Starting phenix.real_space_refine on Mon Sep 23 15:40:07 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws6_32748/09_2024/7ws6_32748.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws6_32748/09_2024/7ws6_32748.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.8 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws6_32748/09_2024/7ws6_32748.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws6_32748/09_2024/7ws6_32748.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws6_32748/09_2024/7ws6_32748.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws6_32748/09_2024/7ws6_32748.cif" } resolution = 3.8 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= -0.002 sd= 0.022 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 15 5.16 5 C 2245 2.51 5 N 597 2.21 5 O 674 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped. Time to flip 14 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: 3531 Number of models: 1 Model: "" Number of chains: 3 Chain: "C" Number of atoms: 1747 Number of conformers: 1 Conformer: "" Number of residues, atoms: 218, 1747 Classifications: {'peptide': 218} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 14, 'TRANS': 203} Unresolved non-hydrogen bonds: 6 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 6 Planarities with less than four sites: {'HIS:plan': 1} Unresolved non-hydrogen planarities: 5 Chain: "H" Number of atoms: 817 Number of conformers: 1 Conformer: "" Number of residues, atoms: 108, 817 Classifications: {'peptide': 108} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 7, 'TRANS': 100} Unresolved non-hydrogen bonds: 4 Unresolved non-hydrogen angles: 4 Unresolved non-hydrogen dihedrals: 4 Chain: "I" Number of atoms: 967 Number of conformers: 1 Conformer: "" Number of residues, atoms: 125, 967 Classifications: {'peptide': 125} Link IDs: {'PTRANS': 3, 'TRANS': 121} Time building chain proxies: 5.11, per 1000 atoms: 1.45 Number of scatterers: 3531 At special positions: 0 Unit cell: (59.072, 94.016, 113.152, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 15 16.00 O 674 8.00 N 597 7.00 C 2245 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=5, symmetry=0 Simple disulfide: pdb=" SG CYS C 336 " - pdb=" SG CYS C 361 " distance=2.03 Simple disulfide: pdb=" SG CYS C 379 " - pdb=" SG CYS C 432 " distance=2.03 Simple disulfide: pdb=" SG CYS C 480 " - pdb=" SG CYS C 488 " distance=2.02 Simple disulfide: pdb=" SG CYS H 23 " - pdb=" SG CYS H 88 " distance=2.03 Simple disulfide: pdb=" SG CYS I 22 " - pdb=" SG CYS I 96 " distance=2.03 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: 0.83 Conformation dependent library (CDL) restraints added in 429.2 milliseconds 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 836 Finding SS restraints... Secondary structure from input PDB file: 7 helices and 10 sheets defined 8.9% alpha, 29.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.48 Creating SS restraints... Processing helix chain 'C' and resid 338 through 343 removed outlier: 3.527A pdb=" N PHE C 342 " --> pdb=" O PHE C 338 " (cutoff:3.500A) Processing helix chain 'C' and resid 365 through 370 removed outlier: 3.539A pdb=" N ASN C 370 " --> pdb=" O SER C 366 " (cutoff:3.500A) Processing helix chain 'C' and resid 383 through 389 removed outlier: 3.512A pdb=" N LEU C 387 " --> pdb=" O PRO C 384 " (cutoff:3.500A) removed outlier: 3.917A pdb=" N ASN C 388 " --> pdb=" O THR C 385 " (cutoff:3.500A) removed outlier: 3.524A pdb=" N ASP C 389 " --> pdb=" O LYS C 386 " (cutoff:3.500A) Processing helix chain 'C' and resid 406 through 410 Processing helix chain 'C' and resid 416 through 422 Processing helix chain 'C' and resid 502 through 506 Processing helix chain 'I' and resid 62 through 65 removed outlier: 3.554A pdb=" N LYS I 65 " --> pdb=" O ASP I 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'I' and resid 62 through 65' Processing sheet with id=AA1, first strand: chain 'C' and resid 354 through 358 removed outlier: 3.542A pdb=" N ASN C 354 " --> pdb=" O SER C 399 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 361 through 362 removed outlier: 6.771A pdb=" N CYS C 361 " --> pdb=" O CYS C 525 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 452 through 454 Processing sheet with id=AA4, first strand: chain 'H' and resid 4 through 6 Processing sheet with id=AA5, first strand: chain 'H' and resid 10 through 13 removed outlier: 5.604A pdb=" N LEU H 11 " --> pdb=" O GLU H 106 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'H' and resid 53 through 54 removed outlier: 6.866A pdb=" N TRP H 35 " --> pdb=" O LEU H 47 " (cutoff:3.500A) removed outlier: 5.430A pdb=" N TYR H 49 " --> pdb=" O LEU H 33 " (cutoff:3.500A) removed outlier: 7.149A pdb=" N LEU H 33 " --> pdb=" O TYR H 49 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'I' and resid 4 through 7 removed outlier: 3.680A pdb=" N SER I 21 " --> pdb=" O SER I 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'I' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.952A pdb=" N ASP I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.530A pdb=" N LYS I 98 " --> pdb=" O ASP I 111 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'I' and resid 58 through 60 removed outlier: 3.952A pdb=" N ASP I 59 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 6.741A pdb=" N TRP I 36 " --> pdb=" O VAL I 48 " (cutoff:3.500A) removed outlier: 4.646A pdb=" N GLY I 50 " --> pdb=" O MET I 34 " (cutoff:3.500A) removed outlier: 6.873A pdb=" N MET I 34 " --> pdb=" O GLY I 50 " (cutoff:3.500A) removed outlier: 3.611A pdb=" N TYR I 94 " --> pdb=" O THR I 117 " (cutoff:3.500A) 100 hydrogen bonds defined for protein. 240 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: 0.91 Time building geometry restraints manager: 0.99 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1132 1.34 - 1.46: 899 1.46 - 1.58: 1573 1.58 - 1.70: 0 1.70 - 1.81: 18 Bond restraints: 3622 Sorted by residual: bond pdb=" N ASP I 31 " pdb=" CA ASP I 31 " ideal model delta sigma weight residual 1.458 1.493 -0.036 1.22e-02 6.72e+03 8.47e+00 bond pdb=" N ASP C 442 " pdb=" CA ASP C 442 " ideal model delta sigma weight residual 1.457 1.489 -0.032 1.16e-02 7.43e+03 7.52e+00 bond pdb=" N ARG C 346 " pdb=" CA ARG C 346 " ideal model delta sigma weight residual 1.455 1.486 -0.031 1.25e-02 6.40e+03 6.12e+00 bond pdb=" N LYS C 440 " pdb=" CA LYS C 440 " ideal model delta sigma weight residual 1.456 1.486 -0.031 1.32e-02 5.74e+03 5.37e+00 bond pdb=" N ARG C 493 " pdb=" CA ARG C 493 " ideal model delta sigma weight residual 1.454 1.482 -0.028 1.19e-02 7.06e+03 5.36e+00 ... (remaining 3617 not shown) Histogram of bond angle deviations from ideal: 0.00 - 1.21: 4597 1.21 - 2.42: 249 2.42 - 3.64: 61 3.64 - 4.85: 11 4.85 - 6.06: 4 Bond angle restraints: 4922 Sorted by residual: angle pdb=" CA TYR H 32 " pdb=" C TYR H 32 " pdb=" O TYR H 32 " ideal model delta sigma weight residual 122.13 118.09 4.04 1.13e+00 7.83e-01 1.28e+01 angle pdb=" C SER C 438 " pdb=" N ASN C 439 " pdb=" CA ASN C 439 " ideal model delta sigma weight residual 121.14 115.95 5.19 1.75e+00 3.27e-01 8.80e+00 angle pdb=" CA ARG C 493 " pdb=" C ARG C 493 " pdb=" O ARG C 493 " ideal model delta sigma weight residual 121.16 118.08 3.08 1.13e+00 7.83e-01 7.43e+00 angle pdb=" CA ARG C 346 " pdb=" C ARG C 346 " pdb=" O ARG C 346 " ideal model delta sigma weight residual 120.66 117.69 2.97 1.15e+00 7.56e-01 6.65e+00 angle pdb=" CA LYS H 45 " pdb=" C LYS H 45 " pdb=" O LYS H 45 " ideal model delta sigma weight residual 121.44 118.43 3.01 1.17e+00 7.31e-01 6.62e+00 ... (remaining 4917 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.96: 1952 17.96 - 35.91: 163 35.91 - 53.87: 24 53.87 - 71.82: 6 71.82 - 89.78: 3 Dihedral angle restraints: 2148 sinusoidal: 836 harmonic: 1312 Sorted by residual: dihedral pdb=" CB CYS C 336 " pdb=" SG CYS C 336 " pdb=" SG CYS C 361 " pdb=" CB CYS C 361 " ideal model delta sinusoidal sigma weight residual 93.00 35.32 57.68 1 1.00e+01 1.00e-02 4.47e+01 dihedral pdb=" CA PRO C 337 " pdb=" C PRO C 337 " pdb=" N PHE C 338 " pdb=" CA PHE C 338 " ideal model delta harmonic sigma weight residual 180.00 160.69 19.31 0 5.00e+00 4.00e-02 1.49e+01 dihedral pdb=" CB CYS H 23 " pdb=" SG CYS H 23 " pdb=" SG CYS H 88 " pdb=" CB CYS H 88 " ideal model delta sinusoidal sigma weight residual 93.00 63.07 29.93 1 1.00e+01 1.00e-02 1.28e+01 ... (remaining 2145 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.041: 375 0.041 - 0.082: 106 0.082 - 0.124: 43 0.124 - 0.165: 3 0.165 - 0.206: 2 Chirality restraints: 529 Sorted by residual: chirality pdb=" CB ILE H 75 " pdb=" CA ILE H 75 " pdb=" CG1 ILE H 75 " pdb=" CG2 ILE H 75 " both_signs ideal model delta sigma weight residual False 2.64 2.44 0.21 2.00e-01 2.50e+01 1.06e+00 chirality pdb=" CA THR H 94 " pdb=" N THR H 94 " pdb=" C THR H 94 " pdb=" CB THR H 94 " both_signs ideal model delta sigma weight residual False 2.53 2.34 0.18 2.00e-01 2.50e+01 8.54e-01 chirality pdb=" CA ARG C 346 " pdb=" N ARG C 346 " pdb=" C ARG C 346 " pdb=" CB ARG C 346 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.60e-01 ... (remaining 526 not shown) Planarity restraints: 638 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CD ARG H 24 " -0.143 9.50e-02 1.11e+02 6.45e-02 3.09e+00 pdb=" NE ARG H 24 " 0.013 2.00e-02 2.50e+03 pdb=" CZ ARG H 24 " -0.011 2.00e-02 2.50e+03 pdb=" NH1 ARG H 24 " 0.006 2.00e-02 2.50e+03 pdb=" NH2 ARG H 24 " -0.001 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C THR I 106 " 0.020 5.00e-02 4.00e+02 2.98e-02 1.42e+00 pdb=" N PRO I 107 " -0.051 5.00e-02 4.00e+02 pdb=" CA PRO I 107 " 0.015 5.00e-02 4.00e+02 pdb=" CD PRO I 107 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR I 60 " -0.006 2.00e-02 2.50e+03 8.32e-03 1.39e+00 pdb=" CG TYR I 60 " 0.020 2.00e-02 2.50e+03 pdb=" CD1 TYR I 60 " -0.004 2.00e-02 2.50e+03 pdb=" CD2 TYR I 60 " -0.010 2.00e-02 2.50e+03 pdb=" CE1 TYR I 60 " -0.003 2.00e-02 2.50e+03 pdb=" CE2 TYR I 60 " 0.003 2.00e-02 2.50e+03 pdb=" CZ TYR I 60 " 0.000 2.00e-02 2.50e+03 pdb=" OH TYR I 60 " 0.000 2.00e-02 2.50e+03 ... (remaining 635 not shown) Histogram of nonbonded interaction distances: 2.28 - 2.81: 1013 2.81 - 3.33: 3100 3.33 - 3.85: 5601 3.85 - 4.38: 6356 4.38 - 4.90: 10946 Nonbonded interactions: 27016 Sorted by model distance: nonbonded pdb=" OD1 ASP C 339 " pdb=" N GLU C 340 " model vdw 2.282 3.120 nonbonded pdb=" OD1 ASP I 62 " pdb=" N SER I 63 " model vdw 2.309 3.120 nonbonded pdb=" OG1 THR C 393 " pdb=" O GLU C 516 " model vdw 2.310 3.040 nonbonded pdb=" OD1 ASN H 34 " pdb=" OG SER I 109 " model vdw 2.313 3.040 nonbonded pdb=" OD1 ASP I 99 " pdb=" N ARG I 100 " model vdw 2.322 3.120 ... (remaining 27011 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.720 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 0.150 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 15.440 Find NCS groups from input model: 0.040 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.800 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 24.240 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7295 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3622 Z= 0.224 Angle : 0.682 6.060 4922 Z= 0.391 Chirality : 0.046 0.206 529 Planarity : 0.004 0.065 638 Dihedral : 13.454 89.776 1297 Min Nonbonded Distance : 2.282 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.72 % Favored : 95.28 % 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: -1.37 (0.36), residues: 445 helix: -3.69 (0.62), residues: 26 sheet: 0.38 (0.45), residues: 133 loop : -1.33 (0.32), residues: 286 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP I 113 HIS 0.003 0.001 HIS I 35 PHE 0.016 0.001 PHE C 486 TYR 0.020 0.001 TYR I 60 ARG 0.013 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 107 time to evaluate : 0.380 Fit side-chains revert: symmetry clash REVERT: H 34 ASN cc_start: 0.8518 (m110) cc_final: 0.7462 (m110) REVERT: H 97 TYR cc_start: 0.8609 (m-80) cc_final: 0.8334 (m-80) outliers start: 0 outliers final: 0 residues processed: 107 average time/residue: 0.1858 time to fit residues: 23.4549 Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 95 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 36 optimal weight: 0.0060 chunk 32 optimal weight: 3.9990 chunk 18 optimal weight: 1.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 17 optimal weight: 2.9990 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.9980 chunk 39 optimal weight: 0.7980 overall best weight: 0.8998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 417 ASN ** C 422 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7389 moved from start: 0.2222 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 3622 Z= 0.272 Angle : 0.664 7.964 4922 Z= 0.344 Chirality : 0.047 0.153 529 Planarity : 0.004 0.033 638 Dihedral : 5.079 18.372 499 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 13.42 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 2.33 % Allowed : 13.18 % Favored : 84.50 % 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: -1.21 (0.37), residues: 445 helix: -3.70 (0.60), residues: 24 sheet: 0.24 (0.44), residues: 141 loop : -1.12 (0.34), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP I 36 HIS 0.002 0.001 HIS I 35 PHE 0.020 0.002 PHE C 486 TYR 0.018 0.002 TYR I 102 ARG 0.005 0.001 ARG H 61 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 98 time to evaluate : 0.412 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.7615 (p90) cc_final: 0.7378 (p90) REVERT: I 31 ASP cc_start: 0.8474 (p0) cc_final: 0.8069 (p0) REVERT: I 59 ASP cc_start: 0.8047 (t0) cc_final: 0.7834 (t0) outliers start: 9 outliers final: 6 residues processed: 101 average time/residue: 0.1662 time to fit residues: 20.3233 Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 89 time to evaluate : 0.425 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 48 ILE Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 32 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 39 optimal weight: 0.5980 chunk 42 optimal weight: 0.0770 chunk 34 optimal weight: 0.9990 chunk 38 optimal weight: 0.9990 chunk 13 optimal weight: 1.9990 chunk 31 optimal weight: 0.4980 overall best weight: 0.5740 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 moved from start: 0.2491 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3622 Z= 0.219 Angle : 0.658 9.504 4922 Z= 0.334 Chirality : 0.046 0.204 529 Planarity : 0.004 0.032 638 Dihedral : 4.837 17.748 499 Min Nonbonded Distance : 2.595 Molprobity Statistics. All-atom Clashscore : 11.40 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.15 % Favored : 96.85 % Rotamer: Outliers : 2.84 % Allowed : 16.54 % Favored : 80.62 % 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: -1.16 (0.37), residues: 445 helix: -3.64 (0.64), residues: 24 sheet: 0.29 (0.46), residues: 132 loop : -1.06 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.012 0.001 PHE C 486 TYR 0.020 0.001 TYR I 102 ARG 0.007 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 107 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 96 time to evaluate : 0.375 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: H 49 TYR cc_start: 0.7527 (p90) cc_final: 0.7273 (p90) REVERT: I 31 ASP cc_start: 0.8421 (p0) cc_final: 0.8060 (p0) REVERT: I 59 ASP cc_start: 0.8062 (t0) cc_final: 0.7708 (t0) outliers start: 11 outliers final: 7 residues processed: 101 average time/residue: 0.1718 time to fit residues: 20.9982 Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 88 time to evaluate : 0.371 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 75 ILE Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 1.9990 chunk 29 optimal weight: 0.6980 chunk 20 optimal weight: 4.9990 chunk 4 optimal weight: 0.4980 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 2.9990 chunk 39 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 37 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 506 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7384 moved from start: 0.2864 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 3622 Z= 0.235 Angle : 0.664 9.776 4922 Z= 0.335 Chirality : 0.046 0.183 529 Planarity : 0.004 0.034 638 Dihedral : 4.881 17.215 499 Min Nonbonded Distance : 2.589 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.17 % Favored : 94.83 % Rotamer: Outliers : 2.33 % Allowed : 20.67 % Favored : 77.00 % 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: -1.15 (0.37), residues: 445 helix: -3.55 (0.65), residues: 24 sheet: 0.30 (0.45), residues: 132 loop : -1.06 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP I 53 HIS 0.003 0.001 HIS I 35 PHE 0.014 0.002 PHE C 486 TYR 0.020 0.001 TYR I 102 ARG 0.008 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 92 time to evaluate : 0.403 Fit side-chains REVERT: I 31 ASP cc_start: 0.8504 (p0) cc_final: 0.8095 (p0) REVERT: I 59 ASP cc_start: 0.8074 (t0) cc_final: 0.7657 (t0) REVERT: I 60 TYR cc_start: 0.8386 (m-10) cc_final: 0.8165 (m-10) outliers start: 9 outliers final: 8 residues processed: 97 average time/residue: 0.1605 time to fit residues: 18.8784 Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.419 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 4.9990 chunk 0 optimal weight: 1.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 21 optimal weight: 0.9980 chunk 37 optimal weight: 0.0050 chunk 10 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 8 optimal weight: 0.3980 overall best weight: 0.6194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 409 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 414 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7377 moved from start: 0.2923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3622 Z= 0.222 Angle : 0.654 8.148 4922 Z= 0.331 Chirality : 0.046 0.174 529 Planarity : 0.004 0.033 638 Dihedral : 4.814 16.950 499 Min Nonbonded Distance : 2.551 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer: Outliers : 3.36 % Allowed : 20.93 % Favored : 75.71 % 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: -1.17 (0.37), residues: 445 helix: -3.39 (0.69), residues: 24 sheet: 0.29 (0.45), residues: 132 loop : -1.09 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.002 HIS I 35 PHE 0.013 0.001 PHE C 490 TYR 0.019 0.001 TYR I 102 ARG 0.004 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 104 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 91 time to evaluate : 0.429 Fit side-chains REVERT: H 81 GLU cc_start: 0.7479 (pp20) cc_final: 0.7241 (pp20) REVERT: I 31 ASP cc_start: 0.8471 (p0) cc_final: 0.8065 (p0) REVERT: I 59 ASP cc_start: 0.8036 (t0) cc_final: 0.7618 (t0) REVERT: I 60 TYR cc_start: 0.8430 (m-10) cc_final: 0.8105 (m-10) outliers start: 13 outliers final: 8 residues processed: 98 average time/residue: 0.1726 time to fit residues: 20.2687 Evaluate side-chains 94 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 86 time to evaluate : 0.369 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain I residue 37 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 3.9990 chunk 10 optimal weight: 0.0770 chunk 41 optimal weight: 0.4980 chunk 34 optimal weight: 0.9980 chunk 19 optimal weight: 0.9980 chunk 3 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.0050 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 0.8980 chunk 23 optimal weight: 1.9990 overall best weight: 0.4752 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** H 89 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7351 moved from start: 0.3283 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3622 Z= 0.204 Angle : 0.654 9.738 4922 Z= 0.328 Chirality : 0.045 0.171 529 Planarity : 0.004 0.033 638 Dihedral : 4.779 19.175 499 Min Nonbonded Distance : 2.557 Molprobity Statistics. All-atom Clashscore : 11.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.04 % Favored : 95.96 % Rotamer: Outliers : 3.88 % Allowed : 21.71 % Favored : 74.42 % 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: -1.18 (0.37), residues: 445 helix: -3.33 (0.69), residues: 24 sheet: 0.36 (0.45), residues: 132 loop : -1.15 (0.33), residues: 289 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.011 0.001 PHE C 490 TYR 0.018 0.001 TYR I 102 ARG 0.006 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 101 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 86 time to evaluate : 0.409 Fit side-chains REVERT: I 31 ASP cc_start: 0.8434 (p0) cc_final: 0.8034 (p0) REVERT: I 59 ASP cc_start: 0.7990 (t0) cc_final: 0.7545 (t0) REVERT: I 60 TYR cc_start: 0.8433 (m-10) cc_final: 0.8168 (m-10) REVERT: I 68 PHE cc_start: 0.7248 (OUTLIER) cc_final: 0.7022 (m-10) REVERT: I 83 MET cc_start: 0.8333 (mmm) cc_final: 0.7221 (mmm) outliers start: 15 outliers final: 9 residues processed: 93 average time/residue: 0.1631 time to fit residues: 18.4621 Evaluate side-chains 95 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 85 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Chi-restraints excluded: chain I residue 68 PHE Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 0.6980 chunk 23 optimal weight: 4.9990 chunk 35 optimal weight: 0.1980 chunk 41 optimal weight: 0.1980 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 24 optimal weight: 0.7980 chunk 12 optimal weight: 0.9980 chunk 8 optimal weight: 0.5980 chunk 26 optimal weight: 0.4980 overall best weight: 0.4380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3368 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.043 3622 Z= 0.200 Angle : 0.666 9.267 4922 Z= 0.334 Chirality : 0.046 0.166 529 Planarity : 0.004 0.033 638 Dihedral : 4.703 21.401 499 Min Nonbonded Distance : 2.568 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.60 % Favored : 96.40 % Rotamer: Outliers : 4.13 % Allowed : 21.71 % Favored : 74.16 % 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: -1.27 (0.37), residues: 445 helix: -3.28 (0.70), residues: 24 sheet: 0.24 (0.44), residues: 139 loop : -1.23 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.010 0.001 PHE I 68 TYR 0.019 0.001 TYR C 473 ARG 0.007 0.000 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 102 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 86 time to evaluate : 0.375 Fit side-chains REVERT: H 71 PHE cc_start: 0.6551 (m-80) cc_final: 0.6278 (m-80) REVERT: I 31 ASP cc_start: 0.8424 (p0) cc_final: 0.8031 (p0) REVERT: I 59 ASP cc_start: 0.7995 (t0) cc_final: 0.7581 (t0) REVERT: I 60 TYR cc_start: 0.8495 (m-10) cc_final: 0.8159 (m-10) outliers start: 16 outliers final: 12 residues processed: 97 average time/residue: 0.1664 time to fit residues: 19.5875 Evaluate side-chains 94 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 425 LEU Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 3 optimal weight: 0.9990 chunk 32 optimal weight: 0.2980 chunk 37 optimal weight: 0.7980 chunk 39 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 0.9980 chunk 23 optimal weight: 1.9990 chunk 16 optimal weight: 0.9980 chunk 30 optimal weight: 0.0970 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7356 moved from start: 0.3532 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.045 3622 Z= 0.223 Angle : 0.675 8.632 4922 Z= 0.342 Chirality : 0.045 0.170 529 Planarity : 0.005 0.056 638 Dihedral : 4.813 20.796 499 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 12.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.27 % Favored : 95.73 % Rotamer: Outliers : 3.62 % Allowed : 22.22 % Favored : 74.16 % 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: -1.40 (0.37), residues: 445 helix: -3.31 (0.70), residues: 24 sheet: 0.09 (0.43), residues: 141 loop : -1.30 (0.33), residues: 280 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.025 0.002 PHE I 68 TYR 0.019 0.001 TYR I 102 ARG 0.013 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 85 time to evaluate : 0.447 Fit side-chains REVERT: C 460 ASN cc_start: 0.8591 (m-40) cc_final: 0.8328 (m-40) REVERT: H 71 PHE cc_start: 0.6472 (m-80) cc_final: 0.6214 (m-80) REVERT: I 31 ASP cc_start: 0.8438 (p0) cc_final: 0.8018 (p0) REVERT: I 59 ASP cc_start: 0.7991 (t0) cc_final: 0.7597 (t0) REVERT: I 60 TYR cc_start: 0.8516 (m-10) cc_final: 0.8118 (m-10) outliers start: 14 outliers final: 13 residues processed: 91 average time/residue: 0.1708 time to fit residues: 19.0360 Evaluate side-chains 96 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 83 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 361 CYS Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.7980 chunk 36 optimal weight: 0.9980 chunk 38 optimal weight: 0.5980 chunk 25 optimal weight: 0.0970 chunk 40 optimal weight: 1.9990 chunk 24 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 28 optimal weight: 3.9990 chunk 42 optimal weight: 0.6980 chunk 39 optimal weight: 0.9990 overall best weight: 0.5578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: H 34 ASN H 89 GLN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7357 moved from start: 0.3603 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 3622 Z= 0.224 Angle : 0.680 8.268 4922 Z= 0.346 Chirality : 0.046 0.173 529 Planarity : 0.005 0.061 638 Dihedral : 4.799 20.636 499 Min Nonbonded Distance : 2.532 Molprobity Statistics. All-atom Clashscore : 11.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.39 % Favored : 94.61 % Rotamer: Outliers : 2.84 % Allowed : 22.48 % Favored : 74.68 % 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: -1.27 (0.36), residues: 445 helix: -2.71 (0.87), residues: 18 sheet: 0.33 (0.43), residues: 137 loop : -1.38 (0.32), residues: 290 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.022 0.002 PHE I 68 TYR 0.019 0.001 TYR I 102 ARG 0.014 0.001 ARG H 24 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.408 Fit side-chains REVERT: C 460 ASN cc_start: 0.8603 (m-40) cc_final: 0.8336 (m-40) REVERT: H 55 GLN cc_start: 0.8594 (tm-30) cc_final: 0.8379 (tm-30) REVERT: H 71 PHE cc_start: 0.6523 (m-80) cc_final: 0.6275 (m-80) REVERT: I 31 ASP cc_start: 0.8435 (p0) cc_final: 0.8009 (p0) REVERT: I 59 ASP cc_start: 0.7999 (t0) cc_final: 0.7610 (t0) REVERT: I 60 TYR cc_start: 0.8497 (m-10) cc_final: 0.8091 (m-10) outliers start: 11 outliers final: 10 residues processed: 88 average time/residue: 0.1599 time to fit residues: 17.1733 Evaluate side-chains 91 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 81 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.8980 chunk 3 optimal weight: 0.9990 chunk 26 optimal weight: 0.4980 chunk 20 optimal weight: 0.6980 chunk 27 optimal weight: 0.6980 chunk 36 optimal weight: 0.7980 chunk 10 optimal weight: 0.0370 chunk 31 optimal weight: 2.9990 chunk 5 optimal weight: 0.0870 chunk 9 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 overall best weight: 0.4036 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7328 moved from start: 0.3738 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.044 3622 Z= 0.202 Angle : 0.690 8.253 4922 Z= 0.346 Chirality : 0.046 0.172 529 Planarity : 0.004 0.040 638 Dihedral : 4.688 20.253 499 Min Nonbonded Distance : 2.498 Molprobity Statistics. All-atom Clashscore : 10.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.49 % Favored : 95.51 % Rotamer: Outliers : 3.10 % Allowed : 23.77 % Favored : 73.13 % 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: -1.37 (0.36), residues: 445 helix: -3.34 (0.69), residues: 24 sheet: 0.26 (0.43), residues: 139 loop : -1.35 (0.33), residues: 282 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP C 436 HIS 0.003 0.001 HIS I 35 PHE 0.019 0.002 PHE I 68 TYR 0.018 0.001 TYR I 102 ARG 0.006 0.000 ARG C 493 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 890 Ramachandran restraints generated. 445 Oldfield, 0 Emsley, 445 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 82 time to evaluate : 0.339 Fit side-chains REVERT: H 55 GLN cc_start: 0.8558 (tm-30) cc_final: 0.8319 (tm-30) REVERT: I 31 ASP cc_start: 0.8397 (p0) cc_final: 0.7975 (p0) REVERT: I 59 ASP cc_start: 0.7990 (t0) cc_final: 0.7590 (t0) REVERT: I 60 TYR cc_start: 0.8510 (m-10) cc_final: 0.8109 (m-10) outliers start: 12 outliers final: 12 residues processed: 88 average time/residue: 0.1619 time to fit residues: 17.3024 Evaluate side-chains 92 residues out of total 389 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.407 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 338 PHE Chi-restraints excluded: chain C residue 350 VAL Chi-restraints excluded: chain C residue 379 CYS Chi-restraints excluded: chain C residue 418 ILE Chi-restraints excluded: chain C residue 494 SER Chi-restraints excluded: chain H residue 22 THR Chi-restraints excluded: chain H residue 33 LEU Chi-restraints excluded: chain H residue 58 VAL Chi-restraints excluded: chain H residue 65 SER Chi-restraints excluded: chain H residue 89 GLN Chi-restraints excluded: chain H residue 94 THR Chi-restraints excluded: chain I residue 5 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 2.9990 chunk 4 optimal weight: 0.7980 chunk 6 optimal weight: 0.8980 chunk 29 optimal weight: 0.8980 chunk 1 optimal weight: 0.0970 chunk 24 optimal weight: 0.8980 chunk 39 optimal weight: 1.9990 chunk 22 optimal weight: 0.4980 chunk 27 optimal weight: 3.9990 chunk 26 optimal weight: 2.9990 chunk 16 optimal weight: 0.9980 overall best weight: 0.6378 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 439 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** H 89 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3949 r_free = 0.3949 target = 0.124694 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 33)----------------| | r_work = 0.3715 r_free = 0.3715 target = 0.108961 restraints weight = 9539.639| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 24)----------------| | r_work = 0.3774 r_free = 0.3774 target = 0.113698 restraints weight = 6841.949| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 28)----------------| | r_work = 0.3800 r_free = 0.3800 target = 0.115545 restraints weight = 3775.900| |-----------------------------------------------------------------------------| r_work (final): 0.3801 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7336 moved from start: 0.3791 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.045 3622 Z= 0.244 Angle : 0.714 9.701 4922 Z= 0.360 Chirality : 0.046 0.178 529 Planarity : 0.005 0.058 638 Dihedral : 4.864 20.291 499 Min Nonbonded Distance : 2.517 Molprobity Statistics. All-atom Clashscore : 11.69 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.07 % Favored : 93.93 % Rotamer: Outliers : 3.62 % Allowed : 23.00 % Favored : 73.39 % 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: -1.36 (0.36), residues: 445 helix: -2.61 (0.91), residues: 18 sheet: 0.34 (0.44), residues: 130 loop : -1.45 (0.32), residues: 297 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 436 HIS 0.004 0.001 HIS I 35 PHE 0.048 0.002 PHE I 68 TYR 0.018 0.001 TYR I 102 ARG 0.015 0.001 ARG H 24 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1613.64 seconds wall clock time: 29 minutes 12.64 seconds (1752.64 seconds total)