Starting phenix.real_space_refine (version: 1.21rc1) on Mon Oct 2 20:46:59 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/10_2023/7ru4_24696.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/10_2023/7ru4_24696.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/10_2023/7ru4_24696.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/10_2023/7ru4_24696.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/10_2023/7ru4_24696.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ru4_24696/10_2023/7ru4_24696.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.001 sd= 0.016 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 14 5.16 5 C 2151 2.51 5 N 564 2.21 5 O 653 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "H TYR 59": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H PHE 63": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "H TYR 102": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 32": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 49": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L TYR 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "L PHE 98": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 338": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 342": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 365": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 374": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 377": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 392": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 449": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 451": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 464": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 473": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 489": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 497": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 505": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 515": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5097/modules/chem_data/mon_lib" Total number of atoms: 3382 Number of models: 1 Model: "" Number of chains: 5 Chain: "H" Number of atoms: 894 Number of conformers: 1 Conformer: "" Number of residues, atoms: 118, 894 Classifications: {'peptide': 118} Link IDs: {'PTRANS': 3, 'TRANS': 114} Chain: "L" Number of atoms: 826 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 826 Classifications: {'peptide': 108} Link IDs: {'PCIS': 1, 'PTRANS': 5, 'TRANS': 101} Chain: "A" Number of atoms: 1610 Number of conformers: 1 Conformer: "" Number of residues, atoms: 202, 1610 Classifications: {'peptide': 202} Link IDs: {'PTRANS': 12, 'TRANS': 189} Chain breaks: 1 Chain: "B" 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 chiralities: 3 Chain: "A" Number of atoms: 14 Number of conformers: 1 Conformer: "" Number of residues, atoms: 1, 14 Unusual residues: {'NAG': 1} Classifications: {'undetermined': 1} Unresolved non-hydrogen bonds: 1 Unresolved non-hydrogen angles: 2 Unresolved non-hydrogen chiralities: 1 Time building chain proxies: 2.43, per 1000 atoms: 0.72 Number of scatterers: 3382 At special positions: 0 Unit cell: (64.89, 99.91, 84.46, 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 14 16.00 O 653 8.00 N 564 7.00 C 2151 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS H 22 " - pdb=" SG CYS H 92 " distance=2.03 Simple disulfide: pdb=" SG CYS L 23 " - pdb=" SG CYS L 88 " distance=2.04 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=2.06 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.04 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " 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 Links applied BETA1-4 " NAG B 1 " - " NAG B 2 " BETA1-6 " NAG B 1 " - " FUC B 3 " ~> Even though FUC is an alpha isomer, a beta linkage is required... NAG-ASN " NAG A1301 " - " ASN A 331 " " NAG B 1 " - " ASN A 343 " Time building additional restraints: 1.47 Conformation dependent library (CDL) restraints added in 495.4 milliseconds 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 786 Finding SS restraints... Secondary structure from input PDB file: 12 helices and 9 sheets defined 15.0% alpha, 36.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'H' and resid 61 through 64 Processing helix chain 'H' and resid 73 through 75 No H-bonds generated for 'chain 'H' and resid 73 through 75' Processing helix chain 'L' and resid 29 through 31 No H-bonds generated for 'chain 'L' and resid 29 through 31' Processing helix chain 'L' and resid 79 through 83 removed outlier: 3.799A pdb=" N PHE L 83 " --> pdb=" O PRO L 80 " (cutoff:3.500A) Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 349 through 353 removed outlier: 3.899A pdb=" N TRP A 353 " --> pdb=" O VAL A 350 " (cutoff:3.500A) Processing helix chain 'A' and resid 364 through 371 removed outlier: 4.233A pdb=" N LEU A 368 " --> pdb=" O ASP A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 383 through 389 removed outlier: 4.886A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) Processing helix chain 'A' and resid 405 through 410 removed outlier: 4.208A 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 438 through 443 Processing helix chain 'A' 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 9 through 11 removed outlier: 4.048A pdb=" N ALA H 9 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR H 110 " --> pdb=" O ALA H 9 " (cutoff:3.500A) removed outlier: 6.519A pdb=" N ILE H 34 " --> pdb=" O GLY H 50 " (cutoff:3.500A) removed outlier: 4.398A pdb=" N GLY H 50 " --> pdb=" O ILE H 34 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TRP H 36 " --> pdb=" O MET H 48 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'H' and resid 9 through 11 removed outlier: 4.048A pdb=" N ALA H 9 " --> pdb=" O LEU H 108 " (cutoff:3.500A) removed outlier: 4.231A pdb=" N THR H 110 " --> pdb=" O ALA H 9 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'L' and resid 4 through 7 Processing sheet with id=AA5, first strand: chain 'L' and resid 10 through 13 removed outlier: 6.482A pdb=" N LEU L 33 " --> pdb=" O TYR L 49 " (cutoff:3.500A) removed outlier: 4.470A pdb=" N TYR L 49 " --> pdb=" O LEU L 33 " (cutoff:3.500A) removed outlier: 6.500A pdb=" N TRP L 35 " --> pdb=" O LEU L 47 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'L' and resid 10 through 13 Processing sheet with id=AA7, first strand: chain 'A' and resid 354 through 358 Processing sheet with id=AA8, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.500A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) Processing sheet with id=AA9, first strand: chain 'A' and resid 452 through 454 127 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: 0.92 Time building geometry restraints manager: 1.52 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 949 1.33 - 1.47: 1110 1.47 - 1.61: 1385 1.61 - 1.74: 4 1.74 - 1.88: 16 Bond restraints: 3464 Sorted by residual: bond pdb=" CB ILE A 326 " pdb=" CG1 ILE A 326 " ideal model delta sigma weight residual 1.530 1.679 -0.149 2.00e-02 2.50e+03 5.55e+01 bond pdb=" CG GLN L 6 " pdb=" CD GLN L 6 " ideal model delta sigma weight residual 1.516 1.384 0.132 2.50e-02 1.60e+03 2.79e+01 bond pdb=" CB TYR L 87 " pdb=" CG TYR L 87 " ideal model delta sigma weight residual 1.512 1.397 0.115 2.20e-02 2.07e+03 2.75e+01 bond pdb=" CB TYR L 36 " pdb=" CG TYR L 36 " ideal model delta sigma weight residual 1.512 1.398 0.114 2.20e-02 2.07e+03 2.67e+01 bond pdb=" CB ILE A 472 " pdb=" CG2 ILE A 472 " ideal model delta sigma weight residual 1.521 1.363 0.158 3.30e-02 9.18e+02 2.29e+01 ... (remaining 3459 not shown) Histogram of bond angle deviations from ideal: 101.15 - 107.78: 260 107.78 - 114.42: 1731 114.42 - 121.06: 1660 121.06 - 127.70: 1025 127.70 - 134.33: 30 Bond angle restraints: 4706 Sorted by residual: angle pdb=" N ARG L 61 " pdb=" CA ARG L 61 " pdb=" C ARG L 61 " ideal model delta sigma weight residual 114.56 101.68 12.88 1.27e+00 6.20e-01 1.03e+02 angle pdb=" N ALA A 520 " pdb=" CA ALA A 520 " pdb=" C ALA A 520 " ideal model delta sigma weight residual 108.13 117.09 -8.96 9.00e-01 1.23e+00 9.91e+01 angle pdb=" N LEU H 54 " pdb=" CA LEU H 54 " pdb=" C LEU H 54 " ideal model delta sigma weight residual 113.97 102.00 11.97 1.28e+00 6.10e-01 8.75e+01 angle pdb=" N GLN A 474 " pdb=" CA GLN A 474 " pdb=" C GLN A 474 " ideal model delta sigma weight residual 110.55 122.38 -11.83 1.35e+00 5.49e-01 7.68e+01 angle pdb=" N PHE L 98 " pdb=" CA PHE L 98 " pdb=" C PHE L 98 " ideal model delta sigma weight residual 113.30 124.82 -11.52 1.34e+00 5.57e-01 7.39e+01 ... (remaining 4701 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 14.72: 1921 14.72 - 29.45: 66 29.45 - 44.17: 15 44.17 - 58.90: 13 58.90 - 73.62: 4 Dihedral angle restraints: 2019 sinusoidal: 784 harmonic: 1235 Sorted by residual: dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual 93.00 138.11 -45.11 1 1.00e+01 1.00e-02 2.82e+01 dihedral pdb=" CB CYS H 22 " pdb=" SG CYS H 22 " pdb=" SG CYS H 92 " pdb=" CB CYS H 92 " ideal model delta sinusoidal sigma weight residual 93.00 64.13 28.87 1 1.00e+01 1.00e-02 1.19e+01 dihedral pdb=" SG CYS A 391 " pdb=" CB CYS A 525 " pdb=" SG CYS A 525 " pdb=" CA CYS A 525 " ideal model delta sinusoidal sigma weight residual 79.00 23.24 55.76 1 2.00e+01 2.50e-03 1.05e+01 ... (remaining 2016 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.087: 322 0.087 - 0.173: 141 0.173 - 0.260: 46 0.260 - 0.346: 11 0.346 - 0.433: 6 Chirality restraints: 526 Sorted by residual: chirality pdb=" C1 NAG B 2 " pdb=" O4 NAG B 1 " pdb=" C2 NAG B 2 " pdb=" O5 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.40 -2.61 0.21 2.00e-02 2.50e+03 1.08e+02 chirality pdb=" C1 FUC B 3 " pdb=" O6 NAG B 1 " pdb=" C2 FUC B 3 " pdb=" O5 FUC B 3 " both_signs ideal model delta sigma weight residual False -2.40 -2.51 0.11 2.00e-02 2.50e+03 2.98e+01 chirality pdb=" C2 NAG B 2 " pdb=" C1 NAG B 2 " pdb=" C3 NAG B 2 " pdb=" N2 NAG B 2 " both_signs ideal model delta sigma weight residual False -2.49 -2.92 0.43 2.00e-01 2.50e+01 4.68e+00 ... (remaining 523 not shown) Planarity restraints: 599 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TRP H 47 " -0.057 2.00e-02 2.50e+03 2.67e-02 1.78e+01 pdb=" CG TRP H 47 " 0.027 2.00e-02 2.50e+03 pdb=" CD1 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TRP H 47 " 0.027 2.00e-02 2.50e+03 pdb=" NE1 TRP H 47 " 0.008 2.00e-02 2.50e+03 pdb=" CE2 TRP H 47 " 0.002 2.00e-02 2.50e+03 pdb=" CE3 TRP H 47 " 0.026 2.00e-02 2.50e+03 pdb=" CZ2 TRP H 47 " -0.031 2.00e-02 2.50e+03 pdb=" CZ3 TRP H 47 " 0.010 2.00e-02 2.50e+03 pdb=" CH2 TRP H 47 " -0.023 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR L 32 " -0.056 2.00e-02 2.50e+03 2.94e-02 1.73e+01 pdb=" CG TYR L 32 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR L 32 " 0.025 2.00e-02 2.50e+03 pdb=" CD2 TYR L 32 " 0.023 2.00e-02 2.50e+03 pdb=" CE1 TYR L 32 " 0.014 2.00e-02 2.50e+03 pdb=" CE2 TYR L 32 " 0.017 2.00e-02 2.50e+03 pdb=" CZ TYR L 32 " -0.002 2.00e-02 2.50e+03 pdb=" OH TYR L 32 " -0.042 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA THR A 478 " 0.018 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C THR A 478 " -0.060 2.00e-02 2.50e+03 pdb=" O THR A 478 " 0.022 2.00e-02 2.50e+03 pdb=" N PRO A 479 " 0.020 2.00e-02 2.50e+03 ... (remaining 596 not shown) Histogram of nonbonded interaction distances: 2.36 - 2.87: 1243 2.87 - 3.38: 2954 3.38 - 3.88: 5675 3.88 - 4.39: 6717 4.39 - 4.90: 10862 Nonbonded interactions: 27451 Sorted by model distance: nonbonded pdb=" OE1 GLU A 340 " pdb=" NZ LYS A 356 " model vdw 2.362 2.520 nonbonded pdb=" N LEU H 54 " pdb=" N ASP H 55 " model vdw 2.363 2.560 nonbonded pdb=" N ARG L 61 " pdb=" N PHE L 62 " model vdw 2.377 2.560 nonbonded pdb=" N PRO A 426 " pdb=" O PRO A 426 " model vdw 2.440 2.496 nonbonded pdb=" N GLN H 97 " pdb=" O GLN H 97 " model vdw 2.463 2.496 ... (remaining 27446 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 3.540 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 17.980 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.770 Find NCS groups from input model: 0.090 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: 0.010 Load rotamer database and sin/cos tables:2.670 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 39.160 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7837 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 : 0.023 0.158 3464 Z= 1.507 Angle : 1.894 12.879 4706 Z= 1.262 Chirality : 0.113 0.433 526 Planarity : 0.008 0.035 597 Dihedral : 9.845 73.619 1215 Min Nonbonded Distance : 2.362 Molprobity Statistics. All-atom Clashscore : 0.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.10 % Favored : 96.90 % Rotamer: Outliers : 0.55 % Allowed : 1.10 % Favored : 98.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: 0.06 (0.40), residues: 420 helix: -3.40 (0.59), residues: 31 sheet: 1.34 (0.44), residues: 150 loop : -0.30 (0.37), residues: 239 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 122 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 120 time to evaluate : 0.403 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 122 average time/residue: 0.2439 time to fit residues: 33.7486 Evaluate side-chains 74 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 74 time to evaluate : 0.459 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5790 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 3.9990 chunk 31 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 10 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 12 optimal weight: 0.7980 chunk 19 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 37 optimal weight: 0.0970 overall best weight: 0.5978 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.3278 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.071 3464 Z= 0.284 Angle : 0.750 10.577 4706 Z= 0.396 Chirality : 0.050 0.247 526 Planarity : 0.005 0.036 597 Dihedral : 5.664 25.512 469 Min Nonbonded Distance : 2.202 Molprobity Statistics. All-atom Clashscore : 8.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 3.84 % Allowed : 9.59 % Favored : 86.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -0.26 (0.40), residues: 420 helix: -1.80 (1.18), residues: 25 sheet: 0.86 (0.42), residues: 149 loop : -0.65 (0.38), residues: 246 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 92 time to evaluate : 0.401 Fit side-chains outliers start: 14 outliers final: 9 residues processed: 97 average time/residue: 0.1628 time to fit residues: 19.1208 Evaluate side-chains 78 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 69 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 9 outliers final: 0 residues processed: 9 average time/residue: 0.0687 time to fit residues: 1.3815 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.9980 chunk 10 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 40 optimal weight: 0.8980 chunk 33 optimal weight: 0.7980 chunk 36 optimal weight: 0.0970 chunk 12 optimal weight: 0.0670 chunk 29 optimal weight: 0.0270 overall best weight: 0.3174 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 97 GLN A 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7888 moved from start: 0.4035 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.049 3464 Z= 0.194 Angle : 0.660 7.464 4706 Z= 0.337 Chirality : 0.048 0.236 526 Planarity : 0.005 0.040 597 Dihedral : 5.174 24.437 469 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 7.95 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.33 % Favored : 96.67 % Rotamer: Outliers : 1.92 % Allowed : 12.60 % Favored : 85.48 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.20 (0.40), residues: 420 helix: -2.16 (1.03), residues: 26 sheet: 0.94 (0.43), residues: 151 loop : -0.59 (0.38), residues: 243 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.415 Fit side-chains revert: symmetry clash outliers start: 7 outliers final: 2 residues processed: 93 average time/residue: 0.1651 time to fit residues: 18.6269 Evaluate side-chains 74 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 72 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0660 time to fit residues: 0.7123 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.1980 chunk 28 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 4 optimal weight: 0.0870 chunk 17 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 37 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 35 optimal weight: 1.9990 chunk 10 optimal weight: 1.9990 chunk 33 optimal weight: 0.9990 overall best weight: 0.5762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** L 100 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.4461 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.050 3464 Z= 0.228 Angle : 0.651 9.512 4706 Z= 0.331 Chirality : 0.048 0.242 526 Planarity : 0.005 0.042 597 Dihedral : 4.992 24.452 469 Min Nonbonded Distance : 2.230 Molprobity Statistics. All-atom Clashscore : 7.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.81 % Favored : 96.19 % Rotamer: Outliers : 2.74 % Allowed : 13.15 % Favored : 84.11 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.37 (0.40), residues: 420 helix: -2.36 (1.01), residues: 26 sheet: 0.88 (0.42), residues: 151 loop : -0.74 (0.38), residues: 243 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.408 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 6 residues processed: 85 average time/residue: 0.1751 time to fit residues: 17.8780 Evaluate side-chains 81 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 75 time to evaluate : 0.403 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0349 time to fit residues: 0.8896 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9980 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 0.0980 chunk 16 optimal weight: 2.9990 chunk 33 optimal weight: 2.9990 chunk 27 optimal weight: 0.7980 chunk 20 optimal weight: 1.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 100 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 moved from start: 0.4896 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.062 3464 Z= 0.328 Angle : 0.688 8.358 4706 Z= 0.350 Chirality : 0.049 0.222 526 Planarity : 0.005 0.040 597 Dihedral : 5.116 25.025 469 Min Nonbonded Distance : 2.163 Molprobity Statistics. All-atom Clashscore : 8.70 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 2.19 % Allowed : 14.79 % Favored : 83.01 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.67 (0.39), residues: 420 helix: -2.48 (0.98), residues: 26 sheet: 0.86 (0.41), residues: 152 loop : -1.11 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 83 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.419 Fit side-chains revert: symmetry clash outliers start: 8 outliers final: 4 residues processed: 78 average time/residue: 0.1821 time to fit residues: 17.0249 Evaluate side-chains 75 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.411 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0492 time to fit residues: 0.8428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 1.9990 chunk 9 optimal weight: 2.9990 chunk 39 optimal weight: 0.6980 chunk 32 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 38 optimal weight: 0.1980 chunk 4 optimal weight: 2.9990 chunk 22 optimal weight: 0.7980 overall best weight: 0.6580 ------------------------------------------------------------------------------- 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: 0.7987 moved from start: 0.5091 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 3464 Z= 0.240 Angle : 0.639 7.825 4706 Z= 0.328 Chirality : 0.047 0.225 526 Planarity : 0.005 0.039 597 Dihedral : 4.995 24.063 469 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 8.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.52 % Favored : 95.48 % Rotamer: Outliers : 3.29 % Allowed : 14.79 % Favored : 81.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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 (0.40), residues: 420 helix: -2.30 (1.00), residues: 26 sheet: 0.90 (0.42), residues: 152 loop : -1.22 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 78 time to evaluate : 0.376 Fit side-chains revert: symmetry clash outliers start: 12 outliers final: 8 residues processed: 81 average time/residue: 0.1846 time to fit residues: 17.8523 Evaluate side-chains 81 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 73 time to evaluate : 0.417 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0426 time to fit residues: 1.0956 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.9990 chunk 22 optimal weight: 0.5980 chunk 33 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 18 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 23 optimal weight: 0.5980 chunk 11 optimal weight: 0.9990 chunk 7 optimal weight: 2.9990 chunk 25 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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: 0.8005 moved from start: 0.5303 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 3464 Z= 0.274 Angle : 0.662 8.841 4706 Z= 0.336 Chirality : 0.047 0.163 526 Planarity : 0.005 0.037 597 Dihedral : 5.037 23.041 469 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % Rotamer: Outliers : 1.64 % Allowed : 15.89 % Favored : 82.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.88 (0.40), residues: 420 helix: -2.45 (0.96), residues: 26 sheet: 0.87 (0.42), residues: 152 loop : -1.40 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 76 time to evaluate : 0.428 Fit side-chains revert: symmetry clash outliers start: 6 outliers final: 3 residues processed: 80 average time/residue: 0.1862 time to fit residues: 17.7545 Evaluate side-chains 76 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 73 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0350 time to fit residues: 0.7125 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.9990 chunk 19 optimal weight: 0.6980 chunk 3 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 35 optimal weight: 3.9990 chunk 37 optimal weight: 0.1980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0770 chunk 22 optimal weight: 0.8980 chunk 16 optimal weight: 2.9990 chunk 28 optimal weight: 1.9990 overall best weight: 0.5538 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.5493 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3464 Z= 0.221 Angle : 0.684 10.310 4706 Z= 0.342 Chirality : 0.048 0.147 526 Planarity : 0.005 0.036 597 Dihedral : 5.044 25.404 469 Min Nonbonded Distance : 2.184 Molprobity Statistics. All-atom Clashscore : 8.85 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.71 % Favored : 94.29 % Rotamer: Outliers : 0.82 % Allowed : 17.81 % Favored : 81.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.92 (0.40), residues: 420 helix: -2.47 (0.98), residues: 26 sheet: 0.91 (0.43), residues: 152 loop : -1.48 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 76 time to evaluate : 0.422 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 76 average time/residue: 0.1728 time to fit residues: 15.9833 Evaluate side-chains 73 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.421 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0918 time to fit residues: 0.9285 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 0.2980 chunk 33 optimal weight: 2.9990 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 0.0570 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 1.9990 chunk 23 optimal weight: 0.7980 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 0.4980 chunk 40 optimal weight: 0.9990 chunk 37 optimal weight: 0.5980 overall best weight: 0.4498 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 493 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7965 moved from start: 0.5628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.052 3464 Z= 0.207 Angle : 0.670 7.975 4706 Z= 0.338 Chirality : 0.048 0.148 526 Planarity : 0.005 0.035 597 Dihedral : 4.988 24.498 469 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 9.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.24 % Favored : 94.76 % Rotamer: Outliers : 0.27 % Allowed : 19.18 % Favored : 80.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.89 (0.40), residues: 420 helix: -2.55 (0.96), residues: 26 sheet: 0.97 (0.44), residues: 152 loop : -1.49 (0.37), residues: 242 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.488 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 75 average time/residue: 0.1675 time to fit residues: 15.4823 Evaluate side-chains 69 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 68 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0498 time to fit residues: 0.6052 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 4.9990 chunk 3 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.9990 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 3.9990 chunk 6 optimal weight: 0.2980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: L 37 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.5792 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.058 3464 Z= 0.264 Angle : 0.683 8.179 4706 Z= 0.347 Chirality : 0.048 0.159 526 Planarity : 0.005 0.034 597 Dihedral : 5.039 23.293 469 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 9.91 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.90 % Favored : 93.10 % Rotamer: Outliers : 0.55 % Allowed : 20.00 % Favored : 79.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.98 (0.40), residues: 420 helix: -2.58 (0.94), residues: 26 sheet: 0.91 (0.44), residues: 152 loop : -1.55 (0.37), residues: 242 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 840 Ramachandran restraints generated. 420 Oldfield, 0 Emsley, 420 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 70 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 68 time to evaluate : 0.409 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 68 average time/residue: 0.1666 time to fit residues: 13.8597 Evaluate side-chains 68 residues out of total 365 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 67 time to evaluate : 0.416 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0562 time to fit residues: 0.7259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.5980 chunk 1 optimal weight: 0.5980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 0.0970 chunk 21 optimal weight: 0.7980 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 0.5980 chunk 24 optimal weight: 0.7980 chunk 16 optimal weight: 3.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.0980 overall best weight: 0.3978 ------------------------------------------------------------------------------- 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 = 0.3529 r_free = 0.3529 target = 0.088228 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 28)----------------| | r_work = 0.3404 r_free = 0.3404 target = 0.081293 restraints weight = 9374.597| |-----------------------------------------------------------------------------| r_work (start): 0.3398 rms_B_bonded: 2.65 r_work: 0.3312 rms_B_bonded: 3.05 restraints_weight: 0.5000 r_work (final): 0.3312 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8101 moved from start: 0.5900 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.051 3464 Z= 0.197 Angle : 0.655 7.540 4706 Z= 0.331 Chirality : 0.047 0.158 526 Planarity : 0.005 0.036 597 Dihedral : 4.868 22.530 469 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 10.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.95 % Favored : 94.05 % Rotamer: Outliers : 0.27 % Allowed : 21.10 % Favored : 78.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 4.76 % 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: -0.87 (0.41), residues: 420 helix: -2.57 (0.95), residues: 26 sheet: 1.00 (0.44), residues: 152 loop : -1.48 (0.37), residues: 242 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1463.50 seconds wall clock time: 26 minutes 56.07 seconds (1616.07 seconds total)