Starting phenix.real_space_refine on Thu Dec 7 18:04:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/12_2023/8p6a_17462.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/12_2023/8p6a_17462.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.63 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/12_2023/8p6a_17462.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/12_2023/8p6a_17462.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/12_2023/8p6a_17462.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8p6a_17462/12_2023/8p6a_17462.pdb" } resolution = 3.63 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 sd= 0.048 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 16 5.16 5 C 2225 2.51 5 N 531 2.21 5 O 565 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 44": "OE1" <-> "OE2" Residue "A PHE 91": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 97": "OD1" <-> "OD2" Residue "A ASP 185": "OD1" <-> "OD2" Residue "A TYR 226": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 314": "OD1" <-> "OD2" 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: 3337 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3337 Number of conformers: 1 Conformer: "" Number of residues, atoms: 432, 3337 Classifications: {'peptide': 432} Link IDs: {'PTRANS': 15, 'TRANS': 416} Chain breaks: 3 Time building chain proxies: 2.25, per 1000 atoms: 0.67 Number of scatterers: 3337 At special positions: 0 Unit cell: (72.384, 67.392, 65.728, 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 16 16.00 O 565 8.00 N 531 7.00 C 2225 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.28 Conformation dependent library (CDL) restraints added in 625.7 milliseconds 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 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: 17 helices and 1 sheets defined 80.6% alpha, 0.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.30 Creating SS restraints... Processing helix chain 'A' and resid 35 through 62 removed outlier: 5.178A pdb=" N VAL A 59 " --> pdb=" O THR A 55 " (cutoff:3.500A) removed outlier: 5.075A pdb=" N LEU A 60 " --> pdb=" O SER A 56 " (cutoff:3.500A) Processing helix chain 'A' and resid 70 through 96 removed outlier: 3.984A pdb=" N SER A 89 " --> pdb=" O THR A 85 " (cutoff:3.500A) Proline residue: A 90 - end of helix Processing helix chain 'A' and resid 103 through 118 Processing helix chain 'A' and resid 157 through 182 removed outlier: 4.188A pdb=" N THR A 176 " --> pdb=" O LYS A 172 " (cutoff:3.500A) Proline residue: A 177 - end of helix Processing helix chain 'A' and resid 183 through 186 Processing helix chain 'A' and resid 187 through 220 Processing helix chain 'A' and resid 221 through 225 removed outlier: 3.685A pdb=" N THR A 224 " --> pdb=" O SER A 221 " (cutoff:3.500A) Processing helix chain 'A' and resid 226 through 244 Processing helix chain 'A' and resid 311 through 346 removed outlier: 3.690A pdb=" N VAL A 322 " --> pdb=" O LEU A 318 " (cutoff:3.500A) Proline residue: A 323 - end of helix Proline residue: A 330 - end of helix Processing helix chain 'A' and resid 347 through 349 No H-bonds generated for 'chain 'A' and resid 347 through 349' Processing helix chain 'A' and resid 367 through 370 removed outlier: 3.915A pdb=" N THR A 370 " --> pdb=" O ALA A 367 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 367 through 370' Processing helix chain 'A' and resid 371 through 396 Proline residue: A 382 - end of helix Proline residue: A 390 - end of helix Processing helix chain 'A' and resid 400 through 433 removed outlier: 3.632A pdb=" N ARG A 404 " --> pdb=" O SER A 400 " (cutoff:3.500A) removed outlier: 3.849A pdb=" N GLU A 432 " --> pdb=" O ASN A 428 " (cutoff:3.500A) Processing helix chain 'A' and resid 450 through 453 Processing helix chain 'A' and resid 454 through 479 removed outlier: 4.047A pdb=" N ILE A 470 " --> pdb=" O ILE A 466 " (cutoff:3.500A) removed outlier: 4.355A pdb=" N ALA A 471 " --> pdb=" O PHE A 467 " (cutoff:3.500A) Processing helix chain 'A' and resid 484 through 511 Processing helix chain 'A' and resid 532 through 559 Processing sheet with id=AA1, first strand: chain 'A' and resid 435 through 436 258 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.92 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1002 1.34 - 1.46: 751 1.46 - 1.58: 1641 1.58 - 1.69: 0 1.69 - 1.81: 26 Bond restraints: 3420 Sorted by residual: bond pdb=" CA VAL A 322 " pdb=" C VAL A 322 " ideal model delta sigma weight residual 1.520 1.532 -0.013 8.80e-03 1.29e+04 2.04e+00 bond pdb=" CB ASP A 185 " pdb=" CG ASP A 185 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.21e+00 bond pdb=" CB ASP A 97 " pdb=" CG ASP A 97 " ideal model delta sigma weight residual 1.516 1.543 -0.027 2.50e-02 1.60e+03 1.20e+00 bond pdb=" C ALA A 65 " pdb=" N PRO A 66 " ideal model delta sigma weight residual 1.340 1.367 -0.027 2.76e-02 1.31e+03 9.38e-01 bond pdb=" CG LEU A 46 " pdb=" CD2 LEU A 46 " ideal model delta sigma weight residual 1.521 1.489 0.032 3.30e-02 9.18e+02 9.25e-01 ... (remaining 3415 not shown) Histogram of bond angle deviations from ideal: 96.77 - 104.21: 40 104.21 - 111.65: 1617 111.65 - 119.10: 1122 119.10 - 126.54: 1814 126.54 - 133.98: 55 Bond angle restraints: 4648 Sorted by residual: angle pdb=" CB MET A 117 " pdb=" CG MET A 117 " pdb=" SD MET A 117 " ideal model delta sigma weight residual 112.70 124.25 -11.55 3.00e+00 1.11e-01 1.48e+01 angle pdb=" CA LEU A 344 " pdb=" CB LEU A 344 " pdb=" CG LEU A 344 " ideal model delta sigma weight residual 116.30 125.21 -8.91 3.50e+00 8.16e-02 6.48e+00 angle pdb=" CA LEU A 79 " pdb=" CB LEU A 79 " pdb=" CG LEU A 79 " ideal model delta sigma weight residual 116.30 124.51 -8.21 3.50e+00 8.16e-02 5.50e+00 angle pdb=" CA LEU A 507 " pdb=" CB LEU A 507 " pdb=" CG LEU A 507 " ideal model delta sigma weight residual 116.30 123.81 -7.51 3.50e+00 8.16e-02 4.61e+00 angle pdb=" CA LEU A 42 " pdb=" CB LEU A 42 " pdb=" CG LEU A 42 " ideal model delta sigma weight residual 116.30 123.70 -7.40 3.50e+00 8.16e-02 4.47e+00 ... (remaining 4643 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.10: 1602 15.10 - 30.19: 252 30.19 - 45.29: 75 45.29 - 60.38: 30 60.38 - 75.48: 4 Dihedral angle restraints: 1963 sinusoidal: 729 harmonic: 1234 Sorted by residual: dihedral pdb=" CG ARG A 193 " pdb=" CD ARG A 193 " pdb=" NE ARG A 193 " pdb=" CZ ARG A 193 " ideal model delta sinusoidal sigma weight residual 180.00 135.59 44.41 2 1.50e+01 4.44e-03 1.04e+01 dihedral pdb=" CG ARG A 404 " pdb=" CD ARG A 404 " pdb=" NE ARG A 404 " pdb=" CZ ARG A 404 " ideal model delta sinusoidal sigma weight residual -180.00 -137.22 -42.78 2 1.50e+01 4.44e-03 9.84e+00 dihedral pdb=" CB ARG A 404 " pdb=" CG ARG A 404 " pdb=" CD ARG A 404 " pdb=" NE ARG A 404 " ideal model delta sinusoidal sigma weight residual 180.00 122.86 57.14 3 1.50e+01 4.44e-03 9.43e+00 ... (remaining 1960 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.043: 401 0.043 - 0.086: 118 0.086 - 0.129: 20 0.129 - 0.173: 4 0.173 - 0.216: 1 Chirality restraints: 544 Sorted by residual: chirality pdb=" CB ILE A 329 " pdb=" CA ILE A 329 " pdb=" CG1 ILE A 329 " pdb=" CG2 ILE A 329 " both_signs ideal model delta sigma weight residual False 2.64 2.43 0.22 2.00e-01 2.50e+01 1.16e+00 chirality pdb=" CB VAL A 246 " pdb=" CA VAL A 246 " pdb=" CG1 VAL A 246 " pdb=" CG2 VAL A 246 " both_signs ideal model delta sigma weight residual False -2.63 -2.49 -0.14 2.00e-01 2.50e+01 5.10e-01 chirality pdb=" CA VAL A 455 " pdb=" N VAL A 455 " pdb=" C VAL A 455 " pdb=" CB VAL A 455 " both_signs ideal model delta sigma weight residual False 2.44 2.30 0.14 2.00e-01 2.50e+01 4.89e-01 ... (remaining 541 not shown) Planarity restraints: 567 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CG GLN A 457 " -0.007 2.00e-02 2.50e+03 1.47e-02 2.15e+00 pdb=" CD GLN A 457 " 0.025 2.00e-02 2.50e+03 pdb=" OE1 GLN A 457 " -0.010 2.00e-02 2.50e+03 pdb=" NE2 GLN A 457 " -0.008 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL A 455 " -0.023 5.00e-02 4.00e+02 3.37e-02 1.81e+00 pdb=" N PRO A 456 " 0.058 5.00e-02 4.00e+02 pdb=" CA PRO A 456 " -0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 456 " -0.019 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA ASP A 385 " -0.005 2.00e-02 2.50e+03 1.10e-02 1.20e+00 pdb=" C ASP A 385 " 0.019 2.00e-02 2.50e+03 pdb=" O ASP A 385 " -0.007 2.00e-02 2.50e+03 pdb=" N LYS A 386 " -0.006 2.00e-02 2.50e+03 ... (remaining 564 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 82 2.71 - 3.26: 3478 3.26 - 3.80: 5677 3.80 - 4.35: 6172 4.35 - 4.90: 10711 Nonbonded interactions: 26120 Sorted by model distance: nonbonded pdb=" OG SER A 415 " pdb=" OE1 GLN A 457 " model vdw 2.161 2.440 nonbonded pdb=" O SER A 415 " pdb=" NE2 GLN A 457 " model vdw 2.239 2.520 nonbonded pdb=" OH TYR A 342 " pdb=" OE1 GLN A 457 " model vdw 2.302 2.440 nonbonded pdb=" O ARG A 394 " pdb=" NH1 ARG A 394 " model vdw 2.372 2.520 nonbonded pdb=" OG SER A 109 " pdb=" O GLY A 167 " model vdw 2.394 2.440 ... (remaining 26115 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 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: 1.000 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: 5.000 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.930 Find NCS groups from input model: 0.090 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 22.880 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8001 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 0.032 3420 Z= 0.201 Angle : 0.656 11.546 4648 Z= 0.313 Chirality : 0.041 0.216 544 Planarity : 0.003 0.034 567 Dihedral : 17.396 75.475 1173 Min Nonbonded Distance : 2.161 Molprobity Statistics. All-atom Clashscore : 10.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 0.29 % Allowed : 39.48 % Favored : 60.23 % 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: 2.80 (0.43), residues: 424 helix: 2.59 (0.29), residues: 325 sheet: -1.95 (1.74), residues: 10 loop : -0.54 (0.73), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.013 0.001 PHE A 247 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 350 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.345 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 74 average time/residue: 0.1454 time to fit residues: 13.4464 Evaluate side-chains 73 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.382 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0368 time to fit residues: 0.5766 ------------------------------------------------------------------------------- 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: 1.9990 chunk 32 optimal weight: 0.5980 chunk 18 optimal weight: 5.9990 chunk 11 optimal weight: 0.6980 chunk 21 optimal weight: 0.3980 chunk 17 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 20 optimal weight: 3.9990 chunk 25 optimal weight: 0.4980 chunk 39 optimal weight: 9.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8018 moved from start: 0.0551 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3420 Z= 0.190 Angle : 0.560 7.046 4648 Z= 0.276 Chirality : 0.039 0.215 544 Planarity : 0.003 0.030 567 Dihedral : 3.628 12.258 457 Min Nonbonded Distance : 2.181 Molprobity Statistics. All-atom Clashscore : 8.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 3.75 % Allowed : 35.45 % Favored : 60.81 % 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: 2.90 (0.43), residues: 424 helix: 2.73 (0.29), residues: 325 sheet: -2.28 (1.59), residues: 10 loop : -0.75 (0.70), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.011 0.001 PHE A 247 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 186 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 74 time to evaluate : 0.381 Fit side-chains outliers start: 13 outliers final: 8 residues processed: 82 average time/residue: 0.1274 time to fit residues: 13.2883 Evaluate side-chains 79 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 71 time to evaluate : 0.373 Switching outliers to nearest non-outliers outliers start: 8 outliers final: 0 residues processed: 8 average time/residue: 0.0350 time to fit residues: 0.9964 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 21 optimal weight: 0.3980 chunk 12 optimal weight: 0.8980 chunk 32 optimal weight: 0.0970 chunk 26 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 39 optimal weight: 5.9990 chunk 42 optimal weight: 0.6980 chunk 34 optimal weight: 0.5980 chunk 38 optimal weight: 4.9990 chunk 13 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 overall best weight: 0.4778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8003 moved from start: 0.0596 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3420 Z= 0.171 Angle : 0.545 7.141 4648 Z= 0.265 Chirality : 0.039 0.227 544 Planarity : 0.003 0.029 567 Dihedral : 3.575 11.887 457 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 8.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % Rotamer: Outliers : 1.15 % Allowed : 36.60 % Favored : 62.25 % 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: 2.99 (0.43), residues: 424 helix: 2.79 (0.29), residues: 325 sheet: -2.30 (1.58), residues: 10 loop : -0.74 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 194 TYR 0.013 0.001 TYR A 444 ARG 0.000 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 79 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 75 time to evaluate : 0.392 Fit side-chains outliers start: 4 outliers final: 1 residues processed: 77 average time/residue: 0.1284 time to fit residues: 12.9025 Evaluate side-chains 76 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0410 time to fit residues: 0.5905 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 38 optimal weight: 4.9990 chunk 29 optimal weight: 0.9990 chunk 20 optimal weight: 0.5980 chunk 4 optimal weight: 0.5980 chunk 18 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 7.9990 chunk 41 optimal weight: 0.6980 chunk 37 optimal weight: 0.9980 chunk 11 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8029 moved from start: 0.0737 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 3420 Z= 0.201 Angle : 0.569 7.108 4648 Z= 0.275 Chirality : 0.040 0.207 544 Planarity : 0.003 0.029 567 Dihedral : 3.604 12.456 457 Min Nonbonded Distance : 2.125 Molprobity Statistics. All-atom Clashscore : 9.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer: Outliers : 3.46 % Allowed : 36.31 % Favored : 60.23 % 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: 2.94 (0.43), residues: 424 helix: 2.77 (0.29), residues: 325 sheet: -2.46 (1.52), residues: 10 loop : -0.76 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 194 TYR 0.012 0.001 TYR A 444 ARG 0.000 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 74 time to evaluate : 0.366 Fit side-chains outliers start: 12 outliers final: 6 residues processed: 80 average time/residue: 0.1344 time to fit residues: 13.4533 Evaluate side-chains 79 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 73 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0540 time to fit residues: 1.0187 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 23 optimal weight: 0.8980 chunk 0 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 17 optimal weight: 0.7980 chunk 35 optimal weight: 0.6980 chunk 28 optimal weight: 0.7980 chunk 21 optimal weight: 0.6980 chunk 37 optimal weight: 3.9990 chunk 10 optimal weight: 0.6980 chunk 13 optimal weight: 0.5980 chunk 8 optimal weight: 3.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8024 moved from start: 0.0799 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3420 Z= 0.206 Angle : 0.593 8.371 4648 Z= 0.282 Chirality : 0.040 0.256 544 Planarity : 0.003 0.030 567 Dihedral : 3.600 12.539 457 Min Nonbonded Distance : 2.133 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 2.88 % Allowed : 36.60 % Favored : 60.52 % 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: 2.91 (0.43), residues: 424 helix: 2.76 (0.29), residues: 325 sheet: -2.57 (1.48), residues: 10 loop : -0.81 (0.71), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 194 TYR 0.010 0.001 TYR A 444 ARG 0.001 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 76 time to evaluate : 0.431 Fit side-chains outliers start: 10 outliers final: 3 residues processed: 84 average time/residue: 0.1423 time to fit residues: 15.0136 Evaluate side-chains 73 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 70 time to evaluate : 0.427 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0381 time to fit residues: 0.8009 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 24 optimal weight: 1.9990 chunk 10 optimal weight: 0.5980 chunk 41 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 13 optimal weight: 0.6980 chunk 21 optimal weight: 0.7980 chunk 40 optimal weight: 0.9980 chunk 4 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8032 moved from start: 0.0902 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.026 3420 Z= 0.213 Angle : 0.604 7.342 4648 Z= 0.290 Chirality : 0.040 0.203 544 Planarity : 0.003 0.030 567 Dihedral : 3.635 12.123 457 Min Nonbonded Distance : 2.142 Molprobity Statistics. All-atom Clashscore : 8.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.36 % Favored : 97.64 % Rotamer: Outliers : 1.15 % Allowed : 38.04 % Favored : 60.81 % 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: 2.89 (0.43), residues: 424 helix: 2.72 (0.29), residues: 326 sheet: -2.69 (1.44), residues: 10 loop : -0.73 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.010 0.001 PHE A 240 TYR 0.014 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 75 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 71 time to evaluate : 0.382 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 74 average time/residue: 0.1236 time to fit residues: 11.7926 Evaluate side-chains 71 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 68 time to evaluate : 0.399 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0359 time to fit residues: 0.6924 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 30 optimal weight: 4.9990 chunk 23 optimal weight: 0.9980 chunk 35 optimal weight: 0.9980 chunk 41 optimal weight: 1.9990 chunk 25 optimal weight: 0.3980 chunk 19 optimal weight: 0.4980 chunk 16 optimal weight: 0.7980 chunk 24 optimal weight: 0.1980 chunk 12 optimal weight: 0.5980 chunk 8 optimal weight: 0.9980 chunk 26 optimal weight: 1.9990 overall best weight: 0.4980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8010 moved from start: 0.0857 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3420 Z= 0.188 Angle : 0.596 7.625 4648 Z= 0.285 Chirality : 0.040 0.269 544 Planarity : 0.003 0.032 567 Dihedral : 3.600 11.941 457 Min Nonbonded Distance : 2.121 Molprobity Statistics. All-atom Clashscore : 8.56 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.58 % Allowed : 37.75 % Favored : 61.67 % 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: 2.99 (0.43), residues: 424 helix: 2.80 (0.29), residues: 326 sheet: -2.67 (1.45), residues: 10 loop : -0.73 (0.71), residues: 88 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.015 0.001 TYR A 444 ARG 0.001 0.000 ARG A 394 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 77 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 75 time to evaluate : 0.378 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 76 average time/residue: 0.1250 time to fit residues: 12.2600 Evaluate side-chains 69 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 69 time to evaluate : 0.393 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5063 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 28 optimal weight: 0.6980 chunk 20 optimal weight: 0.5980 chunk 3 optimal weight: 0.0370 chunk 32 optimal weight: 1.9990 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 0.0980 chunk 36 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 16 optimal weight: 0.8980 chunk 30 optimal weight: 0.9990 overall best weight: 0.4058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7995 moved from start: 0.0915 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3420 Z= 0.184 Angle : 0.608 10.382 4648 Z= 0.287 Chirality : 0.040 0.206 544 Planarity : 0.003 0.031 567 Dihedral : 3.610 11.798 457 Min Nonbonded Distance : 2.139 Molprobity Statistics. All-atom Clashscore : 9.30 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.58 % Allowed : 38.33 % Favored : 61.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.01 (0.43), residues: 424 helix: 2.84 (0.29), residues: 325 sheet: -2.60 (1.48), residues: 10 loop : -0.79 (0.72), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.009 0.001 PHE A 240 TYR 0.014 0.001 TYR A 444 ARG 0.000 0.000 ARG A 393 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 74 time to evaluate : 0.377 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 75 average time/residue: 0.1231 time to fit residues: 11.9169 Evaluate side-chains 72 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 71 time to evaluate : 0.377 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0372 time to fit residues: 0.5693 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 25 optimal weight: 0.0980 chunk 40 optimal weight: 0.8980 chunk 24 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 28 optimal weight: 0.8980 chunk 42 optimal weight: 0.9980 chunk 39 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8022 moved from start: 0.0976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3420 Z= 0.223 Angle : 0.630 12.754 4648 Z= 0.299 Chirality : 0.041 0.238 544 Planarity : 0.003 0.031 567 Dihedral : 3.613 11.786 457 Min Nonbonded Distance : 2.123 Molprobity Statistics. All-atom Clashscore : 10.33 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.30 % Favored : 96.70 % Rotamer: Outliers : 0.29 % Allowed : 39.48 % Favored : 60.23 % 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: 2.97 (0.43), residues: 424 helix: 2.80 (0.29), residues: 325 sheet: -2.75 (1.42), residues: 10 loop : -0.77 (0.72), residues: 89 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.010 0.001 PHE A 194 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 73 time to evaluate : 0.407 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 74 average time/residue: 0.1307 time to fit residues: 12.4289 Evaluate side-chains 70 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 70 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5303 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 34 optimal weight: 0.5980 chunk 3 optimal weight: 1.9990 chunk 26 optimal weight: 0.0970 chunk 20 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 10 optimal weight: 0.0570 chunk 31 optimal weight: 8.9990 chunk 5 optimal weight: 0.3980 chunk 9 optimal weight: 0.9990 chunk 14 optimal weight: 0.9990 overall best weight: 0.3496 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7985 moved from start: 0.1015 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3420 Z= 0.177 Angle : 0.635 12.202 4648 Z= 0.295 Chirality : 0.040 0.205 544 Planarity : 0.003 0.031 567 Dihedral : 3.603 11.887 457 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 9.74 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.07 % Favored : 96.93 % Rotamer: Outliers : 0.29 % Allowed : 40.06 % Favored : 59.65 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 3.03 (0.43), residues: 424 helix: 2.86 (0.29), residues: 324 sheet: -2.56 (1.49), residues: 10 loop : -0.80 (0.72), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 368 HIS 0.002 0.000 HIS A 348 PHE 0.010 0.001 PHE A 240 TYR 0.014 0.001 TYR A 444 ARG 0.000 0.000 ARG A 394 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 848 Ramachandran restraints generated. 424 Oldfield, 0 Emsley, 424 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 76 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 75 time to evaluate : 0.395 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 76 average time/residue: 0.1289 time to fit residues: 12.4749 Evaluate side-chains 73 residues out of total 347 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 72 time to evaluate : 0.388 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0385 time to fit residues: 0.5936 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 43 random chunks: chunk 35 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 6 optimal weight: 0.9980 chunk 29 optimal weight: 4.9990 chunk 1 optimal weight: 0.5980 chunk 24 optimal weight: 4.9990 chunk 39 optimal weight: 0.2980 chunk 22 optimal weight: 0.6980 chunk 27 optimal weight: 0.9980 chunk 26 optimal weight: 0.7980 chunk 16 optimal weight: 0.9980 overall best weight: 0.6580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3922 r_free = 0.3922 target = 0.154893 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 42)----------------| | r_work = 0.3589 r_free = 0.3589 target = 0.127624 restraints weight = 5334.027| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.3632 r_free = 0.3632 target = 0.131350 restraints weight = 2933.098| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 33)----------------| | r_work = 0.3662 r_free = 0.3662 target = 0.133883 restraints weight = 2065.401| |-----------------------------------------------------------------------------| r_work (final): 0.3649 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8014 moved from start: 0.1075 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3420 Z= 0.216 Angle : 0.637 11.574 4648 Z= 0.302 Chirality : 0.041 0.239 544 Planarity : 0.003 0.031 567 Dihedral : 3.581 11.640 457 Min Nonbonded Distance : 2.147 Molprobity Statistics. All-atom Clashscore : 11.22 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.83 % Favored : 97.17 % Rotamer: Outliers : 0.00 % Allowed : 40.92 % Favored : 59.08 % 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: 2.99 (0.43), residues: 424 helix: 2.84 (0.29), residues: 324 sheet: -2.71 (1.43), residues: 10 loop : -0.84 (0.73), residues: 90 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 368 HIS 0.002 0.001 HIS A 348 PHE 0.010 0.001 PHE A 240 TYR 0.013 0.001 TYR A 444 ARG 0.001 0.000 ARG A 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1098.83 seconds wall clock time: 20 minutes 31.90 seconds (1231.90 seconds total)