Starting phenix.real_space_refine on Mon Sep 23 11:59:38 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/09_2024/7zir_14738.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/09_2024/7zir_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_14738/09_2024/7zir_14738.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/09_2024/7zir_14738.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/09_2024/7zir_14738.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7zir_14738/09_2024/7zir_14738.cif" } 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. Time to flip 15 residue(s): 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 2120 Number of models: 1 Model: "" Number of chains: 6 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: "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} Restraints were copied for chains: C, B, E, D Time building chain proxies: 0.99, per 1000 atoms: 0.47 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 - 3.00 Amino acid : True - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.19 Conformation dependent library (CDL) restraints added in 240.2 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: 0.34 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: 0.45 Time building geometry restraints manager: 1.27 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: 0.00 - 0.34: 2351 0.34 - 0.67: 356 0.67 - 1.01: 160 1.01 - 1.34: 28 1.34 - 1.68: 25 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 3.040 nonbonded pdb=" OE1 GLN D 356 " pdb=" O HOH D 501 " model vdw 2.329 3.040 nonbonded pdb=" OE1 GLN A 356 " pdb=" O HOH A 501 " model vdw 2.396 3.040 nonbonded pdb=" OE1 GLN E 356 " pdb=" O HOH E 501 " model vdw 2.467 3.040 nonbonded pdb=" OE1 GLN B 356 " pdb=" O HOH B 501 " model vdw 2.508 3.040 ... (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 Time spend for trying shortcut: 0.00 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: 2.200 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: 0.090 Check model and map are aligned: 0.020 Set scattering table: 0.020 Process input model: 10.300 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.000 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:10.320 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- 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 : 0.217 Fit side-chains REVERT: C 368 ASP cc_start: 0.7486 (p0) cc_final: 0.7214 (m-30) REVERT: D 368 ASP cc_start: 0.7443 (p0) cc_final: 0.7158 (m-30) outliers start: 0 outliers final: 0 residues processed: 28 average time/residue: 0.2539 time to fit residues: 7.9214 Evaluate side-chains 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.217 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 2.9990 chunk 19 optimal weight: 3.9990 chunk 7 optimal weight: 3.9990 chunk 11 optimal weight: 0.9990 chunk 14 optimal weight: 0.8980 chunk 22 optimal weight: 0.9980 chunk 15 optimal weight: 2.9990 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.8863 moved from start: 0.1600 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 2150 Z= 0.267 Angle : 0.466 2.616 2920 Z= 0.284 Chirality : 0.038 0.080 195 Planarity : 0.002 0.006 415 Dihedral : 3.439 12.356 320 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -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 B 350 TYR 0.014 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 23 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.220 Fit side-chains REVERT: C 368 ASP cc_start: 0.7637 (p0) cc_final: 0.7249 (m-30) REVERT: D 355 ASP cc_start: 0.7966 (m-30) cc_final: 0.7719 (m-30) REVERT: D 368 ASP cc_start: 0.7914 (p0) cc_final: 0.7632 (m-30) REVERT: D 389 TYR cc_start: 0.6951 (m-80) cc_final: 0.6739 (m-80) outliers start: 0 outliers final: 0 residues processed: 23 average time/residue: 0.2722 time to fit residues: 7.0227 Evaluate side-chains 23 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.228 ------------------------------------------------------------------------------- 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: 3.9990 chunk 22 optimal weight: 4.9990 chunk 24 optimal weight: 4.9990 chunk 20 optimal weight: 1.9990 chunk 7 optimal weight: 0.2980 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 3.9990 chunk 11 optimal weight: 2.9990 chunk 2 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 15 optimal weight: 1.9990 overall best weight: 1.3986 ------------------------------------------------------------------------------- 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: 0.8877 moved from start: 0.1881 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.016 2150 Z= 0.270 Angle : 0.460 2.612 2920 Z= 0.280 Chirality : 0.038 0.076 195 Planarity : 0.002 0.006 415 Dihedral : 3.588 12.380 320 Min Nonbonded Distance : 2.647 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: -3.99 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.04 (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 0.014 0.002 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 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.221 Fit side-chains REVERT: C 368 ASP cc_start: 0.7627 (p0) cc_final: 0.7348 (m-30) REVERT: D 355 ASP cc_start: 0.8002 (m-30) cc_final: 0.7766 (m-30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2686 time to fit residues: 7.2053 Evaluate side-chains 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.226 ------------------------------------------------------------------------------- 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: 4.9990 chunk 24 optimal weight: 4.9990 chunk 11 optimal weight: 1.9990 chunk 21 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 2.9990 chunk 0 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 9 optimal weight: 0.8980 chunk 16 optimal weight: 0.9980 overall best weight: 1.3584 ------------------------------------------------------------------------------- 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: 0.8881 moved from start: 0.2032 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= 0.261 Angle : 0.453 2.625 2920 Z= 0.275 Chirality : 0.038 0.076 195 Planarity : 0.002 0.006 415 Dihedral : 3.630 12.521 320 Min Nonbonded Distance : 2.646 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.56 % Allowed : 5.56 % 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: -3.98 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.03 (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 0.001 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 27 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.219 Fit side-chains REVERT: C 368 ASP cc_start: 0.7802 (p0) cc_final: 0.7427 (m-30) REVERT: D 355 ASP cc_start: 0.7993 (m-30) cc_final: 0.7769 (m-30) outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.2711 time to fit residues: 7.8499 Evaluate side-chains 26 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 26 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 2.9990 chunk 21 optimal weight: 2.9990 chunk 6 optimal weight: 0.6980 chunk 8 optimal weight: 1.9990 chunk 4 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 24 optimal weight: 1.9990 chunk 20 optimal weight: 0.3980 chunk 11 optimal weight: 0.6980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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: 0.8880 moved from start: 0.2090 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= 0.222 Angle : 0.430 2.433 2920 Z= 0.261 Chirality : 0.037 0.073 195 Planarity : 0.001 0.005 415 Dihedral : 3.572 12.352 320 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % 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: -3.90 (0.25), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.97 (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 0.011 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 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.207 Fit side-chains REVERT: C 368 ASP cc_start: 0.7814 (p0) cc_final: 0.7419 (m-30) REVERT: D 355 ASP cc_start: 0.7989 (m-30) cc_final: 0.7773 (m-30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2742 time to fit residues: 7.3253 Evaluate side-chains 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.221 ------------------------------------------------------------------------------- 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: 0.8980 chunk 12 optimal weight: 1.9990 chunk 23 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 17 optimal weight: 0.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 4.9990 chunk 15 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 11 optimal weight: 0.6980 overall best weight: 1.1184 ------------------------------------------------------------------------------- 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: 0.8880 moved from start: 0.2138 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2150 Z= 0.215 Angle : 0.427 2.441 2920 Z= 0.259 Chirality : 0.037 0.073 195 Planarity : 0.001 0.005 415 Dihedral : 3.580 12.356 320 Min Nonbonded Distance : 2.653 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -3.86 (0.26), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.20), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP B 346 PHE 0.004 0.001 PHE B 350 TYR 0.011 0.001 TYR A 377 *********************** 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 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.224 Fit side-chains REVERT: C 368 ASP cc_start: 0.7823 (p0) cc_final: 0.7515 (m-30) REVERT: A 345 ASN cc_start: 0.7471 (t0) cc_final: 0.7210 (t0) REVERT: D 355 ASP cc_start: 0.8017 (m-30) cc_final: 0.7802 (m-30) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2540 time to fit residues: 6.8177 Evaluate side-chains 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.192 ------------------------------------------------------------------------------- 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: 0.9990 chunk 9 optimal weight: 4.9990 chunk 7 optimal weight: 3.9990 chunk 4 optimal weight: 3.9990 chunk 15 optimal weight: 2.9990 chunk 16 optimal weight: 3.9990 chunk 11 optimal weight: 0.6980 chunk 2 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 21 optimal weight: 2.9990 chunk 23 optimal weight: 3.9990 overall best weight: 2.3388 ------------------------------------------------------------------------------- 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: 0.8898 moved from start: 0.2283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.026 2150 Z= 0.446 Angle : 0.541 3.385 2920 Z= 0.328 Chirality : 0.042 0.087 195 Planarity : 0.002 0.007 415 Dihedral : 4.017 13.509 320 Min Nonbonded Distance : 2.630 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -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 0.002 TRP B 346 PHE 0.005 0.001 PHE B 350 TYR 0.018 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 24 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.221 Fit side-chains REVERT: C 368 ASP cc_start: 0.7850 (p0) cc_final: 0.7344 (m-30) REVERT: A 345 ASN cc_start: 0.7552 (t0) cc_final: 0.7270 (t0) outliers start: 0 outliers final: 0 residues processed: 24 average time/residue: 0.2599 time to fit residues: 6.9996 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 ------------------------------------------------------------------------------- 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: 0.5980 chunk 22 optimal weight: 3.9990 chunk 23 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 17 optimal weight: 3.9990 chunk 6 optimal weight: 0.9990 chunk 20 optimal weight: 1.9990 chunk 14 optimal weight: 0.0870 chunk 11 optimal weight: 0.9990 chunk 16 optimal weight: 0.9990 overall best weight: 0.7364 ------------------------------------------------------------------------------- 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: 0.8873 moved from start: 0.2186 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.008 2150 Z= 0.145 Angle : 0.395 2.204 2920 Z= 0.240 Chirality : 0.036 0.068 195 Planarity : 0.001 0.004 415 Dihedral : 3.528 11.978 320 Min Nonbonded Distance : 2.662 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -3.87 (0.26), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.20), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.000 TRP A 346 PHE 0.003 0.001 PHE B 350 TYR 0.010 0.001 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 : 0.231 Fit side-chains REVERT: C 368 ASP cc_start: 0.7821 (p0) cc_final: 0.7493 (m-30) REVERT: A 345 ASN cc_start: 0.7506 (t0) cc_final: 0.7210 (t0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2765 time to fit residues: 6.8192 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 ------------------------------------------------------------------------------- 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: 5.9990 chunk 22 optimal weight: 5.9990 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: 0.6980 chunk 6 optimal weight: 0.9990 chunk 18 optimal weight: 3.9990 chunk 5 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 overall best weight: 1.0786 ------------------------------------------------------------------------------- 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: 0.8881 moved from start: 0.2250 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= 0.208 Angle : 0.427 2.430 2920 Z= 0.259 Chirality : 0.038 0.073 195 Planarity : 0.001 0.005 415 Dihedral : 3.630 12.634 320 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.00 % Allowed : 5.00 % Favored : 95.00 % 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: -3.86 (0.26), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.93 (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 *********************** 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 : 0.254 Fit side-chains REVERT: C 368 ASP cc_start: 0.7800 (p0) cc_final: 0.7443 (m-30) REVERT: A 345 ASN cc_start: 0.7523 (t0) cc_final: 0.7186 (t0) outliers start: 0 outliers final: 0 residues processed: 22 average time/residue: 0.2685 time to fit residues: 6.6285 Evaluate side-chains 22 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.220 ------------------------------------------------------------------------------- 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: 3.9990 chunk 2 optimal weight: 4.9990 chunk 3 optimal weight: 0.0050 chunk 17 optimal weight: 1.9990 chunk 1 optimal weight: 3.9990 chunk 14 optimal weight: 1.9990 chunk 22 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 0 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 4.9990 overall best weight: 1.1198 ------------------------------------------------------------------------------- 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: 0.8881 moved from start: 0.2254 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.013 2150 Z= 0.215 Angle : 0.429 2.426 2920 Z= 0.260 Chirality : 0.038 0.075 195 Planarity : 0.001 0.005 415 Dihedral : 3.637 12.657 320 Min Nonbonded Distance : 2.655 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.86 % Favored : 97.14 % Rotamer: Outliers : 0.56 % Allowed : 4.44 % Favored : 95.00 % 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: -3.87 (0.27), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.94 (0.20), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 346 PHE 0.004 0.001 PHE B 350 TYR 0.011 0.001 TYR A 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: 1 poor density : 22 time to evaluate : 0.219 Fit side-chains REVERT: C 368 ASP cc_start: 0.7795 (p0) cc_final: 0.7434 (m-30) REVERT: A 345 ASN cc_start: 0.7546 (t0) cc_final: 0.7209 (t0) outliers start: 1 outliers final: 1 residues processed: 23 average time/residue: 0.2551 time to fit residues: 6.6155 Evaluate side-chains 23 residues out of total 180 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 22 time to evaluate : 0.214 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 372 SER 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: 3.9990 chunk 0 optimal weight: 4.9990 chunk 4 optimal weight: 0.9990 chunk 3 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 20 optimal weight: 0.5980 chunk 23 optimal weight: 0.8980 chunk 10 optimal weight: 2.9990 chunk 2 optimal weight: 4.9990 chunk 6 optimal weight: 0.7980 overall best weight: 1.2584 ------------------------------------------------------------------------------- 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 = 0.3526 r_free = 0.3526 target = 0.108516 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.2907 r_free = 0.2907 target = 0.069661 restraints weight = 2158.834| |-----------------------------------------------------------------------------| r_work (start): 0.2901 rms_B_bonded: 1.92 r_work: 0.2779 rms_B_bonded: 2.22 restraints_weight: 0.5000 r_work: 0.2662 rms_B_bonded: 3.39 restraints_weight: 0.2500 r_work (final): 0.2662 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.9095 moved from start: 0.2283 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= 0.243 Angle : 0.444 2.536 2920 Z= 0.269 Chirality : 0.038 0.077 195 Planarity : 0.002 0.005 415 Dihedral : 3.694 12.763 320 Min Nonbonded Distance : 2.650 Molprobity Statistics. All-atom Clashscore : 0.28 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.45 % Favored : 97.55 % Rotamer: Outliers : 0.56 % Allowed : 5.56 % 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: -3.90 (0.26), residues: 245 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -2.96 (0.20), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.002 0.001 TRP A 346 PHE 0.004 0.001 PHE B 350 TYR 0.012 0.001 TYR A 377 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1132.12 seconds wall clock time: 20 minutes 49.16 seconds (1249.16 seconds total)