Starting phenix.real_space_refine on Thu Jul 18 18:39:14 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/07_2024/7r7n_24299.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/07_2024/7r7n_24299.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.95 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/07_2024/7r7n_24299.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/07_2024/7r7n_24299.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/07_2024/7r7n_24299.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7r7n_24299/07_2024/7r7n_24299.cif" } resolution = 3.95 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= 0.000 sd= 0.018 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 17 5.16 5 C 1795 2.51 5 N 481 2.21 5 O 497 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 60": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 113": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 380": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 396": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 421": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E ASP 428": "OD1" <-> "OD2" Residue "E TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 453": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 495": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 71": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 2790 Number of models: 1 Model: "" Number of chains: 4 Chain: "H" Number of atoms: 735 Number of conformers: 1 Conformer: "" Number of residues, atoms: 109, 735 Classifications: {'peptide': 109} Incomplete info: {'truncation_to_alanine': 33} Link IDs: {'PTRANS': 4, 'TRANS': 104} Chain breaks: 3 Unresolved non-hydrogen bonds: 80 Unresolved non-hydrogen angles: 100 Unresolved non-hydrogen dihedrals: 60 Unresolved non-hydrogen chiralities: 9 Planarities with less than four sites: {'GLU:plan': 5, 'ARG:plan': 2, 'ASP:plan': 4} Unresolved non-hydrogen planarities: 42 Chain: "E" Number of atoms: 1382 Number of conformers: 1 Conformer: "" Number of residues, atoms: 189, 1382 Classifications: {'peptide': 189} Incomplete info: {'truncation_to_alanine': 43} Link IDs: {'PTRANS': 10, 'TRANS': 178} Chain breaks: 1 Unresolved non-hydrogen bonds: 118 Unresolved non-hydrogen angles: 149 Unresolved non-hydrogen dihedrals: 92 Unresolved non-hydrogen chiralities: 12 Planarities with less than four sites: {'GLN:plan1': 1, 'TYR:plan': 1, 'ASN:plan1': 4, 'ASP:plan': 4, 'PHE:plan': 1, 'GLU:plan': 5} Unresolved non-hydrogen planarities: 61 Chain: "L" Number of atoms: 635 Number of conformers: 1 Conformer: "" Number of residues, atoms: 93, 635 Classifications: {'peptide': 93} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 2, 'PTRANS': 3, 'TRANS': 87} Chain breaks: 2 Unresolved non-hydrogen bonds: 75 Unresolved non-hydrogen angles: 91 Unresolved non-hydrogen dihedrals: 61 Unresolved non-hydrogen chiralities: 6 Planarities with less than four sites: {'GLN:plan1': 5, 'PHE:plan': 1, 'ARG:plan': 1, 'ASP:plan': 2} Unresolved non-hydrogen planarities: 37 Chain: "A" Number of atoms: 38 Number of conformers: 1 Conformer: "" Number of residues, atoms: 3, 38 Unusual residues: {'FUC': 1, 'NAG': 2} Classifications: {'undetermined': 3} Link IDs: {None: 2} Unresolved non-hydrogen bonds: 3 Unresolved non-hydrogen angles: 6 Unresolved non-hydrogen dihedrals: 9 Unresolved non-hydrogen chiralities: 3 Time building chain proxies: 3.42, per 1000 atoms: 1.23 Number of scatterers: 2790 At special positions: 0 Unit cell: (77.7, 66.15, 76.65, 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 17 16.00 O 497 8.00 N 481 7.00 C 1795 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=7, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 96 " distance=2.03 Simple disulfide: pdb=" SG CYS H 103 " - pdb=" SG CYS H 108 " distance=2.12 Simple disulfide: pdb=" SG CYS E 336 " - pdb=" SG CYS E 361 " distance=2.03 Simple disulfide: pdb=" SG CYS E 379 " - pdb=" SG CYS E 432 " distance=2.09 Simple disulfide: pdb=" SG CYS E 391 " - pdb=" SG CYS E 525 " distance=2.03 Simple disulfide: pdb=" SG CYS E 480 " - pdb=" SG CYS E 488 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.21 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 Links applied BETA1-4 " NAG A 1 " - " NAG A 2 " BETA1-6 " NAG A 1 " - " FUC A 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A 1 " - " ASN E 343 " Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 672.7 milliseconds 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 714 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 12.3% alpha, 38.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.47 Creating SS restraints... Processing helix chain 'H' and resid 74 through 76 No H-bonds generated for 'chain 'H' and resid 74 through 76' Processing helix chain 'H' and resid 87 through 91 Processing helix chain 'E' and resid 338 through 343 Processing helix chain 'E' and resid 349 through 353 removed outlier: 3.808A pdb=" N TRP E 353 " --> pdb=" O VAL E 350 " (cutoff:3.500A) Processing helix chain 'E' and resid 365 through 370 Processing helix chain 'E' and resid 405 through 410 removed outlier: 4.413A pdb=" N ARG E 408 " --> pdb=" O ASP E 405 " (cutoff:3.500A) Processing helix chain 'E' and resid 416 through 422 Processing helix chain 'E' and resid 438 through 443 Processing helix chain 'E' and resid 502 through 505 Processing sheet with id=AA1, first strand: chain 'H' and resid 3 through 6 Processing sheet with id=AA2, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.667A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 58 through 60 removed outlier: 5.667A pdb=" N TRP H 47 " --> pdb=" O ARG H 38 " (cutoff:3.500A) removed outlier: 6.607A pdb=" N ARG H 38 " --> pdb=" O TRP H 47 " (cutoff:3.500A) removed outlier: 4.138A pdb=" N GLY H 49 " --> pdb=" O TRP H 36 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'E' and resid 354 through 358 removed outlier: 3.537A pdb=" N VAL E 395 " --> pdb=" O ILE E 358 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'E' and resid 361 through 362 removed outlier: 6.320A pdb=" N CYS E 361 " --> pdb=" O CYS E 525 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'E' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 473 through 474 Processing sheet with id=AA8, first strand: chain 'L' and resid 4 through 7 removed outlier: 3.603A pdb=" N ASP L 70 " --> pdb=" O SER L 67 " (cutoff:3.500A) removed outlier: 3.651A pdb=" N SER L 67 " --> pdb=" O ASP L 70 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'L' and resid 53 through 54 removed outlier: 6.564A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) removed outlier: 5.190A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 7.294A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) 128 hydrogen bonds defined for protein. 297 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: 0.68 Time building geometry restraints manager: 1.11 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 808 1.33 - 1.46: 747 1.46 - 1.58: 1283 1.58 - 1.71: 0 1.71 - 1.83: 20 Bond restraints: 2858 Sorted by residual: bond pdb=" NE ARG L 18 " pdb=" CZ ARG L 18 " ideal model delta sigma weight residual 1.326 1.367 -0.041 1.10e-02 8.26e+03 1.40e+01 bond pdb=" C5 NAG A 2 " pdb=" O5 NAG A 2 " ideal model delta sigma weight residual 1.413 1.470 -0.057 2.00e-02 2.50e+03 8.07e+00 bond pdb=" CB ILE L 2 " pdb=" CG1 ILE L 2 " ideal model delta sigma weight residual 1.530 1.582 -0.052 2.00e-02 2.50e+03 6.86e+00 bond pdb=" CB LEU E 517 " pdb=" CG LEU E 517 " ideal model delta sigma weight residual 1.530 1.579 -0.049 2.00e-02 2.50e+03 5.94e+00 bond pdb=" C5 FUC A 3 " pdb=" O5 FUC A 3 " ideal model delta sigma weight residual 1.423 1.471 -0.048 2.00e-02 2.50e+03 5.81e+00 ... (remaining 2853 not shown) Histogram of bond angle deviations from ideal: 98.92 - 105.91: 81 105.91 - 112.89: 1429 112.89 - 119.88: 846 119.88 - 126.87: 1525 126.87 - 133.86: 26 Bond angle restraints: 3907 Sorted by residual: angle pdb=" C GLY H 27 " pdb=" N PRO H 28 " pdb=" CA PRO H 28 " ideal model delta sigma weight residual 119.85 127.39 -7.54 1.01e+00 9.80e-01 5.58e+01 angle pdb=" C SER E 383 " pdb=" N PRO E 384 " pdb=" CA PRO E 384 " ideal model delta sigma weight residual 119.56 126.71 -7.15 1.02e+00 9.61e-01 4.91e+01 angle pdb=" C GLN E 498 " pdb=" N PRO E 499 " pdb=" CA PRO E 499 " ideal model delta sigma weight residual 119.87 126.95 -7.08 1.04e+00 9.25e-01 4.63e+01 angle pdb=" C ALA L 43 " pdb=" N PRO L 44 " pdb=" CA PRO L 44 " ideal model delta sigma weight residual 119.85 126.57 -6.72 1.01e+00 9.80e-01 4.42e+01 angle pdb=" C PHE E 490 " pdb=" N PRO E 491 " pdb=" CA PRO E 491 " ideal model delta sigma weight residual 119.87 126.77 -6.90 1.04e+00 9.25e-01 4.40e+01 ... (remaining 3902 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 13.05: 1577 13.05 - 26.10: 77 26.10 - 39.14: 14 39.14 - 52.19: 9 52.19 - 65.24: 6 Dihedral angle restraints: 1683 sinusoidal: 561 harmonic: 1122 Sorted by residual: dihedral pdb=" CB CYS H 103 " pdb=" SG CYS H 103 " pdb=" SG CYS H 108 " pdb=" CB CYS H 108 " ideal model delta sinusoidal sigma weight residual -86.00 -151.24 65.24 1 1.00e+01 1.00e-02 5.58e+01 dihedral pdb=" CB CYS E 391 " pdb=" SG CYS E 391 " pdb=" SG CYS E 525 " pdb=" CB CYS E 525 " ideal model delta sinusoidal sigma weight residual 93.00 45.49 47.51 1 1.00e+01 1.00e-02 3.12e+01 dihedral pdb=" CB CYS L 23 " pdb=" SG CYS L 23 " pdb=" SG CYS L 88 " pdb=" CB CYS L 88 " ideal model delta sinusoidal sigma weight residual 93.00 62.52 30.48 1 1.00e+01 1.00e-02 1.33e+01 ... (remaining 1680 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.057: 306 0.057 - 0.114: 93 0.114 - 0.171: 26 0.171 - 0.228: 9 0.228 - 0.285: 6 Chirality restraints: 440 Sorted by residual: chirality pdb=" C1 NAG A 2 " pdb=" O4 NAG A 1 " pdb=" C2 NAG A 2 " pdb=" O5 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.53 0.13 2.00e-02 2.50e+03 4.12e+01 chirality pdb=" C1 FUC A 3 " pdb=" O6 NAG A 1 " pdb=" C2 FUC A 3 " pdb=" O5 FUC A 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.44 0.04 2.00e-02 2.50e+03 4.68e+00 chirality pdb=" C2 NAG A 2 " pdb=" C1 NAG A 2 " pdb=" C3 NAG A 2 " pdb=" N2 NAG A 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.78 0.29 2.00e-01 2.50e+01 2.03e+00 ... (remaining 437 not shown) Planarity restraints: 505 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA TYR E 489 " 0.008 2.00e-02 2.50e+03 1.63e-02 2.66e+00 pdb=" C TYR E 489 " -0.028 2.00e-02 2.50e+03 pdb=" O TYR E 489 " 0.011 2.00e-02 2.50e+03 pdb=" N PHE E 490 " 0.009 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 92 " -0.021 2.00e-02 2.50e+03 1.12e-02 2.53e+00 pdb=" CG TYR L 92 " 0.006 2.00e-02 2.50e+03 pdb=" CD1 TYR L 92 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR L 92 " 0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR L 92 " 0.005 2.00e-02 2.50e+03 pdb=" CE2 TYR L 92 " 0.007 2.00e-02 2.50e+03 pdb=" CZ TYR L 92 " 0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 92 " -0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 449 " 0.019 2.00e-02 2.50e+03 1.06e-02 2.23e+00 pdb=" CG TYR E 449 " -0.008 2.00e-02 2.50e+03 pdb=" CD1 TYR E 449 " -0.006 2.00e-02 2.50e+03 pdb=" CD2 TYR E 449 " -0.008 2.00e-02 2.50e+03 pdb=" CE1 TYR E 449 " -0.006 2.00e-02 2.50e+03 pdb=" CE2 TYR E 449 " -0.005 2.00e-02 2.50e+03 pdb=" CZ TYR E 449 " -0.003 2.00e-02 2.50e+03 pdb=" OH TYR E 449 " 0.017 2.00e-02 2.50e+03 ... (remaining 502 not shown) Histogram of nonbonded interaction distances: 2.55 - 3.02: 1515 3.02 - 3.49: 2477 3.49 - 3.96: 4310 3.96 - 4.43: 4896 4.43 - 4.90: 7917 Nonbonded interactions: 21115 Sorted by model distance: nonbonded pdb=" N ASP E 428 " pdb=" OD1 ASP E 428 " model vdw 2.553 2.520 nonbonded pdb=" N LYS E 462 " pdb=" O LYS E 462 " model vdw 2.609 2.496 nonbonded pdb=" N GLN L 3 " pdb=" OE1 GLN L 3 " model vdw 2.616 2.520 nonbonded pdb=" N THR H 76 " pdb=" N SER H 77 " model vdw 2.623 2.560 nonbonded pdb=" N ALA E 372 " pdb=" N SER E 373 " model vdw 2.627 2.560 ... (remaining 21110 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 2.590 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: 0.100 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 13.910 Find NCS groups from input model: 0.030 Set up NCS constraints: 0.010 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:2.780 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 19.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7587 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 : 0.010 0.057 2858 Z= 0.670 Angle : 1.245 7.544 3907 Z= 0.835 Chirality : 0.069 0.285 440 Planarity : 0.005 0.016 504 Dihedral : 9.309 63.153 948 Min Nonbonded Distance : 2.553 Molprobity Statistics. All-atom Clashscore : 0.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.22 % Favored : 96.78 % Rotamer: Outliers : 0.45 % Allowed : 0.90 % Favored : 98.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: 0.00 (0.43), residues: 373 helix: -4.27 (0.43), residues: 26 sheet: 0.66 (0.46), residues: 126 loop : 0.27 (0.41), residues: 221 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.005 TRP L 35 PHE 0.016 0.003 PHE L 98 TYR 0.021 0.004 TYR L 92 ARG 0.003 0.000 ARG E 454 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 100 time to evaluate : 0.308 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8454 (mp10) cc_final: 0.8035 (tp40) REVERT: E 513 LEU cc_start: 0.8949 (mt) cc_final: 0.8631 (tt) outliers start: 1 outliers final: 1 residues processed: 100 average time/residue: 0.1919 time to fit residues: 22.0919 Evaluate side-chains 56 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 55 time to evaluate : 0.295 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 109 TYR Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 31 optimal weight: 0.6980 chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 0.5980 chunk 9 optimal weight: 0.6980 chunk 18 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 29 optimal weight: 0.8980 chunk 11 optimal weight: 0.3980 chunk 17 optimal weight: 0.0050 chunk 21 optimal weight: 0.6980 chunk 33 optimal weight: 0.9990 overall best weight: 0.4594 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN L 6 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7732 moved from start: 0.2853 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.102 2858 Z= 0.333 Angle : 0.682 10.267 3907 Z= 0.358 Chirality : 0.048 0.184 440 Planarity : 0.004 0.031 504 Dihedral : 5.273 50.700 484 Min Nonbonded Distance : 2.207 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.61 % Favored : 98.39 % Rotamer: Outliers : 6.28 % Allowed : 16.59 % Favored : 77.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.04 (0.42), residues: 373 helix: -3.73 (0.81), residues: 20 sheet: 0.74 (0.46), residues: 130 loop : 0.03 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 PHE 0.017 0.002 PHE H 29 TYR 0.017 0.002 TYR H 95 ARG 0.005 0.001 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.291 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8288 (mp10) cc_final: 0.7938 (tp40) REVERT: E 513 LEU cc_start: 0.9039 (mt) cc_final: 0.8654 (tt) REVERT: L 49 TYR cc_start: 0.8136 (p90) cc_final: 0.7781 (p90) REVERT: L 96 ARG cc_start: 0.7242 (ttt-90) cc_final: 0.6790 (ttm170) outliers start: 14 outliers final: 10 residues processed: 62 average time/residue: 0.1080 time to fit residues: 8.5468 Evaluate side-chains 60 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 50 time to evaluate : 0.292 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 34 ILE Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 349 SER Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 18 optimal weight: 0.3980 chunk 10 optimal weight: 0.6980 chunk 27 optimal weight: 0.4980 chunk 22 optimal weight: 0.5980 chunk 9 optimal weight: 0.9980 chunk 33 optimal weight: 0.9990 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 25 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7817 moved from start: 0.3629 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.082 2858 Z= 0.313 Angle : 0.630 6.193 3907 Z= 0.334 Chirality : 0.046 0.143 440 Planarity : 0.004 0.026 504 Dihedral : 5.331 44.461 484 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 5.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.68 % Favored : 97.32 % Rotamer: Outliers : 7.17 % Allowed : 17.04 % Favored : 75.78 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.11 (0.43), residues: 373 helix: -2.92 (0.93), residues: 26 sheet: 0.97 (0.47), residues: 119 loop : -0.25 (0.40), residues: 228 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP H 47 PHE 0.033 0.002 PHE E 374 TYR 0.014 0.002 TYR H 95 ARG 0.004 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 55 time to evaluate : 0.309 Fit side-chains REVERT: H 3 GLN cc_start: 0.8224 (mp10) cc_final: 0.7939 (tp40) REVERT: E 506 GLN cc_start: 0.8024 (mt0) cc_final: 0.7662 (mt0) REVERT: E 512 VAL cc_start: 0.9472 (t) cc_final: 0.9192 (m) REVERT: E 513 LEU cc_start: 0.9067 (mt) cc_final: 0.8623 (tt) REVERT: L 49 TYR cc_start: 0.8164 (p90) cc_final: 0.7695 (p90) outliers start: 16 outliers final: 12 residues processed: 64 average time/residue: 0.1333 time to fit residues: 10.4746 Evaluate side-chains 60 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.304 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.9980 chunk 16 optimal weight: 0.9990 chunk 22 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 35 optimal weight: 0.9990 chunk 17 optimal weight: 0.3980 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 1.9990 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 6 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7951 moved from start: 0.4438 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.119 2858 Z= 0.490 Angle : 0.745 6.605 3907 Z= 0.395 Chirality : 0.048 0.163 440 Planarity : 0.006 0.072 504 Dihedral : 6.516 47.064 484 Min Nonbonded Distance : 2.169 Molprobity Statistics. All-atom Clashscore : 9.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 8.52 % Allowed : 17.49 % Favored : 73.99 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.64 (0.42), residues: 373 helix: -2.98 (0.95), residues: 26 sheet: 0.91 (0.47), residues: 120 loop : -0.87 (0.38), residues: 227 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.018 0.002 TRP H 47 PHE 0.024 0.003 PHE E 374 TYR 0.015 0.002 TYR H 95 ARG 0.005 0.001 ARG H 98 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 57 time to evaluate : 0.323 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8337 (mp10) cc_final: 0.8023 (tp40) REVERT: E 513 LEU cc_start: 0.9145 (mt) cc_final: 0.8699 (tt) REVERT: L 2 ILE cc_start: 0.7899 (mt) cc_final: 0.7684 (pt) REVERT: L 49 TYR cc_start: 0.8352 (p90) cc_final: 0.7932 (p90) outliers start: 19 outliers final: 17 residues processed: 67 average time/residue: 0.1144 time to fit residues: 9.5646 Evaluate side-chains 68 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 51 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 511 VAL Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 20 THR Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 33 LEU Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.9990 chunk 0 optimal weight: 1.9990 chunk 18 optimal weight: 0.6980 chunk 32 optimal weight: 0.5980 chunk 9 optimal weight: 0.8980 chunk 12 optimal weight: 0.0010 chunk 7 optimal weight: 0.5980 chunk 20 optimal weight: 0.8980 overall best weight: 0.5386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 118 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7925 moved from start: 0.4709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 2858 Z= 0.321 Angle : 0.642 6.289 3907 Z= 0.333 Chirality : 0.046 0.139 440 Planarity : 0.005 0.030 504 Dihedral : 5.888 45.963 484 Min Nonbonded Distance : 2.236 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 6.28 % Allowed : 21.52 % Favored : 72.20 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.71 (0.42), residues: 373 helix: -2.70 (1.02), residues: 26 sheet: 0.84 (0.48), residues: 118 loop : -0.94 (0.38), residues: 229 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 PHE 0.023 0.002 PHE H 29 TYR 0.012 0.001 TYR H 95 ARG 0.006 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 69 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 55 time to evaluate : 0.333 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8304 (mp10) cc_final: 0.8045 (tp40) REVERT: E 511 VAL cc_start: 0.8929 (t) cc_final: 0.8688 (m) REVERT: E 513 LEU cc_start: 0.9095 (mt) cc_final: 0.8670 (tt) REVERT: L 49 TYR cc_start: 0.8317 (p90) cc_final: 0.7917 (p90) outliers start: 14 outliers final: 13 residues processed: 62 average time/residue: 0.1055 time to fit residues: 8.4442 Evaluate side-chains 64 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 51 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 88 CYS Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 8 optimal weight: 0.1980 chunk 35 optimal weight: 0.6980 chunk 29 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 2 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 4 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 26 optimal weight: 0.0980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.4973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.069 2858 Z= 0.269 Angle : 0.609 5.743 3907 Z= 0.314 Chirality : 0.045 0.135 440 Planarity : 0.004 0.028 504 Dihedral : 5.653 42.857 484 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 6.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.29 % Favored : 95.71 % Rotamer: Outliers : 7.62 % Allowed : 21.52 % Favored : 70.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -0.94 (0.42), residues: 373 helix: -2.77 (0.77), residues: 39 sheet: 0.75 (0.47), residues: 118 loop : -1.01 (0.39), residues: 216 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP H 47 PHE 0.031 0.002 PHE H 29 TYR 0.010 0.001 TYR H 95 ARG 0.002 0.000 ARG E 403 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 59 time to evaluate : 0.272 Fit side-chains revert: symmetry clash REVERT: H 3 GLN cc_start: 0.8279 (mp10) cc_final: 0.8070 (tp40) REVERT: E 513 LEU cc_start: 0.9106 (mt) cc_final: 0.8638 (tt) REVERT: L 49 TYR cc_start: 0.8238 (p90) cc_final: 0.7868 (p90) outliers start: 17 outliers final: 16 residues processed: 68 average time/residue: 0.1188 time to fit residues: 10.1683 Evaluate side-chains 68 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 52 time to evaluate : 0.329 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 391 CYS Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 20 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 chunk 19 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 21 optimal weight: 0.7980 chunk 16 optimal weight: 0.7980 chunk 14 optimal weight: 0.9990 chunk 10 optimal weight: 0.6980 chunk 7 optimal weight: 0.5980 chunk 6 optimal weight: 1.9990 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.5233 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.094 2858 Z= 0.377 Angle : 0.671 6.055 3907 Z= 0.349 Chirality : 0.046 0.137 440 Planarity : 0.005 0.029 504 Dihedral : 6.207 43.770 484 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.90 % Favored : 94.10 % Rotamer: Outliers : 8.07 % Allowed : 23.32 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.12 (0.42), residues: 373 helix: -2.60 (0.81), residues: 39 sheet: 0.65 (0.46), residues: 120 loop : -1.23 (0.39), residues: 214 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.016 0.002 TRP H 47 PHE 0.019 0.002 PHE H 29 TYR 0.012 0.001 TYR H 95 ARG 0.005 0.000 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 55 time to evaluate : 0.312 Fit side-chains revert: symmetry clash REVERT: E 513 LEU cc_start: 0.9120 (mt) cc_final: 0.8658 (tt) REVERT: L 49 TYR cc_start: 0.8353 (p90) cc_final: 0.8056 (p90) outliers start: 18 outliers final: 18 residues processed: 65 average time/residue: 0.1116 time to fit residues: 9.0614 Evaluate side-chains 71 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.284 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 58 VAL Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 22 optimal weight: 0.8980 chunk 24 optimal weight: 0.9990 chunk 17 optimal weight: 0.5980 chunk 3 optimal weight: 0.5980 chunk 28 optimal weight: 0.9980 chunk 32 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 31 optimal weight: 0.0060 chunk 33 optimal weight: 0.6980 chunk 20 optimal weight: 0.8980 chunk 14 optimal weight: 0.6980 overall best weight: 0.5196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7940 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.086 2858 Z= 0.312 Angle : 0.645 6.432 3907 Z= 0.332 Chirality : 0.045 0.132 440 Planarity : 0.005 0.037 504 Dihedral : 6.082 43.802 484 Min Nonbonded Distance : 2.248 Molprobity Statistics. All-atom Clashscore : 7.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.83 % Favored : 95.17 % Rotamer: Outliers : 8.52 % Allowed : 22.87 % Favored : 68.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.25 (0.41), residues: 373 helix: -3.44 (0.75), residues: 33 sheet: 0.59 (0.47), residues: 118 loop : -1.25 (0.39), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP H 47 PHE 0.019 0.002 PHE H 29 TYR 0.011 0.001 TYR H 95 ARG 0.007 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 0.315 Fit side-chains revert: symmetry clash REVERT: E 513 LEU cc_start: 0.9132 (mt) cc_final: 0.8647 (tt) REVERT: L 49 TYR cc_start: 0.8307 (p90) cc_final: 0.8045 (p90) outliers start: 19 outliers final: 19 residues processed: 67 average time/residue: 0.1131 time to fit residues: 9.5381 Evaluate side-chains 73 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 54 time to evaluate : 0.305 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 467 ASP Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 26 optimal weight: 0.9980 chunk 10 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 31 optimal weight: 2.9990 chunk 33 optimal weight: 0.4980 chunk 21 optimal weight: 0.9990 chunk 35 optimal weight: 0.9980 chunk 16 optimal weight: 0.2980 chunk 24 optimal weight: 0.8980 chunk 36 optimal weight: 0.6980 chunk 29 optimal weight: 1.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7955 moved from start: 0.5591 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.095 2858 Z= 0.353 Angle : 0.667 6.187 3907 Z= 0.344 Chirality : 0.045 0.132 440 Planarity : 0.005 0.033 504 Dihedral : 6.475 50.477 484 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.43 % Favored : 93.57 % Rotamer: Outliers : 8.52 % Allowed : 25.11 % Favored : 66.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.41), residues: 373 helix: -3.49 (0.74), residues: 33 sheet: 0.43 (0.46), residues: 122 loop : -1.38 (0.39), residues: 218 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.002 TRP H 47 PHE 0.018 0.002 PHE H 29 TYR 0.013 0.001 TYR H 95 ARG 0.005 0.001 ARG L 96 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 56 time to evaluate : 0.309 Fit side-chains revert: symmetry clash REVERT: E 513 LEU cc_start: 0.9153 (mt) cc_final: 0.8675 (tt) REVERT: L 49 TYR cc_start: 0.8401 (p90) cc_final: 0.8168 (p90) outliers start: 19 outliers final: 18 residues processed: 67 average time/residue: 0.1318 time to fit residues: 10.8577 Evaluate side-chains 71 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 53 time to evaluate : 0.314 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 47 LEU Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.1980 chunk 22 optimal weight: 0.0980 chunk 17 optimal weight: 0.3980 chunk 23 optimal weight: 0.9990 chunk 31 optimal weight: 0.5980 chunk 8 optimal weight: 0.5980 chunk 27 optimal weight: 0.3980 chunk 4 optimal weight: 0.9990 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 0.4980 chunk 30 optimal weight: 0.9980 overall best weight: 0.3180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7906 moved from start: 0.5652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.063 2858 Z= 0.229 Angle : 0.625 6.644 3907 Z= 0.316 Chirality : 0.044 0.128 440 Planarity : 0.004 0.031 504 Dihedral : 5.954 48.976 484 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 7.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.02 % Favored : 95.98 % Rotamer: Outliers : 7.62 % Allowed : 25.56 % Favored : 66.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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 (0.42), residues: 373 helix: -3.32 (0.79), residues: 33 sheet: 0.48 (0.47), residues: 118 loop : -1.24 (0.40), residues: 222 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.015 0.001 TRP E 436 PHE 0.018 0.002 PHE H 29 TYR 0.010 0.001 TYR E 423 ARG 0.005 0.001 ARG L 96 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 746 Ramachandran restraints generated. 373 Oldfield, 0 Emsley, 373 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 60 time to evaluate : 0.234 Fit side-chains revert: symmetry clash REVERT: H 5 VAL cc_start: 0.9109 (t) cc_final: 0.8826 (m) REVERT: E 386 LYS cc_start: 0.9339 (mmtm) cc_final: 0.7541 (pttt) REVERT: E 429 PHE cc_start: 0.8654 (t80) cc_final: 0.8240 (t80) REVERT: E 513 LEU cc_start: 0.9136 (mt) cc_final: 0.8637 (tt) REVERT: L 49 TYR cc_start: 0.8268 (p90) cc_final: 0.8049 (p90) outliers start: 17 outliers final: 17 residues processed: 70 average time/residue: 0.1273 time to fit residues: 11.2262 Evaluate side-chains 72 residues out of total 331 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 55 time to evaluate : 0.302 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain H residue 2 VAL Chi-restraints excluded: chain H residue 68 VAL Chi-restraints excluded: chain H residue 71 THR Chi-restraints excluded: chain H residue 103 CYS Chi-restraints excluded: chain H residue 108 CYS Chi-restraints excluded: chain H residue 109 TYR Chi-restraints excluded: chain E residue 362 VAL Chi-restraints excluded: chain E residue 385 THR Chi-restraints excluded: chain E residue 392 PHE Chi-restraints excluded: chain E residue 415 THR Chi-restraints excluded: chain E residue 433 VAL Chi-restraints excluded: chain E residue 434 ILE Chi-restraints excluded: chain E residue 517 LEU Chi-restraints excluded: chain L residue 23 CYS Chi-restraints excluded: chain L residue 32 TYR Chi-restraints excluded: chain L residue 88 CYS Chi-restraints excluded: chain L residue 97 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 37 random chunks: chunk 3 optimal weight: 0.4980 chunk 5 optimal weight: 0.3980 chunk 25 optimal weight: 0.5980 chunk 1 optimal weight: 0.0170 chunk 21 optimal weight: 0.9990 chunk 33 optimal weight: 0.0010 chunk 19 optimal weight: 0.9980 chunk 0 optimal weight: 1.9990 chunk 23 optimal weight: 0.2980 chunk 22 optimal weight: 0.9980 chunk 14 optimal weight: 0.6980 overall best weight: 0.2424 ------------------------------------------------------------------------------- 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 = 0.3400 r_free = 0.3400 target = 0.093877 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 32)----------------| | r_work = 0.3262 r_free = 0.3262 target = 0.086332 restraints weight = 7338.459| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 34)----------------| | r_work = 0.3294 r_free = 0.3294 target = 0.088070 restraints weight = 4069.482| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 30)----------------| | r_work = 0.3316 r_free = 0.3316 target = 0.089250 restraints weight = 2568.523| |-----------------------------------------------------------------------------| r_work (final): 0.3315 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7986 moved from start: 0.5694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 2858 Z= 0.195 Angle : 0.627 7.719 3907 Z= 0.313 Chirality : 0.044 0.129 440 Planarity : 0.004 0.027 504 Dihedral : 5.711 47.617 484 Min Nonbonded Distance : 2.313 Molprobity Statistics. All-atom Clashscore : 7.75 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.75 % Favored : 96.25 % Rotamer: Outliers : 7.17 % Allowed : 24.66 % Favored : 68.16 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 10.53 % 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: -1.04 (0.42), residues: 373 helix: -3.37 (0.78), residues: 33 sheet: 0.63 (0.48), residues: 117 loop : -1.01 (0.40), residues: 223 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP E 436 PHE 0.017 0.002 PHE H 29 TYR 0.012 0.001 TYR H 95 ARG 0.003 0.000 ARG E 403 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1150.41 seconds wall clock time: 22 minutes 58.45 seconds (1378.45 seconds total)