.07 (0.33), residues: 256 loop : -0.97 (0.26), residues: 532 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 0.002 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.02505 ( 186) hydrogen bonds : angle 5.87919 ( 459) SS BOND : bond 0.00462 ( 14) SS BOND : angle 0.98768 ( 28) covalent geometry : bond 0.00278 ( 6742) covalent geometry : angle 0.53126 ( 9184) *********************** 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 110 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 14 poor density : 96 time to evaluate : 0.685 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8351 (pt0) cc_final: 0.8117 (pt0) REVERT: B 376 THR cc_start: 0.8707 (m) cc_final: 0.8259 (p) REVERT: B 420 ASP cc_start: 0.8587 (OUTLIER) cc_final: 0.8297 (t0) REVERT: D 96 ASP cc_start: 0.8170 (p0) cc_final: 0.7287 (p0) outliers start: 14 outliers final: 12 residues processed: 103 average time/residue: 0.1934 time to fit residues: 26.9922 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 : 0.696 ------------------------------------------------------------------------------- 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 420 ASP 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 46 GLU 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 63 optimal weight: 2.9990 chunk 40 optimal weight: 0.3980 chunk 6 optimal weight: 0.0980 chunk 54 optimal weight: 0.0980 chunk 8 optimal weight: 0.0670 chunk 28 optimal weight: 0.9990 chunk 65 optimal weight: 0.0060 chunk 70 optimal weight: 2.9990 chunk 46 optimal weight: 1.9990 chunk 15 optimal weight: 0.1980 chunk 1 optimal weight: 2.9990 overall best weight: 0.0934 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3365 r_free = 0.3365 target = 0.084032 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3095 r_free = 0.3095 target = 0.069989 restraints weight = 16716.684| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 39)----------------| | r_work = 0.3147 r_free = 0.3147 target = 0.072628 restraints weight = 7784.068| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3180 r_free = 0.3180 target = 0.074332 restraints weight = 4898.060| |-----------------------------------------------------------------------------| r_work (final): 0.3183 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8303 moved from start: 0.2372 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.031 6756 Z= 0.094 Angle : 0.524 8.038 9212 Z= 0.273 Chirality : 0.042 0.132 1000 Planarity : 0.004 0.048 1184 Dihedral : 3.758 15.727 932 Min Nonbonded Distance : 2.421 Molprobity Statistics. All-atom Clashscore : 5.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 0.99 % Allowed : 16.62 % Favored : 82.39 % 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: -1.22 (0.28), residues: 842 helix: -3.97 (0.43), residues: 54 sheet: 0.07 (0.33), residues: 252 loop : -0.91 (0.26), residues: 536 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.001 0.000 HIS B 519 PHE 0.010 0.001 PHE B 486 TYR 0.009 0.001 TYR A 380 ARG 0.001 0.000 ARG G 98 Details of bonding type rmsd hydrogen bonds : bond 0.02279 ( 186) hydrogen bonds : angle 5.59822 ( 459) SS BOND : bond 0.00449 ( 14) SS BOND : angle 0.94698 ( 28) covalent geometry : bond 0.00203 ( 6742) covalent geometry : angle 0.52248 ( 9184) ********************** 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 108 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 7 poor density : 101 time to evaluate : 0.782 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 340 GLU cc_start: 0.8329 (pt0) cc_final: 0.8102 (pt0) REVERT: B 376 THR cc_start: 0.8620 (m) cc_final: 0.8235 (p) REVERT: B 420 ASP cc_start: 0.8574 (m-30) cc_final: 0.8278 (t0) REVERT: B 515 PHE cc_start: 0.7192 (m-10) cc_final: 0.6974 (m-80) REVERT: D 96 ASP cc_start: 0.8123 (p0) cc_final: 0.7270 (p0) outliers start: 7 outliers final: 5 residues processed: 104 average time/residue: 0.1831 time to fit residues: 25.8601 Evaluate side-chains 96 residues out of total 710 (non-[ALA,GLY,PRO]) need to be fit. rotamer outliers: 5 poor density : 91 time to evaluate : 0.810 ------------------------------------------------------------------------------- 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 480 CYS Chi-restraints excluded: chain G residue 59 ILE 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 57 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 5 optimal weight: 0.3980 chunk 62 optimal weight: 0.5980 chunk 73 optimal weight: 1.9990 chunk 7 optimal weight: 0.9980 chunk 10 optimal weight: 0.9980 chunk 60 optimal weight: 0.8980 chunk 28 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 ** F 31 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3325 r_free = 0.3325 target = 0.082208 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3053 r_free = 0.3053 target = 0.068345 restraints weight = 16937.763| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.070891 restraints weight = 8070.730| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.3135 r_free = 0.3135 target = 0.072520 restraints weight = 5133.276| |-----------------------------------------------------------------------------| r_work (final): 0.3131 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8370 moved from start: 0.2388 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 6756 Z= 0.151 Angle : 0.544 7.598 9212 Z= 0.288 Chirality : 0.042 0.145 1000 Planarity : 0.004 0.047 1184 Dihedral : 3.967 16.180 932 Min Nonbonded Distance : 2.404 Molprobity Statistics. All-atom Clashscore : 6.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 0.85 % Allowed : 17.46 % 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: -1.28 (0.28), residues: 842 helix: -3.92 (0.45), residues: 54 sheet: -0.01 (0.32), residues: 266 loop : -0.95 (0.26), residues: 522 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP B 436 HIS 0.001 0.000 HIS A 505 PHE 0.011 0.001 PHE E 95 TYR 0.019 0.001 TYR A 365 ARG 0.003 0.000 ARG B 454 Details of bonding type rmsd hydrogen bonds : bond 0.02545 ( 186) hydrogen bonds : angle 5.72860 ( 459) SS BOND : bond 0.00439 ( 14) SS BOND : angle 0.99213 ( 28) covalent geometry : bond 0.00343 ( 6742) covalent geometry : angle 0.54220 ( 9184) Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3107.51 seconds wall clock time: 56 minutes 46.82 seconds (3406.82 seconds total)