Starting phenix.real_space_refine on Sat Apr 6 01:26:08 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzz_34406/04_2024/8gzz_34406.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzz_34406/04_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/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzz_34406/04_2024/8gzz_34406.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzz_34406/04_2024/8gzz_34406.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzz_34406/04_2024/8gzz_34406.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8gzz_34406/04_2024/8gzz_34406.pdb" } 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 Residue "A ARG 357": "NH1" <-> "NH2" Residue "D GLU 106": "OE1" <-> "OE2" Residue "F TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F PHE 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "G GLU 5": "OE1" <-> "OE2" Residue "G GLU 46": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/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: 4.06, per 1000 atoms: 0.62 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 - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.27 Conformation dependent library (CDL) restraints added in 1.3 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: 0.82 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: 1.87 Time building geometry restraints manager: 2.53 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: 99.05 - 106.04: 158 106.04 - 113.02: 3488 113.02 - 120.00: 2282 120.00 - 126.99: 3180 126.99 - 133.97: 76 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 2.440 nonbonded pdb=" O SER E 29 " pdb=" OG1 THR E 53 " model vdw 2.299 2.440 nonbonded pdb=" O SER G 29 " pdb=" OG1 THR G 53 " model vdw 2.334 2.440 nonbonded pdb=" NE2 GLN F 90 " pdb=" O SER F 93 " model vdw 2.337 2.520 nonbonded pdb=" OD2 ASP A 364 " pdb=" OG SER A 366 " model vdw 2.340 2.440 ... (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 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: 7.180 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.010 Extract box with map and model: 27.120 Check model and map are aligned: 0.090 Set scattering table: 0.070 Process input model: 21.590 Find NCS groups from input model: 0.370 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:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 59.300 ------------------------------------------------------------------------------- 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 fitting. rotamer outliers: 0 poor density : 113 time to evaluate : 0.732 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 113 average time/residue: 0.2196 time to fit residues: 32.2347 Evaluate side-chains 93 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 93 time to evaluate : 0.707 ------------------------------------------------------------------------------- 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: 1.9990 chunk 63 optimal weight: 2.9990 chunk 35 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 42 optimal weight: 1.9990 chunk 34 optimal weight: 3.9990 chunk 65 optimal weight: 0.0270 chunk 25 optimal weight: 0.6980 chunk 40 optimal weight: 1.9990 chunk 49 optimal weight: 0.9990 chunk 76 optimal weight: 0.8980 overall best weight: 0.9242 ------------------------------------------------------------------------------- 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** D 31 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8395 moved from start: 0.1017 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.034 6742 Z= 0.255 Angle : 0.543 5.005 9184 Z= 0.293 Chirality : 0.043 0.141 1000 Planarity : 0.004 0.039 1184 Dihedral : 4.263 16.566 932 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 7.24 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 1.55 % Allowed : 7.46 % Favored : 90.99 % 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: -3.80 (0.45), residues: 54 sheet: 0.30 (0.32), residues: 284 loop : -0.93 (0.27), residues: 504 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 0.044 0.001 PHE B 374 TYR 0.011 0.001 TYR D 49 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 109 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 98 time to evaluate : 0.880 Fit side-chains revert: symmetry clash outliers start: 11 outliers final: 8 residues processed: 102 average time/residue: 0.2194 time to fit residues: 29.4935 Evaluate side-chains 101 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 93 time to evaluate : 1.068 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 415 THR Chi-restraints excluded: chain B residue 398 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 117 LEU Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 42 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 63 optimal weight: 3.9990 chunk 51 optimal weight: 3.9990 chunk 21 optimal weight: 0.9980 chunk 76 optimal weight: 0.4980 chunk 82 optimal weight: 0.8980 chunk 68 optimal weight: 0.6980 chunk 75 optimal weight: 0.9990 chunk 26 optimal weight: 1.9990 chunk 61 optimal weight: 0.9980 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** A 505 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8390 moved from start: 0.1254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 6742 Z= 0.222 Angle : 0.514 4.833 9184 Z= 0.276 Chirality : 0.042 0.144 1000 Planarity : 0.004 0.035 1184 Dihedral : 4.199 15.800 932 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 1.83 % Allowed : 11.27 % Favored : 86.90 % 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: -1.09 (0.29), residues: 842 helix: -3.94 (0.45), residues: 54 sheet: 0.25 (0.32), residues: 284 loop : -0.92 (0.27), residues: 504 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 0.010 0.001 PHE A 347 TYR 0.010 0.001 TYR D 49 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 110 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 97 time to evaluate : 0.706 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 376 THR cc_start: 0.8893 (m) cc_final: 0.8311 (p) outliers start: 13 outliers final: 9 residues processed: 104 average time/residue: 0.1779 time to fit residues: 25.3146 Evaluate side-chains 102 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 93 time to evaluate : 0.819 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 398 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=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 57 optimal weight: 4.9990 chunk 39 optimal weight: 0.0570 chunk 8 optimal weight: 1.9990 chunk 36 optimal weight: 0.5980 chunk 51 optimal weight: 2.9990 chunk 76 optimal weight: 1.9990 chunk 81 optimal weight: 0.7980 chunk 40 optimal weight: 0.8980 chunk 72 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 overall best weight: 0.8700 ------------------------------------------------------------------------------- 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: 0.8399 moved from start: 0.1495 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6742 Z= 0.236 Angle : 0.515 6.093 9184 Z= 0.276 Chirality : 0.042 0.140 1000 Planarity : 0.004 0.037 1184 Dihedral : 4.178 16.842 932 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 7.63 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.92 % Favored : 96.08 % Rotamer: Outliers : 1.97 % Allowed : 13.38 % Favored : 84.65 % 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: -1.13 (0.29), residues: 842 helix: -3.97 (0.45), residues: 54 sheet: 0.13 (0.32), residues: 296 loop : -0.91 (0.28), residues: 492 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP B 436 HIS 0.002 0.000 HIS A 505 PHE 0.010 0.001 PHE E 95 TYR 0.009 0.001 TYR D 49 ARG 0.003 0.000 ARG B 454 *********************** 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 114 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 100 time to evaluate : 0.765 Fit side-chains revert: symmetry clash REVERT: B 376 THR cc_start: 0.8885 (m) cc_final: 0.8233 (p) outliers start: 14 outliers final: 11 residues processed: 105 average time/residue: 0.1709 time to fit residues: 25.0966 Evaluate side-chains 108 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 97 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE 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: 5.9990 chunk 46 optimal weight: 1.9990 chunk 1 optimal weight: 2.9990 chunk 60 optimal weight: 0.6980 chunk 33 optimal weight: 1.9990 chunk 69 optimal weight: 2.9990 chunk 56 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 41 optimal weight: 1.9990 chunk 72 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 overall best weight: 1.7388 ------------------------------------------------------------------------------- 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: 0.8469 moved from start: 0.1765 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.068 6742 Z= 0.432 Angle : 0.613 7.999 9184 Z= 0.329 Chirality : 0.045 0.140 1000 Planarity : 0.004 0.042 1184 Dihedral : 4.737 17.018 932 Min Nonbonded Distance : 2.145 Molprobity Statistics. All-atom Clashscore : 8.87 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.18 % Favored : 93.82 % Rotamer: Outliers : 2.39 % Allowed : 15.63 % Favored : 81.97 % 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: -1.36 (0.29), residues: 842 helix: -3.84 (0.49), residues: 54 sheet: 0.17 (0.35), residues: 246 loop : -1.14 (0.26), residues: 542 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP B 436 HIS 0.003 0.001 HIS A 505 PHE 0.016 0.002 PHE E 95 TYR 0.015 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 110 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 93 time to evaluate : 0.694 Fit side-chains REVERT: B 376 THR cc_start: 0.9138 (m) cc_final: 0.8637 (p) outliers start: 17 outliers final: 13 residues processed: 100 average time/residue: 0.1676 time to fit residues: 23.0017 Evaluate side-chains 100 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 87 time to evaluate : 0.839 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE 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 27 optimal weight: 2.9990 chunk 73 optimal weight: 4.9990 chunk 16 optimal weight: 0.9980 chunk 47 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 81 optimal weight: 0.2980 chunk 67 optimal weight: 4.9990 chunk 37 optimal weight: 0.9990 chunk 6 optimal weight: 0.6980 chunk 26 optimal weight: 0.9990 chunk 42 optimal weight: 0.9990 overall best weight: 0.7782 ------------------------------------------------------------------------------- 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: 0.8423 moved from start: 0.1852 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 6742 Z= 0.228 Angle : 0.539 6.346 9184 Z= 0.288 Chirality : 0.042 0.139 1000 Planarity : 0.004 0.048 1184 Dihedral : 4.453 16.506 932 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.96 % Allowed : 15.63 % Favored : 81.41 % 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: -1.52 (0.28), residues: 842 helix: -3.92 (0.46), residues: 54 sheet: 0.00 (0.33), residues: 260 loop : -1.25 (0.26), residues: 528 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 0.009 0.001 PHE E 95 TYR 0.009 0.001 TYR D 49 ARG 0.003 0.000 ARG B 454 *********************** 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 119 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 98 time to evaluate : 0.741 Fit side-chains REVERT: B 376 THR cc_start: 0.8983 (m) cc_final: 0.8417 (p) REVERT: B 474 GLN cc_start: 0.8228 (tm-30) cc_final: 0.7931 (tm-30) REVERT: D 7 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8265 (p) REVERT: D 42 GLN cc_start: 0.8641 (OUTLIER) cc_final: 0.8140 (mp10) REVERT: D 96 ASP cc_start: 0.8096 (p0) cc_final: 0.7140 (p0) outliers start: 21 outliers final: 16 residues processed: 108 average time/residue: 0.1844 time to fit residues: 26.8224 Evaluate side-chains 110 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 92 time to evaluate : 0.773 ------------------------------------------------------------------------------- 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 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain B residue 480 CYS Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 42 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 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: 1.9990 chunk 59 optimal weight: 2.9990 chunk 45 optimal weight: 0.6980 chunk 68 optimal weight: 0.9980 chunk 80 optimal weight: 4.9990 chunk 50 optimal weight: 2.9990 chunk 49 optimal weight: 1.9990 chunk 37 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8449 moved from start: 0.2067 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.037 6742 Z= 0.331 Angle : 0.571 6.123 9184 Z= 0.306 Chirality : 0.044 0.138 1000 Planarity : 0.004 0.046 1184 Dihedral : 4.579 18.136 932 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.46 % Favored : 94.54 % Rotamer: Outliers : 3.10 % Allowed : 16.76 % Favored : 80.14 % 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: -1.55 (0.28), residues: 842 helix: -3.82 (0.49), residues: 54 sheet: -0.01 (0.34), residues: 248 loop : -1.26 (0.26), residues: 540 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 0.044 0.002 PHE B 374 TYR 0.012 0.001 TYR E 103 ARG 0.004 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 112 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 90 time to evaluate : 0.709 Fit side-chains REVERT: B 340 GLU cc_start: 0.8150 (pt0) cc_final: 0.7932 (pt0) REVERT: B 376 THR cc_start: 0.9056 (m) cc_final: 0.8593 (p) REVERT: D 7 THR cc_start: 0.8511 (OUTLIER) cc_final: 0.8288 (p) REVERT: D 42 GLN cc_start: 0.8649 (OUTLIER) cc_final: 0.8151 (mp10) REVERT: D 96 ASP cc_start: 0.8119 (p0) cc_final: 0.7155 (p0) outliers start: 22 outliers final: 15 residues processed: 102 average time/residue: 0.1823 time to fit residues: 24.9468 Evaluate side-chains 105 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 88 time to evaluate : 0.780 ------------------------------------------------------------------------------- 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 415 THR Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 42 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=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 48 optimal weight: 0.7980 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 0.9980 chunk 51 optimal weight: 2.9990 chunk 55 optimal weight: 1.9990 chunk 40 optimal weight: 1.9990 chunk 7 optimal weight: 0.9990 chunk 63 optimal weight: 3.9990 chunk 73 optimal weight: 3.9990 chunk 77 optimal weight: 0.6980 chunk 70 optimal weight: 0.9980 overall best weight: 0.8982 ------------------------------------------------------------------------------- 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: 0.8427 moved from start: 0.2151 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 6742 Z= 0.243 Angle : 0.541 7.818 9184 Z= 0.287 Chirality : 0.042 0.137 1000 Planarity : 0.004 0.045 1184 Dihedral : 4.380 15.896 932 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 2.82 % Allowed : 17.61 % Favored : 79.58 % 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: -1.61 (0.28), residues: 842 helix: -3.80 (0.49), residues: 54 sheet: 0.05 (0.34), residues: 248 loop : -1.37 (0.26), residues: 540 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 0.010 0.001 PHE E 95 TYR 0.009 0.001 TYR E 103 ARG 0.003 0.000 ARG B 454 *********************** 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 fitting. rotamer outliers: 20 poor density : 96 time to evaluate : 0.799 Fit side-chains REVERT: A 365 TYR cc_start: 0.7289 (p90) cc_final: 0.6802 (p90) REVERT: B 340 GLU cc_start: 0.8153 (pt0) cc_final: 0.7935 (pt0) REVERT: B 376 THR cc_start: 0.8938 (m) cc_final: 0.8623 (p) REVERT: B 430 THR cc_start: 0.9168 (OUTLIER) cc_final: 0.8961 (p) REVERT: D 7 THR cc_start: 0.8478 (OUTLIER) cc_final: 0.8261 (p) REVERT: D 42 GLN cc_start: 0.8622 (OUTLIER) cc_final: 0.8121 (mp10) REVERT: D 96 ASP cc_start: 0.8092 (p0) cc_final: 0.7152 (p0) outliers start: 20 outliers final: 15 residues processed: 107 average time/residue: 0.1710 time to fit residues: 24.8417 Evaluate side-chains 107 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 89 time to evaluate : 0.738 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 402 ILE Chi-restraints excluded: chain B residue 430 THR Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 42 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=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 84 random chunks: chunk 75 optimal weight: 2.9990 chunk 77 optimal weight: 4.9990 chunk 45 optimal weight: 0.5980 chunk 32 optimal weight: 3.9990 chunk 59 optimal weight: 1.9990 chunk 23 optimal weight: 0.8980 chunk 68 optimal weight: 0.9980 chunk 71 optimal weight: 0.0270 chunk 49 optimal weight: 3.9990 chunk 79 optimal weight: 0.9990 chunk 48 optimal weight: 0.7980 overall best weight: 0.6638 ------------------------------------------------------------------------------- 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: 0.8408 moved from start: 0.2234 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= 0.201 Angle : 0.549 12.571 9184 Z= 0.284 Chirality : 0.042 0.135 1000 Planarity : 0.004 0.045 1184 Dihedral : 4.223 16.248 932 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 7.86 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.28 % Favored : 95.72 % Rotamer: Outliers : 2.54 % Allowed : 18.03 % Favored : 79.44 % 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: -1.59 (0.28), residues: 842 helix: -3.82 (0.48), residues: 54 sheet: 0.11 (0.34), residues: 246 loop : -1.37 (0.26), residues: 542 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 0.013 0.001 PHE B 486 TYR 0.009 0.001 TYR D 49 ARG 0.003 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 112 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 94 time to evaluate : 0.797 Fit side-chains REVERT: A 365 TYR cc_start: 0.7326 (p90) cc_final: 0.6826 (p90) REVERT: B 340 GLU cc_start: 0.8169 (pt0) cc_final: 0.7956 (pt0) REVERT: B 376 THR cc_start: 0.8893 (m) cc_final: 0.8674 (p) REVERT: D 7 THR cc_start: 0.8483 (OUTLIER) cc_final: 0.8262 (p) REVERT: D 42 GLN cc_start: 0.8575 (OUTLIER) cc_final: 0.8080 (mp10) REVERT: D 96 ASP cc_start: 0.8050 (p0) cc_final: 0.7102 (p0) outliers start: 18 outliers final: 13 residues processed: 104 average time/residue: 0.1802 time to fit residues: 25.3328 Evaluate side-chains 106 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 91 time to evaluate : 0.647 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 42 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 37 optimal weight: 2.9990 chunk 55 optimal weight: 2.9990 chunk 83 optimal weight: 1.9990 chunk 77 optimal weight: 2.9990 chunk 66 optimal weight: 2.9990 chunk 6 optimal weight: 0.8980 chunk 51 optimal weight: 0.6980 chunk 40 optimal weight: 0.6980 chunk 52 optimal weight: 0.9980 chunk 70 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 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** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8435 moved from start: 0.2291 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= 0.277 Angle : 0.560 9.452 9184 Z= 0.294 Chirality : 0.043 0.146 1000 Planarity : 0.004 0.044 1184 Dihedral : 4.353 16.318 932 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 8.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.99 % Favored : 95.01 % Rotamer: Outliers : 2.54 % Allowed : 18.73 % Favored : 78.73 % 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: -1.62 (0.28), residues: 842 helix: -3.73 (0.51), residues: 54 sheet: 0.11 (0.34), residues: 244 loop : -1.43 (0.26), residues: 544 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 0.013 0.001 PHE B 486 TYR 0.010 0.001 TYR E 103 ARG 0.003 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 108 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 90 time to evaluate : 0.757 Fit side-chains REVERT: B 340 GLU cc_start: 0.8167 (pt0) cc_final: 0.7953 (pt0) REVERT: D 7 THR cc_start: 0.8493 (OUTLIER) cc_final: 0.8273 (p) REVERT: D 42 GLN cc_start: 0.8612 (OUTLIER) cc_final: 0.8125 (mp10) REVERT: D 96 ASP cc_start: 0.8071 (p0) cc_final: 0.7115 (p0) outliers start: 18 outliers final: 14 residues processed: 100 average time/residue: 0.1736 time to fit residues: 23.5566 Evaluate side-chains 104 residues out of total 710 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 88 time to evaluate : 0.770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 350 VAL Chi-restraints excluded: chain A residue 379 CYS Chi-restraints excluded: chain A residue 392 PHE Chi-restraints excluded: chain A residue 440 LYS Chi-restraints excluded: chain B residue 364 ASP Chi-restraints excluded: chain B residue 398 ASP Chi-restraints excluded: chain B residue 468 ILE Chi-restraints excluded: chain D residue 7 THR Chi-restraints excluded: chain D residue 42 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 61 optimal weight: 1.9990 chunk 9 optimal weight: 0.0370 chunk 18 optimal weight: 0.9990 chunk 66 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 68 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 58 optimal weight: 0.7980 chunk 3 optimal weight: 0.8980 chunk 48 optimal weight: 0.4980 overall best weight: 0.5858 ------------------------------------------------------------------------------- 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 = 0.3309 r_free = 0.3309 target = 0.081186 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3036 r_free = 0.3036 target = 0.067421 restraints weight = 16542.836| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.3089 r_free = 0.3089 target = 0.070006 restraints weight = 7887.491| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3124 r_free = 0.3124 target = 0.071683 restraints weight = 5000.413| |-----------------------------------------------------------------------------| r_work (final): 0.3120 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8381 moved from start: 0.2347 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= 0.181 Angle : 0.531 8.373 9184 Z= 0.279 Chirality : 0.042 0.141 1000 Planarity : 0.004 0.041 1184 Dihedral : 4.161 16.332 932 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 7.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.39 % Favored : 95.61 % Rotamer: Outliers : 2.39 % Allowed : 18.87 % Favored : 78.73 % 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: -1.55 (0.28), residues: 842 helix: -3.81 (0.49), residues: 54 sheet: 0.19 (0.34), residues: 242 loop : -1.37 (0.26), residues: 546 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 0.012 0.001 PHE B 486 TYR 0.008 0.001 TYR D 49 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: 2051.92 seconds wall clock time: 38 minutes 30.45 seconds (2310.45 seconds total)