Starting phenix.real_space_refine on Thu Dec 7 18:15:26 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws2_32741/12_2023/7ws2_32741.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws2_32741/12_2023/7ws2_32741.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.3 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws2_32741/12_2023/7ws2_32741.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws2_32741/12_2023/7ws2_32741.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws2_32741/12_2023/7ws2_32741.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ws2_32741/12_2023/7ws2_32741.pdb" } resolution = 3.3 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.003 sd= 0.025 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 2120 2.51 5 N 558 2.21 5 O 650 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "E TYR 95": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 103": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3343 Number of models: 1 Model: "" Number of chains: 3 Chain: "D" 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: "A" Number of atoms: 1578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 200, 1578 Classifications: {'peptide': 200} Incomplete info: {'truncation_to_alanine': 1} Link IDs: {'PTRANS': 11, 'TRANS': 188} 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: "E" Number of atoms: 948 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 948 Classifications: {'peptide': 123} Incomplete info: {'truncation_to_alanine': 2} Link IDs: {'PTRANS': 3, 'TRANS': 119} Unresolved non-hydrogen bonds: 8 Unresolved non-hydrogen angles: 8 Unresolved non-hydrogen dihedrals: 8 Time building chain proxies: 2.30, per 1000 atoms: 0.69 Number of scatterers: 3343 At special positions: 0 Unit cell: (91.84, 55.76, 95.94, 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 650 8.00 N 558 7.00 C 2120 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=6, symmetry=0 Simple disulfide: pdb=" SG CYS D 23 " - pdb=" SG CYS D 88 " distance=2.04 Simple disulfide: pdb=" SG CYS A 336 " - pdb=" SG CYS A 361 " distance=2.02 Simple disulfide: pdb=" SG CYS A 379 " - pdb=" SG CYS A 432 " distance=2.03 Simple disulfide: pdb=" SG CYS A 391 " - pdb=" SG CYS A 525 " distance=2.03 Simple disulfide: pdb=" SG CYS A 480 " - pdb=" SG CYS A 488 " distance=2.03 Simple disulfide: pdb=" SG CYS E 22 " - pdb=" SG CYS E 96 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.20 Conformation dependent library (CDL) restraints added in 604.5 milliseconds 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 790 Finding SS restraints... Secondary structure from input PDB file: 9 helices and 10 sheets defined 12.3% alpha, 30.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.43 Creating SS restraints... Processing helix chain 'A' and resid 338 through 343 Processing helix chain 'A' and resid 365 through 371 Processing helix chain 'A' and resid 383 through 389 removed outlier: 3.596A pdb=" N LEU A 387 " --> pdb=" O PRO A 384 " (cutoff:3.500A) removed outlier: 4.091A pdb=" N ASN A 388 " --> pdb=" O THR A 385 " (cutoff:3.500A) removed outlier: 3.558A pdb=" N ASP A 389 " --> pdb=" O LYS A 386 " (cutoff:3.500A) Processing helix chain 'A' and resid 404 through 410 removed outlier: 3.534A pdb=" N VAL A 407 " --> pdb=" O GLY A 404 " (cutoff:3.500A) removed outlier: 3.825A pdb=" N ARG A 408 " --> pdb=" O ASP A 405 " (cutoff:3.500A) Processing helix chain 'A' and resid 416 through 422 Processing helix chain 'A' and resid 502 through 506 Processing helix chain 'E' and resid 28 through 32 removed outlier: 3.987A pdb=" N ASP E 31 " --> pdb=" O THR E 28 " (cutoff:3.500A) removed outlier: 4.051A pdb=" N TYR E 32 " --> pdb=" O PHE E 29 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 28 through 32' Processing helix chain 'E' and resid 62 through 65 removed outlier: 3.547A pdb=" N LYS E 65 " --> pdb=" O ASP E 62 " (cutoff:3.500A) No H-bonds generated for 'chain 'E' and resid 62 through 65' Processing helix chain 'E' and resid 87 through 91 removed outlier: 3.819A pdb=" N THR E 91 " --> pdb=" O ALA E 88 " (cutoff:3.500A) Processing sheet with id=AA1, first strand: chain 'D' and resid 4 through 6 removed outlier: 3.741A pdb=" N ASP D 70 " --> pdb=" O SER D 67 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'D' and resid 10 through 11 Processing sheet with id=AA3, first strand: chain 'D' and resid 53 through 54 removed outlier: 6.922A pdb=" N TRP D 35 " --> pdb=" O LEU D 47 " (cutoff:3.500A) removed outlier: 5.177A pdb=" N TYR D 49 " --> pdb=" O LEU D 33 " (cutoff:3.500A) removed outlier: 6.867A pdb=" N LEU D 33 " --> pdb=" O TYR D 49 " (cutoff:3.500A) removed outlier: 3.582A pdb=" N THR D 98 " --> pdb=" O GLN D 90 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'A' and resid 356 through 358 removed outlier: 4.111A pdb=" N ASN A 394 " --> pdb=" O GLU A 516 " (cutoff:3.500A) removed outlier: 3.759A pdb=" N GLU A 516 " --> pdb=" O ASN A 394 " (cutoff:3.500A) removed outlier: 3.778A pdb=" N GLY A 431 " --> pdb=" O TYR A 380 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 361 through 362 removed outlier: 5.893A pdb=" N CYS A 361 " --> pdb=" O CYS A 525 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA5 Processing sheet with id=AA6, first strand: chain 'A' and resid 452 through 454 Processing sheet with id=AA7, first strand: chain 'E' and resid 4 through 7 removed outlier: 3.744A pdb=" N SER E 21 " --> pdb=" O SER E 7 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'E' and resid 11 through 12 Processing sheet with id=AA9, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.963A pdb=" N TYR E 112 " --> pdb=" O LYS E 98 " (cutoff:3.500A) Processing sheet with id=AB1, first strand: chain 'E' and resid 58 through 60 removed outlier: 6.676A pdb=" N TRP E 36 " --> pdb=" O VAL E 48 " (cutoff:3.500A) removed outlier: 4.501A pdb=" N GLY E 50 " --> pdb=" O MET E 34 " (cutoff:3.500A) removed outlier: 6.804A pdb=" N MET E 34 " --> pdb=" O GLY E 50 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N TYR E 94 " --> pdb=" O THR E 117 " (cutoff:3.500A) 105 hydrogen bonds defined for protein. 258 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: 0.87 Time building geometry restraints manager: 1.34 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: 1071 1.34 - 1.46: 843 1.46 - 1.58: 1496 1.58 - 1.69: 0 1.69 - 1.81: 18 Bond restraints: 3428 Sorted by residual: bond pdb=" N ASP E 31 " pdb=" CA ASP E 31 " ideal model delta sigma weight residual 1.458 1.492 -0.034 1.25e-02 6.40e+03 7.53e+00 bond pdb=" N GLN D 6 " pdb=" CA GLN D 6 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.19e-02 7.06e+03 7.17e+00 bond pdb=" N ASN A 450 " pdb=" CA ASN A 450 " ideal model delta sigma weight residual 1.456 1.491 -0.035 1.32e-02 5.74e+03 7.02e+00 bond pdb=" N THR A 500 " pdb=" CA THR A 500 " ideal model delta sigma weight residual 1.456 1.490 -0.035 1.32e-02 5.74e+03 6.85e+00 bond pdb=" N THR A 345 " pdb=" CA THR A 345 " ideal model delta sigma weight residual 1.458 1.490 -0.032 1.26e-02 6.30e+03 6.34e+00 ... (remaining 3423 not shown) Histogram of bond angle deviations from ideal: 99.77 - 106.61: 92 106.61 - 113.46: 1764 113.46 - 120.31: 1208 120.31 - 127.16: 1564 127.16 - 134.01: 32 Bond angle restraints: 4660 Sorted by residual: angle pdb=" CA LEU E 105 " pdb=" C LEU E 105 " pdb=" O LEU E 105 " ideal model delta sigma weight residual 122.13 118.28 3.85 1.13e+00 7.83e-01 1.16e+01 angle pdb=" CA ASN A 501 " pdb=" C ASN A 501 " pdb=" O ASN A 501 " ideal model delta sigma weight residual 121.87 118.39 3.48 1.16e+00 7.43e-01 9.02e+00 angle pdb=" N LYS D 39 " pdb=" CA LYS D 39 " pdb=" C LYS D 39 " ideal model delta sigma weight residual 109.50 105.76 3.74 1.47e+00 4.63e-01 6.47e+00 angle pdb=" N TYR E 102 " pdb=" CA TYR E 102 " pdb=" C TYR E 102 " ideal model delta sigma weight residual 113.61 109.90 3.71 1.50e+00 4.44e-01 6.12e+00 angle pdb=" CA GLU E 103 " pdb=" C GLU E 103 " pdb=" O GLU E 103 " ideal model delta sigma weight residual 121.78 118.63 3.15 1.28e+00 6.10e-01 6.04e+00 ... (remaining 4655 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.53: 1795 15.53 - 31.07: 170 31.07 - 46.60: 45 46.60 - 62.13: 7 62.13 - 77.67: 4 Dihedral angle restraints: 2021 sinusoidal: 775 harmonic: 1246 Sorted by residual: dihedral pdb=" CA CYS A 361 " pdb=" C CYS A 361 " pdb=" N VAL A 362 " pdb=" CA VAL A 362 " ideal model delta harmonic sigma weight residual 180.00 154.25 25.75 0 5.00e+00 4.00e-02 2.65e+01 dihedral pdb=" CB CYS A 480 " pdb=" SG CYS A 480 " pdb=" SG CYS A 488 " pdb=" CB CYS A 488 " ideal model delta sinusoidal sigma weight residual -86.00 -121.73 35.73 1 1.00e+01 1.00e-02 1.81e+01 dihedral pdb=" CB CYS A 391 " pdb=" SG CYS A 391 " pdb=" SG CYS A 525 " pdb=" CB CYS A 525 " ideal model delta sinusoidal sigma weight residual 93.00 122.28 -29.28 1 1.00e+01 1.00e-02 1.23e+01 ... (remaining 2018 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.031: 297 0.031 - 0.062: 135 0.062 - 0.092: 33 0.092 - 0.123: 25 0.123 - 0.154: 9 Chirality restraints: 499 Sorted by residual: chirality pdb=" CA LYS D 39 " pdb=" N LYS D 39 " pdb=" C LYS D 39 " pdb=" CB LYS D 39 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.90e-01 chirality pdb=" CA THR D 94 " pdb=" N THR D 94 " pdb=" C THR D 94 " pdb=" CB THR D 94 " both_signs ideal model delta sigma weight residual False 2.53 2.37 0.15 2.00e-01 2.50e+01 5.87e-01 chirality pdb=" CA LYS A 444 " pdb=" N LYS A 444 " pdb=" C LYS A 444 " pdb=" CB LYS A 444 " both_signs ideal model delta sigma weight residual False 2.51 2.66 -0.15 2.00e-01 2.50e+01 5.64e-01 ... (remaining 496 not shown) Planarity restraints: 606 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C THR A 478 " 0.034 5.00e-02 4.00e+02 5.24e-02 4.39e+00 pdb=" N PRO A 479 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 479 " 0.028 5.00e-02 4.00e+02 pdb=" CD PRO A 479 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY A 526 " -0.034 5.00e-02 4.00e+02 5.09e-02 4.14e+00 pdb=" N PRO A 527 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 527 " -0.027 5.00e-02 4.00e+02 pdb=" CD PRO A 527 " -0.028 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 383 " 0.033 5.00e-02 4.00e+02 5.04e-02 4.06e+00 pdb=" N PRO A 384 " -0.087 5.00e-02 4.00e+02 pdb=" CA PRO A 384 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 384 " 0.028 5.00e-02 4.00e+02 ... (remaining 603 not shown) Histogram of nonbonded interaction distances: 2.26 - 2.79: 747 2.79 - 3.32: 2829 3.32 - 3.84: 5241 3.84 - 4.37: 6298 4.37 - 4.90: 11020 Nonbonded interactions: 26135 Sorted by model distance: nonbonded pdb=" NH1 ARG D 61 " pdb=" OD2 ASP D 82 " model vdw 2.258 2.520 nonbonded pdb=" OH TYR D 97 " pdb=" O ILE E 104 " model vdw 2.260 2.440 nonbonded pdb=" OD1 ASN A 439 " pdb=" OG SER A 443 " model vdw 2.269 2.440 nonbonded pdb=" O THR A 393 " pdb=" OG1 THR A 523 " model vdw 2.292 2.440 nonbonded pdb=" O SER A 530 " pdb=" OG SER A 530 " model vdw 2.302 2.440 ... (remaining 26130 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 5.410 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: 26.880 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 13.800 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.740 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 49.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7518 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 : 0.003 0.035 3428 Z= 0.229 Angle : 0.636 5.672 4660 Z= 0.375 Chirality : 0.045 0.154 499 Planarity : 0.005 0.052 606 Dihedral : 13.310 77.666 1213 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 7.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.53 % Favored : 96.47 % 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: -1.86 (0.40), residues: 425 helix: -4.57 (0.37), residues: 33 sheet: -0.50 (0.44), residues: 158 loop : -1.21 (0.39), residues: 234 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.003 0.001 TRP E 53 HIS 0.001 0.000 HIS E 35 PHE 0.009 0.001 PHE D 83 TYR 0.007 0.001 TYR A 495 ARG 0.004 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 90 time to evaluate : 0.440 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 90 average time/residue: 0.1867 time to fit residues: 19.8893 Evaluate side-chains 82 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5137 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.0980 chunk 31 optimal weight: 0.6980 chunk 17 optimal weight: 0.9980 chunk 10 optimal weight: 0.7980 chunk 21 optimal weight: 0.9990 chunk 32 optimal weight: 0.0030 chunk 12 optimal weight: 0.8980 chunk 20 optimal weight: 0.6980 chunk 24 optimal weight: 0.9980 chunk 38 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 overall best weight: 0.4390 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 487 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 501 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7632 moved from start: 0.1733 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3428 Z= 0.216 Angle : 0.582 5.800 4660 Z= 0.306 Chirality : 0.045 0.156 499 Planarity : 0.005 0.051 606 Dihedral : 4.650 25.734 475 Min Nonbonded Distance : 2.170 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 1.65 % Allowed : 9.89 % Favored : 88.46 % 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: -1.77 (0.39), residues: 425 helix: -3.48 (0.69), residues: 27 sheet: -0.55 (0.44), residues: 144 loop : -1.29 (0.37), residues: 254 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP E 47 HIS 0.002 0.001 HIS E 35 PHE 0.010 0.001 PHE A 490 TYR 0.016 0.002 TYR E 80 ARG 0.005 0.001 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 94 time to evaluate : 0.375 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 95 average time/residue: 0.1715 time to fit residues: 19.6349 Evaluate side-chains 92 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 88 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 0 residues processed: 4 average time/residue: 0.0361 time to fit residues: 0.7835 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 0.7980 chunk 25 optimal weight: 0.0470 chunk 10 optimal weight: 0.4980 chunk 38 optimal weight: 0.6980 chunk 41 optimal weight: 0.2980 chunk 34 optimal weight: 0.6980 chunk 37 optimal weight: 1.9990 chunk 13 optimal weight: 0.0670 chunk 30 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.3016 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.1923 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3428 Z= 0.173 Angle : 0.538 4.977 4660 Z= 0.279 Chirality : 0.044 0.150 499 Planarity : 0.004 0.044 606 Dihedral : 4.462 24.845 475 Min Nonbonded Distance : 2.182 Molprobity Statistics. All-atom Clashscore : 7.67 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 1.37 % Allowed : 11.54 % Favored : 87.09 % 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: -1.75 (0.39), residues: 425 helix: -3.47 (0.73), residues: 27 sheet: -0.62 (0.42), residues: 153 loop : -1.22 (0.38), residues: 245 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS E 35 PHE 0.007 0.001 PHE D 83 TYR 0.014 0.001 TYR E 80 ARG 0.002 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 87 time to evaluate : 0.380 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 88 average time/residue: 0.1643 time to fit residues: 17.5712 Evaluate side-chains 86 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 84 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0362 time to fit residues: 0.6450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 0.7980 chunk 18 optimal weight: 0.0000 chunk 25 optimal weight: 0.4980 chunk 38 optimal weight: 1.9990 chunk 40 optimal weight: 0.0770 chunk 20 optimal weight: 0.5980 chunk 36 optimal weight: 0.8980 chunk 10 optimal weight: 0.5980 chunk 33 optimal weight: 2.9990 chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 overall best weight: 0.3542 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7631 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3428 Z= 0.187 Angle : 0.556 9.050 4660 Z= 0.282 Chirality : 0.043 0.145 499 Planarity : 0.004 0.041 606 Dihedral : 4.478 24.163 475 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 8.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 2.47 % Allowed : 13.74 % Favored : 83.79 % 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: -1.70 (0.40), residues: 425 helix: -3.44 (0.75), residues: 27 sheet: -0.53 (0.42), residues: 152 loop : -1.23 (0.39), residues: 246 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS E 35 PHE 0.009 0.001 PHE A 490 TYR 0.021 0.001 TYR E 80 ARG 0.002 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 94 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 85 time to evaluate : 0.378 Fit side-chains outliers start: 9 outliers final: 6 residues processed: 88 average time/residue: 0.1751 time to fit residues: 18.4186 Evaluate side-chains 84 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 78 time to evaluate : 0.375 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0345 time to fit residues: 0.8851 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 28 optimal weight: 0.5980 chunk 0 optimal weight: 1.9990 chunk 20 optimal weight: 0.9980 chunk 36 optimal weight: 0.2980 chunk 10 optimal weight: 0.9980 chunk 13 optimal weight: 0.0980 chunk 8 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.2325 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.031 3428 Z= 0.277 Angle : 0.600 7.224 4660 Z= 0.310 Chirality : 0.045 0.146 499 Planarity : 0.004 0.044 606 Dihedral : 4.783 24.591 475 Min Nonbonded Distance : 2.120 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.65 % Allowed : 15.38 % Favored : 82.97 % 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: -1.81 (0.39), residues: 425 helix: -3.31 (0.77), residues: 27 sheet: -0.60 (0.41), residues: 151 loop : -1.33 (0.38), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.003 0.001 HIS E 35 PHE 0.013 0.001 PHE A 490 TYR 0.022 0.002 TYR E 80 ARG 0.002 0.000 ARG D 24 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 82 time to evaluate : 0.382 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 85 average time/residue: 0.1853 time to fit residues: 18.6729 Evaluate side-chains 84 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 81 time to evaluate : 0.379 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0365 time to fit residues: 0.6736 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 0.7980 chunk 40 optimal weight: 0.7980 chunk 33 optimal weight: 0.7980 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 1.9990 chunk 13 optimal weight: 0.8980 chunk 21 optimal weight: 0.4980 chunk 39 optimal weight: 0.9990 chunk 4 optimal weight: 0.5980 chunk 23 optimal weight: 1.9990 chunk 29 optimal weight: 1.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7723 moved from start: 0.2517 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 3428 Z= 0.315 Angle : 0.635 7.879 4660 Z= 0.328 Chirality : 0.047 0.165 499 Planarity : 0.005 0.047 606 Dihedral : 5.154 28.884 475 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 8.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.12 % Favored : 93.88 % Rotamer: Outliers : 1.65 % Allowed : 18.13 % Favored : 80.22 % 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: -1.94 (0.38), residues: 425 helix: -3.25 (0.77), residues: 27 sheet: -0.63 (0.41), residues: 151 loop : -1.48 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP E 47 HIS 0.003 0.002 HIS E 35 PHE 0.015 0.002 PHE A 490 TYR 0.020 0.002 TYR E 80 ARG 0.002 0.001 ARG A 346 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 79 time to evaluate : 0.388 Fit side-chains outliers start: 6 outliers final: 5 residues processed: 81 average time/residue: 0.2056 time to fit residues: 19.5681 Evaluate side-chains 83 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 78 time to evaluate : 0.394 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 0 residues processed: 5 average time/residue: 0.0407 time to fit residues: 0.8752 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 40 optimal weight: 0.0670 chunk 25 optimal weight: 0.0570 chunk 24 optimal weight: 0.6980 chunk 18 optimal weight: 0.0060 chunk 16 optimal weight: 0.9990 chunk 12 optimal weight: 0.9980 chunk 7 optimal weight: 1.9990 chunk 27 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 overall best weight: 0.3252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7651 moved from start: 0.2490 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3428 Z= 0.187 Angle : 0.568 8.221 4660 Z= 0.286 Chirality : 0.044 0.172 499 Planarity : 0.004 0.047 606 Dihedral : 4.723 26.061 475 Min Nonbonded Distance : 2.156 Molprobity Statistics. All-atom Clashscore : 7.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.47 % Favored : 95.53 % Rotamer: Outliers : 0.82 % Allowed : 19.78 % Favored : 79.40 % 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: -1.84 (0.38), residues: 425 helix: -3.24 (0.78), residues: 27 sheet: -0.57 (0.41), residues: 151 loop : -1.40 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS E 35 PHE 0.009 0.001 PHE D 83 TYR 0.020 0.001 TYR E 80 ARG 0.004 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 79 time to evaluate : 0.360 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 81 average time/residue: 0.1773 time to fit residues: 17.1863 Evaluate side-chains 77 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0372 time to fit residues: 0.5833 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.0020 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 0.5980 chunk 35 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 11 optimal weight: 0.9990 chunk 34 optimal weight: 0.5980 overall best weight: 0.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7703 moved from start: 0.2663 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 3428 Z= 0.273 Angle : 0.613 7.810 4660 Z= 0.314 Chirality : 0.046 0.163 499 Planarity : 0.005 0.047 606 Dihedral : 5.000 26.429 475 Min Nonbonded Distance : 2.109 Molprobity Statistics. All-atom Clashscore : 8.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 1.37 % Allowed : 19.78 % Favored : 78.85 % 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: -1.84 (0.38), residues: 425 helix: -3.22 (0.78), residues: 27 sheet: -0.56 (0.42), residues: 151 loop : -1.41 (0.37), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.003 0.001 HIS E 35 PHE 0.015 0.001 PHE A 490 TYR 0.018 0.002 TYR D 92 ARG 0.004 0.001 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 76 time to evaluate : 0.355 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 80 average time/residue: 0.1939 time to fit residues: 18.4530 Evaluate side-chains 81 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0543 time to fit residues: 0.7689 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.1980 chunk 37 optimal weight: 1.9990 chunk 24 optimal weight: 0.3980 chunk 39 optimal weight: 1.9990 chunk 18 optimal weight: 0.5980 chunk 27 optimal weight: 0.9990 chunk 41 optimal weight: 0.5980 chunk 38 optimal weight: 0.8980 chunk 33 optimal weight: 0.5980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 0.0170 overall best weight: 0.3618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 394 ASN ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7661 moved from start: 0.2645 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.028 3428 Z= 0.199 Angle : 0.578 7.684 4660 Z= 0.289 Chirality : 0.044 0.170 499 Planarity : 0.004 0.046 606 Dihedral : 4.738 24.183 475 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 7.82 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.27 % Allowed : 20.60 % Favored : 79.12 % 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: -1.83 (0.38), residues: 425 helix: -3.21 (0.80), residues: 27 sheet: -0.50 (0.42), residues: 151 loop : -1.45 (0.36), residues: 247 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.001 0.001 HIS E 35 PHE 0.008 0.001 PHE D 83 TYR 0.017 0.001 TYR E 80 ARG 0.006 0.000 ARG E 19 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 77 time to evaluate : 0.379 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 78 average time/residue: 0.1824 time to fit residues: 17.0943 Evaluate side-chains 75 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.384 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5253 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 0.8980 chunk 26 optimal weight: 0.0370 chunk 35 optimal weight: 0.7980 chunk 10 optimal weight: 1.9990 chunk 30 optimal weight: 2.9990 chunk 4 optimal weight: 0.9980 chunk 9 optimal weight: 0.0670 chunk 33 optimal weight: 1.9990 chunk 13 optimal weight: 0.0000 chunk 34 optimal weight: 0.7980 chunk 6 optimal weight: 0.9990 overall best weight: 0.3400 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7654 moved from start: 0.2709 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3428 Z= 0.193 Angle : 0.578 7.650 4660 Z= 0.289 Chirality : 0.044 0.166 499 Planarity : 0.004 0.044 606 Dihedral : 4.670 23.340 475 Min Nonbonded Distance : 2.153 Molprobity Statistics. All-atom Clashscore : 7.98 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.35 % Favored : 93.65 % Rotamer: Outliers : 0.27 % Allowed : 21.15 % Favored : 78.57 % 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: -1.74 (0.39), residues: 425 helix: -3.19 (0.81), residues: 27 sheet: -0.48 (0.40), residues: 160 loop : -1.37 (0.38), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 436 HIS 0.002 0.001 HIS E 35 PHE 0.009 0.001 PHE A 490 TYR 0.017 0.001 TYR D 92 ARG 0.006 0.000 ARG E 19 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 850 Ramachandran restraints generated. 425 Oldfield, 0 Emsley, 425 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.399 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1886 time to fit residues: 16.6071 Evaluate side-chains 75 residues out of total 368 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 74 time to evaluate : 0.369 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0377 time to fit residues: 0.5951 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 0.9990 chunk 1 optimal weight: 1.9990 chunk 24 optimal weight: 0.0000 chunk 38 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 28 optimal weight: 0.8980 chunk 26 optimal weight: 0.1980 chunk 25 optimal weight: 0.4980 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 1.9990 chunk 41 optimal weight: 0.8980 overall best weight: 0.4584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 474 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3686 r_free = 0.3686 target = 0.134990 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3532 r_free = 0.3532 target = 0.123640 restraints weight = 5318.168| |-----------------------------------------------------------------------------| r_work (start): 0.3529 rms_B_bonded: 1.96 r_work: 0.3456 rms_B_bonded: 2.16 restraints_weight: 0.5000 r_work: 0.3341 rms_B_bonded: 3.89 restraints_weight: 0.2500 r_work (final): 0.3341 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2774 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.030 3428 Z= 0.231 Angle : 0.595 7.474 4660 Z= 0.301 Chirality : 0.045 0.166 499 Planarity : 0.004 0.044 606 Dihedral : 4.793 23.356 475 Min Nonbonded Distance : 2.132 Molprobity Statistics. All-atom Clashscore : 8.44 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.55 % Allowed : 20.60 % Favored : 78.85 % 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: -1.79 (0.38), residues: 425 helix: -3.16 (0.82), residues: 27 sheet: -0.47 (0.40), residues: 160 loop : -1.45 (0.37), residues: 238 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 436 HIS 0.002 0.001 HIS E 35 PHE 0.011 0.001 PHE A 490 TYR 0.018 0.001 TYR E 80 ARG 0.003 0.000 ARG E 19 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1630.54 seconds wall clock time: 29 minutes 49.05 seconds (1789.05 seconds total)