Starting phenix.real_space_refine on Thu Dec 7 16:08:44 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/12_2023/7zir_14738.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/12_2023/7zir_14738.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/12_2023/7zir_14738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/12_2023/7zir_14738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/12_2023/7zir_14738.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/12_2023/7zir_14738.pdb" } resolution = 2.5 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= 0.005 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: 3 Type Number sf(0) Gaussians C 1300 2.51 5 N 325 2.21 5 O 495 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "C TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 354": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 382": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B TYR 387": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 2120 Number of models: 1 Model: "" Number of chains: 10 Chain: "C" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain: "A" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain: "E" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain: "D" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain: "B" Number of atoms: 414 Number of conformers: 1 Conformer: "" Number of residues, atoms: 51, 414 Classifications: {'peptide': 51} Link IDs: {'TRANS': 50} Chain: "C" Number of atoms: 11 Number of conformers: 1 Conformer: "" Number of residues, atoms: 11, 11 Classifications: {'water': 11} Link IDs: {None: 10} Chain: "A" Number of atoms: 8 Number of conformers: 1 Conformer: "" Number of residues, atoms: 8, 8 Classifications: {'water': 8} Link IDs: {None: 7} Chain: "E" Number of atoms: 12 Number of conformers: 1 Conformer: "" Number of residues, atoms: 12, 12 Classifications: {'water': 12} Link IDs: {None: 11} Chain: "D" Number of atoms: 10 Number of conformers: 1 Conformer: "" Number of residues, atoms: 10, 10 Classifications: {'water': 10} Link IDs: {None: 9} Chain: "B" Number of atoms: 9 Number of conformers: 1 Conformer: "" Number of residues, atoms: 9, 9 Classifications: {'water': 9} Link IDs: {None: 8} Time building chain proxies: 1.36, per 1000 atoms: 0.64 Number of scatterers: 2120 At special positions: 0 Unit cell: (61.341, 64.897, 45.339, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 3 Type Number sf(0) O 495 8.00 N 325 7.00 C 1300 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.65 Conformation dependent library (CDL) restraints added in 323.3 milliseconds 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 380 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 27.8% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 346 through 347 removed outlier: 6.743A pdb=" N TRP A 346 " --> pdb=" O ASN B 347 " (cutoff:3.500A) removed outlier: 6.785A pdb=" N TRP C 346 " --> pdb=" O ASN D 347 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'A' and resid 352 through 353 removed outlier: 6.597A pdb=" N ASN C 352 " --> pdb=" O TYR B 353 " (cutoff:3.500A) removed outlier: 6.735A pdb=" N ASN E 352 " --> pdb=" O TYR D 353 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'A' and resid 361 through 362 removed outlier: 6.459A pdb=" N TYR A 361 " --> pdb=" O ASN B 362 " (cutoff:3.500A) removed outlier: 8.444A pdb=" N ASN D 362 " --> pdb=" O GLY C 359 " (cutoff:3.500A) removed outlier: 6.440A pdb=" N TYR C 361 " --> pdb=" O ASN D 362 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 369 through 371 removed outlier: 6.630A pdb=" N ASN A 370 " --> pdb=" O TYR B 371 " (cutoff:3.500A) removed outlier: 6.645A pdb=" N ASN C 370 " --> pdb=" O TYR D 371 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 380 through 383 removed outlier: 6.615A pdb=" N THR C 380 " --> pdb=" O GLY B 381 " (cutoff:3.500A) removed outlier: 8.052A pdb=" N ASN B 383 " --> pdb=" O THR C 380 " (cutoff:3.500A) removed outlier: 6.793A pdb=" N TYR C 382 " --> pdb=" O ASN B 383 " (cutoff:3.500A) removed outlier: 6.677A pdb=" N THR E 380 " --> pdb=" O GLY D 381 " (cutoff:3.500A) removed outlier: 8.118A pdb=" N ASN D 383 " --> pdb=" O THR E 380 " (cutoff:3.500A) removed outlier: 6.841A pdb=" N TYR E 382 " --> pdb=" O ASN D 383 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 389 through 394 removed outlier: 5.912A pdb=" N TYR A 389 " --> pdb=" O GLY B 390 " (cutoff:3.500A) removed outlier: 7.544A pdb=" N GLY B 392 " --> pdb=" O TYR A 389 " (cutoff:3.500A) removed outlier: 9.391A pdb=" N GLN A 391 " --> pdb=" O GLY B 392 " (cutoff:3.500A) removed outlier: 7.743A pdb=" N ALA B 394 " --> pdb=" O GLN A 391 " (cutoff:3.500A) removed outlier: 9.406A pdb=" N TYR A 393 " --> pdb=" O ALA B 394 " (cutoff:3.500A) removed outlier: 3.565A pdb=" N GLN B 391 " --> pdb=" O GLY C 390 " (cutoff:3.500A) removed outlier: 3.532A pdb=" N GLY C 392 " --> pdb=" O GLN B 391 " (cutoff:3.500A) removed outlier: 7.340A pdb=" N TYR B 393 " --> pdb=" O GLY C 392 " (cutoff:3.500A) removed outlier: 7.438A pdb=" N ALA C 394 " --> pdb=" O TYR B 393 " (cutoff:3.500A) removed outlier: 5.842A pdb=" N TYR C 389 " --> pdb=" O GLY D 390 " (cutoff:3.500A) removed outlier: 7.455A pdb=" N GLY D 392 " --> pdb=" O TYR C 389 " (cutoff:3.500A) removed outlier: 9.414A pdb=" N GLN C 391 " --> pdb=" O GLY D 392 " (cutoff:3.500A) removed outlier: 7.720A pdb=" N ALA D 394 " --> pdb=" O GLN C 391 " (cutoff:3.500A) removed outlier: 9.469A pdb=" N TYR C 393 " --> pdb=" O ALA D 394 " (cutoff:3.500A) removed outlier: 3.507A pdb=" N GLY E 392 " --> pdb=" O GLN D 391 " (cutoff:3.500A) removed outlier: 7.271A pdb=" N TYR D 393 " --> pdb=" O GLY E 392 " (cutoff:3.500A) removed outlier: 7.408A pdb=" N ALA E 394 " --> pdb=" O TYR D 393 " (cutoff:3.500A) 22 hydrogen bonds defined for protein. 66 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: 0.46 Time building geometry restraints manager: 0.72 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.29: 360 1.29 - 1.35: 315 1.35 - 1.41: 565 1.41 - 1.47: 275 1.47 - 1.54: 635 Bond restraints: 2150 Sorted by residual: bond pdb=" CA GLY E 357 " pdb=" C GLY E 357 " ideal model delta sigma weight residual 1.521 1.516 0.005 1.28e-02 6.10e+03 1.56e-01 bond pdb=" CA GLY C 357 " pdb=" C GLY C 357 " ideal model delta sigma weight residual 1.521 1.516 0.005 1.28e-02 6.10e+03 1.44e-01 bond pdb=" CA GLY B 357 " pdb=" C GLY B 357 " ideal model delta sigma weight residual 1.521 1.516 0.005 1.28e-02 6.10e+03 1.37e-01 bond pdb=" C GLY E 357 " pdb=" O GLY E 357 " ideal model delta sigma weight residual 1.231 1.235 -0.004 1.11e-02 8.12e+03 1.30e-01 bond pdb=" C GLY D 357 " pdb=" O GLY D 357 " ideal model delta sigma weight residual 1.231 1.235 -0.004 1.11e-02 8.12e+03 1.30e-01 ... (remaining 2145 not shown) Histogram of bond angle deviations from ideal: 106.25 - 111.80: 625 111.80 - 117.34: 530 117.34 - 122.88: 1466 122.88 - 128.42: 289 128.42 - 133.96: 10 Bond angle restraints: 2920 Sorted by residual: angle pdb=" N TYR E 384 " pdb=" CA TYR E 384 " pdb=" C TYR E 384 " ideal model delta sigma weight residual 113.02 111.34 1.68 1.49e+00 4.50e-01 1.27e+00 angle pdb=" N TYR D 384 " pdb=" CA TYR D 384 " pdb=" C TYR D 384 " ideal model delta sigma weight residual 113.02 111.34 1.68 1.49e+00 4.50e-01 1.27e+00 angle pdb=" N TYR B 384 " pdb=" CA TYR B 384 " pdb=" C TYR B 384 " ideal model delta sigma weight residual 113.02 111.39 1.63 1.49e+00 4.50e-01 1.19e+00 angle pdb=" N TYR C 384 " pdb=" CA TYR C 384 " pdb=" C TYR C 384 " ideal model delta sigma weight residual 113.02 111.40 1.62 1.49e+00 4.50e-01 1.19e+00 angle pdb=" N TYR A 384 " pdb=" CA TYR A 384 " pdb=" C TYR A 384 " ideal model delta sigma weight residual 113.02 111.40 1.62 1.49e+00 4.50e-01 1.18e+00 ... (remaining 2915 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.77: 1045 15.77 - 31.53: 15 31.53 - 47.30: 0 47.30 - 63.06: 0 63.06 - 78.83: 5 Dihedral angle restraints: 1065 sinusoidal: 365 harmonic: 700 Sorted by residual: dihedral pdb=" CB GLN C 356 " pdb=" CG GLN C 356 " pdb=" CD GLN C 356 " pdb=" OE1 GLN C 356 " ideal model delta sinusoidal sigma weight residual 0.00 -78.83 78.83 2 3.00e+01 1.11e-03 5.13e+00 dihedral pdb=" CB GLN E 356 " pdb=" CG GLN E 356 " pdb=" CD GLN E 356 " pdb=" OE1 GLN E 356 " ideal model delta sinusoidal sigma weight residual 0.00 -78.82 78.82 2 3.00e+01 1.11e-03 5.13e+00 dihedral pdb=" CB GLN A 356 " pdb=" CG GLN A 356 " pdb=" CD GLN A 356 " pdb=" OE1 GLN A 356 " ideal model delta sinusoidal sigma weight residual 0.00 -78.78 78.78 2 3.00e+01 1.11e-03 5.13e+00 ... (remaining 1062 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.013: 59 0.013 - 0.025: 43 0.025 - 0.038: 43 0.038 - 0.050: 20 0.050 - 0.063: 30 Chirality restraints: 195 Sorted by residual: chirality pdb=" CA ALA B 364 " pdb=" N ALA B 364 " pdb=" C ALA B 364 " pdb=" CB ALA B 364 " both_signs ideal model delta sigma weight residual False 2.48 2.55 -0.06 2.00e-01 2.50e+01 9.90e-02 chirality pdb=" CA GLN D 356 " pdb=" N GLN D 356 " pdb=" C GLN D 356 " pdb=" CB GLN D 356 " both_signs ideal model delta sigma weight residual False 2.51 2.45 0.06 2.00e-01 2.50e+01 9.66e-02 chirality pdb=" CA ALA A 364 " pdb=" N ALA A 364 " pdb=" C ALA A 364 " pdb=" CB ALA A 364 " both_signs ideal model delta sigma weight residual False 2.48 2.55 -0.06 2.00e-01 2.50e+01 9.61e-02 ... (remaining 192 not shown) Planarity restraints: 415 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB TYR D 384 " 0.006 2.00e-02 2.50e+03 3.76e-03 2.82e-01 pdb=" CG TYR D 384 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR D 384 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR D 384 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR D 384 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR D 384 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR D 384 " 0.001 2.00e-02 2.50e+03 pdb=" OH TYR D 384 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR C 384 " 0.005 2.00e-02 2.50e+03 3.61e-03 2.60e-01 pdb=" CG TYR C 384 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR C 384 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR C 384 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR C 384 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR C 384 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR C 384 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR C 384 " 0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR E 384 " 0.005 2.00e-02 2.50e+03 3.57e-03 2.54e-01 pdb=" CG TYR E 384 " -0.009 2.00e-02 2.50e+03 pdb=" CD1 TYR E 384 " 0.000 2.00e-02 2.50e+03 pdb=" CD2 TYR E 384 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR E 384 " 0.001 2.00e-02 2.50e+03 pdb=" CE2 TYR E 384 " 0.001 2.00e-02 2.50e+03 pdb=" CZ TYR E 384 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR E 384 " 0.001 2.00e-02 2.50e+03 ... (remaining 412 not shown) Histogram of nonbonded interaction distances: 2.32 - 2.83: 759 2.83 - 3.35: 1424 3.35 - 3.87: 3846 3.87 - 4.38: 4784 4.38 - 4.90: 7612 Nonbonded interactions: 18425 Sorted by model distance: nonbonded pdb=" OE1 GLN C 356 " pdb=" O HOH C 501 " model vdw 2.317 2.440 nonbonded pdb=" OE1 GLN D 356 " pdb=" O HOH D 501 " model vdw 2.329 2.440 nonbonded pdb=" OE1 GLN A 356 " pdb=" O HOH A 501 " model vdw 2.396 2.440 nonbonded pdb=" OE1 GLN E 356 " pdb=" O HOH E 501 " model vdw 2.467 2.440 nonbonded pdb=" OE1 GLN B 356 " pdb=" O HOH B 501 " model vdw 2.508 2.440 ... (remaining 18420 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' } 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: 2.210 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: 10.470 Check model and map are aligned: 0.020 Set scattering table: 0.030 Process input model: 9.870 Find NCS groups from input model: 0.130 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:13.940 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 36.690 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8781 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 : 0.002 0.007 2150 Z= 0.099 Angle : 0.336 1.678 2920 Z= 0.210 Chirality : 0.032 0.063 195 Planarity : 0.001 0.004 415 Dihedral : 9.018 78.827 685 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 1.65 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.82 (0.28), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.22), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.001 0.000 TRP E 346 PHE 0.001 0.000 PHE A 350 TYR 0.009 0.001 TYR D 384 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 28 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 28 time to evaluate : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2544 time to fit residues: 7.9420 Evaluate side-chains 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2661 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 10 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.9980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.2980 chunk 15 optimal weight: 2.9990 overall best weight: 1.2184 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 352 ASN C 386 ASN D 386 ASN B 386 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8856 moved from start: 0.1649 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2150 Z= 0.237 Angle : 0.448 2.521 2920 Z= 0.271 Chirality : 0.038 0.078 195 Planarity : 0.002 0.006 415 Dihedral : 3.419 12.375 320 Min Nonbonded Distance : 2.295 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.09 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.11 (0.19), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 346 PHE 0.003 0.001 PHE E 350 TYR 0.013 0.002 TYR A 377 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.181 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2658 time to fit residues: 7.1304 Evaluate side-chains 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.233 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2665 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 7 optimal weight: 0.8980 chunk 18 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 0.2980 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 overall best weight: 1.1784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8867 moved from start: 0.1888 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.013 2150 Z= 0.226 Angle : 0.427 2.392 2920 Z= 0.259 Chirality : 0.037 0.074 195 Planarity : 0.002 0.006 415 Dihedral : 3.505 12.286 320 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.04 % Favored : 97.96 % Rotamer: Outliers : 0.00 % Allowed : 4.44 % Favored : 95.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.96 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.19), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 346 PHE 0.003 0.001 PHE B 350 TYR 0.013 0.001 TYR A 377 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.189 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2529 time to fit residues: 7.0420 Evaluate side-chains 25 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.193 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2306 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 22 optimal weight: 5.9990 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 2.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.5980 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 352 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8873 moved from start: 0.2025 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.015 2150 Z= 0.238 Angle : 0.435 2.529 2920 Z= 0.263 Chirality : 0.037 0.075 195 Planarity : 0.002 0.006 415 Dihedral : 3.608 12.747 320 Min Nonbonded Distance : 2.308 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.96 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.01 (0.19), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 346 PHE 0.004 0.001 PHE B 350 TYR 0.012 0.001 TYR A 377 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.193 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2667 time to fit residues: 6.8729 Evaluate side-chains 23 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.199 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2453 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 0 optimal weight: 4.9990 chunk 12 optimal weight: 3.9990 chunk 21 optimal weight: 3.9990 chunk 6 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 11 optimal weight: 0.0870 overall best weight: 0.9762 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8869 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.011 2150 Z= 0.186 Angle : 0.402 2.315 2920 Z= 0.244 Chirality : 0.036 0.071 195 Planarity : 0.001 0.005 415 Dihedral : 3.510 12.204 320 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.56 % Allowed : 6.11 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.89 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.19), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 346 PHE 0.003 0.001 PHE B 350 TYR 0.011 0.001 TYR A 377 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.214 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 21 average time/residue: 0.2547 time to fit residues: 6.0398 Evaluate side-chains 21 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 21 time to evaluate : 0.215 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2368 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 2 optimal weight: 4.9990 chunk 8 optimal weight: 2.9990 chunk 12 optimal weight: 2.9990 chunk 23 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.7980 chunk 20 optimal weight: 3.9990 chunk 24 optimal weight: 2.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.4980 overall best weight: 1.6586 ------------------------------------------------------------------------------- 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: 0.8886 moved from start: 0.2200 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 2150 Z= 0.317 Angle : 0.474 2.945 2920 Z= 0.286 Chirality : 0.039 0.079 195 Planarity : 0.002 0.007 415 Dihedral : 3.826 13.211 320 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.67 % Favored : 96.33 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.95 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.00 (0.19), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 346 PHE 0.004 0.001 PHE B 350 TYR 0.013 0.002 TYR E 365 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.211 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2548 time to fit residues: 6.3334 Evaluate side-chains 22 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.248 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2836 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 14 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.8980 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 0.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 2.9990 overall best weight: 1.7786 ------------------------------------------------------------------------------- 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: 0.8890 moved from start: 0.2234 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.020 2150 Z= 0.340 Angle : 0.484 3.098 2920 Z= 0.293 Chirality : 0.039 0.078 195 Planarity : 0.002 0.007 415 Dihedral : 3.900 13.167 320 Min Nonbonded Distance : 2.301 Molprobity Statistics. All-atom Clashscore : 0.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.04 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.07 (0.19), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 346 PHE 0.005 0.001 PHE B 350 TYR 0.014 0.002 TYR E 365 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.216 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.2685 time to fit residues: 7.4919 Evaluate side-chains 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.216 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2653 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 21 optimal weight: 2.9990 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 9 optimal weight: 4.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.5980 chunk 16 optimal weight: 0.8980 overall best weight: 1.6184 ------------------------------------------------------------------------------- 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: 0.8889 moved from start: 0.2252 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.019 2150 Z= 0.308 Angle : 0.471 2.919 2920 Z= 0.285 Chirality : 0.039 0.077 195 Planarity : 0.002 0.006 415 Dihedral : 3.890 13.249 320 Min Nonbonded Distance : 2.306 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.27 % Favored : 96.73 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -4.07 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.09 (0.19), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP B 346 PHE 0.004 0.001 PHE B 350 TYR 0.013 0.002 TYR A 377 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.253 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2695 time to fit residues: 6.6802 Evaluate side-chains 22 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.227 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2702 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 24 optimal weight: 3.9990 chunk 22 optimal weight: 4.9990 chunk 19 optimal weight: 4.9990 chunk 2 optimal weight: 0.6980 chunk 15 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 18 optimal weight: 0.6980 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 overall best weight: 1.0182 ------------------------------------------------------------------------------- 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: 0.8877 moved from start: 0.2217 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2150 Z= 0.193 Angle : 0.419 2.389 2920 Z= 0.254 Chirality : 0.037 0.073 195 Planarity : 0.001 0.007 415 Dihedral : 3.672 12.624 320 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 6.11 % Favored : 93.89 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.97 (0.26), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.02 (0.20), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP D 346 PHE 0.003 0.001 PHE B 350 TYR 0.011 0.001 TYR D 377 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.212 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2561 time to fit residues: 6.3488 Evaluate side-chains 22 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.224 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2762 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 20 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.8980 chunk 17 optimal weight: 0.6980 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 0.6980 chunk 22 optimal weight: 0.7980 chunk 13 optimal weight: 0.0470 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 9 optimal weight: 4.9990 overall best weight: 0.5678 ------------------------------------------------------------------------------- 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: 0.8862 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.007 2150 Z= 0.110 Angle : 0.378 2.211 2920 Z= 0.228 Chirality : 0.036 0.069 195 Planarity : 0.001 0.008 415 Dihedral : 3.394 11.587 320 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.82 (0.27), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.90 (0.20), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.000 TRP A 346 PHE 0.003 0.001 PHE B 350 TYR 0.008 0.001 TYR C 377 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 490 Ramachandran restraints generated. 245 Oldfield, 0 Emsley, 245 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.218 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2798 time to fit residues: 7.2736 Evaluate side-chains 23 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.219 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.2769 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 25 random chunks: chunk 9 optimal weight: 4.9990 chunk 24 optimal weight: 2.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 2.9990 chunk 3 optimal weight: 0.5980 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.6980 chunk 23 optimal weight: 0.5980 chunk 10 optimal weight: 3.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.0980 overall best weight: 0.9982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 386 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3523 r_free = 0.3523 target = 0.108829 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.2909 r_free = 0.2909 target = 0.069976 restraints weight = 2143.618| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.93 r_work: 0.2776 rms_B_bonded: 2.23 restraints_weight: 0.5000 r_work: 0.2655 rms_B_bonded: 3.41 restraints_weight: 0.2500 r_work (final): 0.2655 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9080 moved from start: 0.2204 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.012 2150 Z= 0.188 Angle : 0.417 2.403 2920 Z= 0.252 Chirality : 0.037 0.074 195 Planarity : 0.001 0.006 415 Dihedral : 3.592 12.713 320 Min Nonbonded Distance : 2.315 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % 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: -3.83 (0.27), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.91 (0.20), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP E 346 PHE 0.004 0.001 PHE B 350 TYR 0.011 0.001 TYR A 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1132.38 seconds wall clock time: 20 minutes 52.15 seconds (1252.15 seconds total)