Starting phenix.real_space_refine on Sun Mar 10 19:47:05 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/03_2024/7ul2_26589_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/03_2024/7ul2_26589.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.4 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/03_2024/7ul2_26589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/03_2024/7ul2_26589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/03_2024/7ul2_26589_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/03_2024/7ul2_26589_updated.pdb" } resolution = 2.4 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= 0.088 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Anisotropic ADP refinement not supported. Converting 1879 atoms to isotropic. 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: 6 Type Number sf(0) Gaussians S 15 5.16 5 Cl 1 4.86 5 Na 1 4.78 5 C 1724 2.51 5 N 428 2.21 5 O 455 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "R TYR 346": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 107": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 2624 Number of models: 1 Model: "" Number of chains: 3 Chain: "R" Number of atoms: 2185 Number of conformers: 1 Conformer: "" Number of residues, atoms: 287, 2185 Classifications: {'peptide': 287} Incomplete info: {'truncation_to_alanine': 32} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 277} Chain breaks: 3 Unresolved non-hydrogen bonds: 126 Unresolved non-hydrogen angles: 153 Unresolved non-hydrogen dihedrals: 110 Unresolved non-hydrogen chiralities: 7 Planarities with less than four sites: {'TYR:plan': 1, 'ASN:plan1': 1, 'HIS:plan': 3, 'PHE:plan': 1, 'GLU:plan': 2, 'ARG:plan': 6} Unresolved non-hydrogen planarities: 69 Chain: "D" Number of atoms: 383 Number of conformers: 1 Conformer: "" Number of residues, atoms: 60, 383 Classifications: {'peptide': 60} Incomplete info: {'truncation_to_alanine': 30} Link IDs: {'TRANS': 59} Chain breaks: 4 Unresolved non-hydrogen bonds: 96 Unresolved non-hydrogen angles: 126 Unresolved non-hydrogen dihedrals: 79 Unresolved non-hydrogen chiralities: 11 Planarities with less than four sites: {'GLN:plan1': 3, 'TYR:plan': 2, 'ASN:plan1': 3, 'TRP:plan': 1, 'ASP:plan': 1, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 51 Chain: "R" Number of atoms: 56 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 56 Unusual residues: {' NA': 1, 'Q6Q': 1} Classifications: {'undetermined': 2, 'water': 13} Link IDs: {None: 14} Time building chain proxies: 2.14, per 1000 atoms: 0.82 Number of scatterers: 2624 At special positions: 0 Unit cell: (69.416, 50.3266, 103.256, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 6 Type Number sf(0) Cl 1 17.00 S 15 16.00 Na 1 11.00 O 455 8.00 N 428 7.00 C 1724 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS R 141 " - pdb=" SG CYS R 224 " distance=2.05 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: 1.30 Conformation dependent library (CDL) restraints added in 498.0 milliseconds 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 660 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 2 sheets defined 67.1% alpha, 7.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.49 Creating SS restraints... Processing helix chain 'R' and resid 61 through 89 removed outlier: 3.575A pdb=" N PHE R 86 " --> pdb=" O THR R 82 " (cutoff:3.500A) Processing helix chain 'R' and resid 100 through 117 removed outlier: 3.919A pdb=" N HIS R 104 " --> pdb=" O THR R 100 " (cutoff:3.500A) Processing helix chain 'R' and resid 119 through 126 Processing helix chain 'R' and resid 137 through 171 removed outlier: 3.574A pdb=" N TYR R 145 " --> pdb=" O CYS R 141 " (cutoff:3.500A) Processing helix chain 'R' and resid 173 through 179 removed outlier: 3.784A pdb=" N LYS R 177 " --> pdb=" O PRO R 173 " (cutoff:3.500A) removed outlier: 4.433A pdb=" N THR R 178 " --> pdb=" O PHE R 174 " (cutoff:3.500A) Processing helix chain 'R' and resid 182 through 199 Processing helix chain 'R' and resid 201 through 206 removed outlier: 3.877A pdb=" N PHE R 205 " --> pdb=" O VAL R 201 " (cutoff:3.500A) Processing helix chain 'R' and resid 230 through 244 Processing helix chain 'R' and resid 246 through 263 Processing helix chain 'R' and resid 273 through 328 Proline residue: R 318 - end of helix removed outlier: 3.545A pdb=" N PHE R 326 " --> pdb=" O ARG R 322 " (cutoff:3.500A) removed outlier: 3.694A pdb=" N CYS R 327 " --> pdb=" O ARG R 323 " (cutoff:3.500A) Processing helix chain 'R' and resid 336 through 367 removed outlier: 3.505A pdb=" N PHE R 353 " --> pdb=" O THR R 349 " (cutoff:3.500A) removed outlier: 3.939A pdb=" N TYR R 354 " --> pdb=" O ASN R 350 " (cutoff:3.500A) removed outlier: 4.065A pdb=" N SER R 357 " --> pdb=" O PHE R 353 " (cutoff:3.500A) removed outlier: 3.588A pdb=" N THR R 358 " --> pdb=" O TYR R 354 " (cutoff:3.500A) removed outlier: 4.698A pdb=" N ASN R 360 " --> pdb=" O SER R 356 " (cutoff:3.500A) Proline residue: R 361 - end of helix Processing helix chain 'R' and resid 369 through 378 Processing sheet with id= A, first strand: chain 'R' and resid 207 through 212 Processing sheet with id= B, first strand: chain 'D' and resid 51 through 54 removed outlier: 4.160A pdb=" N ASP D 35 " --> pdb=" O GLU D 100 " (cutoff:3.500A) 185 hydrogen bonds defined for protein. 543 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: 0.78 Time building geometry restraints manager: 1.29 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.19 - 1.33: 605 1.33 - 1.47: 939 1.47 - 1.60: 1106 1.60 - 1.74: 1 1.74 - 1.88: 24 Bond restraints: 2675 Sorted by residual: bond pdb=" C2 Q6Q R 501 " pdb=" O1 Q6Q R 501 " ideal model delta sigma weight residual 1.246 1.196 0.050 2.00e-02 2.50e+03 6.36e+00 bond pdb=" C2 Q6Q R 501 " pdb=" O2 Q6Q R 501 " ideal model delta sigma weight residual 1.244 1.194 0.050 2.00e-02 2.50e+03 6.14e+00 bond pdb=" C1 Q6Q R 501 " pdb=" C2 Q6Q R 501 " ideal model delta sigma weight residual 1.573 1.524 0.049 2.00e-02 2.50e+03 6.10e+00 bond pdb=" CB CYS R 224 " pdb=" SG CYS R 224 " ideal model delta sigma weight residual 1.808 1.878 -0.070 3.30e-02 9.18e+02 4.44e+00 bond pdb=" CB ARG R 303 " pdb=" CG ARG R 303 " ideal model delta sigma weight residual 1.520 1.467 0.053 3.00e-02 1.11e+03 3.09e+00 ... (remaining 2670 not shown) Histogram of bond angle deviations from ideal: 100.27 - 107.04: 70 107.04 - 113.82: 1491 113.82 - 120.59: 1136 120.59 - 127.36: 934 127.36 - 134.13: 34 Bond angle restraints: 3665 Sorted by residual: angle pdb=" N ILE R 359 " pdb=" CA ILE R 359 " pdb=" C ILE R 359 " ideal model delta sigma weight residual 110.72 114.28 -3.56 1.01e+00 9.80e-01 1.24e+01 angle pdb=" N ASN R 360 " pdb=" CA ASN R 360 " pdb=" C ASN R 360 " ideal model delta sigma weight residual 109.81 117.53 -7.72 2.21e+00 2.05e-01 1.22e+01 angle pdb=" CA LEU R 258 " pdb=" CB LEU R 258 " pdb=" CG LEU R 258 " ideal model delta sigma weight residual 116.30 105.45 10.85 3.50e+00 8.16e-02 9.61e+00 angle pdb=" N TYR R 328 " pdb=" CA TYR R 328 " pdb=" C TYR R 328 " ideal model delta sigma weight residual 113.30 117.38 -4.08 1.34e+00 5.57e-01 9.28e+00 angle pdb=" CA TYR R 256 " pdb=" CB TYR R 256 " pdb=" CG TYR R 256 " ideal model delta sigma weight residual 113.90 108.43 5.47 1.80e+00 3.09e-01 9.25e+00 ... (remaining 3660 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.86: 1460 17.86 - 35.72: 60 35.72 - 53.58: 22 53.58 - 71.45: 3 71.45 - 89.31: 2 Dihedral angle restraints: 1547 sinusoidal: 530 harmonic: 1017 Sorted by residual: dihedral pdb=" N ASN R 126 " pdb=" CA ASN R 126 " pdb=" CB ASN R 126 " pdb=" CG ASN R 126 " ideal model delta sinusoidal sigma weight residual -180.00 -120.54 -59.46 3 1.50e+01 4.44e-03 9.48e+00 dihedral pdb=" CA ARG R 323 " pdb=" CB ARG R 323 " pdb=" CG ARG R 323 " pdb=" CD ARG R 323 " ideal model delta sinusoidal sigma weight residual -60.00 -113.69 53.69 3 1.50e+01 4.44e-03 9.23e+00 dihedral pdb=" CA ARG D 32 " pdb=" CB ARG D 32 " pdb=" CG ARG D 32 " pdb=" CD ARG D 32 " ideal model delta sinusoidal sigma weight residual -60.00 -111.39 51.39 3 1.50e+01 4.44e-03 9.01e+00 ... (remaining 1544 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.052: 280 0.052 - 0.103: 125 0.103 - 0.155: 28 0.155 - 0.207: 9 0.207 - 0.258: 1 Chirality restraints: 443 Sorted by residual: chirality pdb=" CA ASN R 360 " pdb=" N ASN R 360 " pdb=" C ASN R 360 " pdb=" CB ASN R 360 " both_signs ideal model delta sigma weight residual False 2.51 2.25 0.26 2.00e-01 2.50e+01 1.67e+00 chirality pdb=" CA TYR R 145 " pdb=" N TYR R 145 " pdb=" C TYR R 145 " pdb=" CB TYR R 145 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 9.09e-01 chirality pdb=" CA PHE R 127 " pdb=" N PHE R 127 " pdb=" C PHE R 127 " pdb=" CB PHE R 127 " both_signs ideal model delta sigma weight residual False 2.51 2.32 0.19 2.00e-01 2.50e+01 8.68e-01 ... (remaining 440 not shown) Planarity restraints: 440 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C Q6Q R 501 " -0.015 2.00e-02 2.50e+03 2.26e-02 1.03e+01 pdb=" C12 Q6Q R 501 " 0.036 2.00e-02 2.50e+03 pdb=" C13 Q6Q R 501 " 0.006 2.00e-02 2.50e+03 pdb=" C14 Q6Q R 501 " -0.011 2.00e-02 2.50e+03 pdb=" C22 Q6Q R 501 " 0.009 2.00e-02 2.50e+03 pdb=" C23 Q6Q R 501 " 0.027 2.00e-02 2.50e+03 pdb=" N1 Q6Q R 501 " -0.014 2.00e-02 2.50e+03 pdb=" N2 Q6Q R 501 " -0.038 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C23 Q6Q R 501 " -0.046 2.00e-02 2.50e+03 1.77e-02 9.37e+00 pdb=" C24 Q6Q R 501 " 0.003 2.00e-02 2.50e+03 pdb=" C25 Q6Q R 501 " -0.010 2.00e-02 2.50e+03 pdb=" C26 Q6Q R 501 " -0.005 2.00e-02 2.50e+03 pdb=" C27 Q6Q R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C28 Q6Q R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C29 Q6Q R 501 " 0.001 2.00e-02 2.50e+03 pdb=" C30 Q6Q R 501 " 0.008 2.00e-02 2.50e+03 pdb=" C31 Q6Q R 501 " -0.001 2.00e-02 2.50e+03 pdb=" N2 Q6Q R 501 " 0.037 2.00e-02 2.50e+03 pdb=" N3 Q6Q R 501 " 0.000 2.00e-02 2.50e+03 pdb="CL Q6Q R 501 " 0.005 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TRP R 334 " 0.019 2.00e-02 2.50e+03 1.28e-02 4.11e+00 pdb=" CG TRP R 334 " -0.032 2.00e-02 2.50e+03 pdb=" CD1 TRP R 334 " 0.012 2.00e-02 2.50e+03 pdb=" CD2 TRP R 334 " -0.001 2.00e-02 2.50e+03 pdb=" NE1 TRP R 334 " -0.002 2.00e-02 2.50e+03 pdb=" CE2 TRP R 334 " -0.006 2.00e-02 2.50e+03 pdb=" CE3 TRP R 334 " -0.003 2.00e-02 2.50e+03 pdb=" CZ2 TRP R 334 " 0.007 2.00e-02 2.50e+03 pdb=" CZ3 TRP R 334 " 0.001 2.00e-02 2.50e+03 pdb=" CH2 TRP R 334 " 0.004 2.00e-02 2.50e+03 ... (remaining 437 not shown) Histogram of nonbonded interaction distances: 2.38 - 2.88: 962 2.88 - 3.39: 2547 3.39 - 3.89: 4310 3.89 - 4.40: 4769 4.40 - 4.90: 7873 Nonbonded interactions: 20461 Sorted by model distance: nonbonded pdb=" O PHE R 74 " pdb=" OG1 THR R 78 " model vdw 2.379 2.440 nonbonded pdb=" OD1 ASP R 112 " pdb="NA NA R 502 " model vdw 2.385 2.470 nonbonded pdb=" O LYS R 63 " pdb=" OG1 THR R 67 " model vdw 2.428 2.440 nonbonded pdb=" O PHE R 353 " pdb=" O HOH R 601 " model vdw 2.547 2.440 nonbonded pdb=" O MET R 249 " pdb=" OG SER R 253 " model vdw 2.592 2.440 ... (remaining 20456 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=0.00 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.030 Construct map_model_manager: 0.000 Extract box with map and model: 6.890 Check model and map are aligned: 0.040 Set scattering table: 0.030 Process input model: 12.960 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.170 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.560 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8119 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 : 0.008 0.070 2675 Z= 0.486 Angle : 1.016 10.850 3665 Z= 0.560 Chirality : 0.061 0.258 443 Planarity : 0.006 0.040 440 Dihedral : 12.544 89.306 884 Min Nonbonded Distance : 2.379 Molprobity Statistics. All-atom Clashscore : 6.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.52 % Favored : 98.48 % Rotamer: Outliers : 0.84 % Allowed : 7.56 % Favored : 91.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 1.60 (0.41), residues: 329 helix: 1.95 (0.30), residues: 224 sheet: 1.57 (1.66), residues: 9 loop : -1.17 (0.52), residues: 96 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.032 0.004 TRP R 334 HIS 0.004 0.002 HIS R 172 PHE 0.026 0.004 PHE R 337 TYR 0.031 0.004 TYR R 256 ARG 0.012 0.002 ARG R 299 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.299 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 1.0585 time to fit residues: 54.4395 Evaluate side-chains 40 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.287 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 126 ASN Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 2.9990 chunk 25 optimal weight: 0.5980 chunk 14 optimal weight: 2.9990 chunk 8 optimal weight: 0.9980 chunk 17 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 26 optimal weight: 0.7980 chunk 10 optimal weight: 0.0870 chunk 16 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 3.9990 overall best weight: 0.5558 ------------------------------------------------------------------------------- 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: 0.8009 moved from start: 0.2154 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2675 Z= 0.185 Angle : 0.562 8.646 3665 Z= 0.315 Chirality : 0.041 0.175 443 Planarity : 0.004 0.027 440 Dihedral : 5.779 49.673 430 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer: Outliers : 2.10 % Allowed : 7.56 % Favored : 90.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.84 (0.44), residues: 329 helix: 3.18 (0.31), residues: 226 sheet: 1.15 (1.52), residues: 9 loop : -1.53 (0.51), residues: 94 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.002 0.001 HIS R 343 PHE 0.019 0.002 PHE R 375 TYR 0.013 0.002 TYR R 144 ARG 0.002 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 37 time to evaluate : 0.270 Fit side-chains REVERT: R 65 LEU cc_start: 0.7376 (OUTLIER) cc_final: 0.7022 (tt) outliers start: 5 outliers final: 3 residues processed: 41 average time/residue: 1.0505 time to fit residues: 44.3911 Evaluate side-chains 40 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.290 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 65 LEU Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 322 ARG Chi-restraints excluded: chain R residue 340 ASP Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 0.2980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 8 optimal weight: 0.5980 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 0.9990 chunk 27 optimal weight: 0.0070 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 overall best weight: 0.4998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8004 moved from start: 0.2565 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2675 Z= 0.168 Angle : 0.503 7.854 3665 Z= 0.282 Chirality : 0.038 0.144 443 Planarity : 0.004 0.031 440 Dihedral : 4.907 43.288 428 Min Nonbonded Distance : 2.324 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.91 % Favored : 99.09 % Rotamer: Outliers : 3.36 % Allowed : 6.72 % Favored : 89.92 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.95 (0.45), residues: 329 helix: 3.32 (0.32), residues: 227 sheet: 0.91 (1.75), residues: 9 loop : -1.69 (0.52), residues: 93 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 PHE 0.016 0.002 PHE R 375 TYR 0.013 0.002 TYR R 256 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 42 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 34 time to evaluate : 0.294 Fit side-chains REVERT: R 123 GLU cc_start: 0.8119 (OUTLIER) cc_final: 0.7617 (tt0) outliers start: 8 outliers final: 2 residues processed: 37 average time/residue: 1.0599 time to fit residues: 40.4819 Evaluate side-chains 36 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 33 time to evaluate : 0.288 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.5980 chunk 20 optimal weight: 0.0970 chunk 31 optimal weight: 7.9990 chunk 32 optimal weight: 0.6980 chunk 29 optimal weight: 0.9990 chunk 8 optimal weight: 0.9980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6578 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2628 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.024 2675 Z= 0.188 Angle : 0.523 7.941 3665 Z= 0.291 Chirality : 0.039 0.145 443 Planarity : 0.004 0.034 440 Dihedral : 4.921 43.881 428 Min Nonbonded Distance : 2.334 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer: Outliers : 2.94 % Allowed : 9.24 % Favored : 87.82 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.74 (0.45), residues: 329 helix: 3.09 (0.32), residues: 233 sheet: 0.43 (1.67), residues: 9 loop : -1.86 (0.52), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 PHE 0.015 0.002 PHE R 375 TYR 0.015 0.002 TYR R 256 ARG 0.001 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 36 time to evaluate : 0.301 Fit side-chains REVERT: R 123 GLU cc_start: 0.8109 (OUTLIER) cc_final: 0.7584 (tt0) outliers start: 7 outliers final: 2 residues processed: 39 average time/residue: 0.9895 time to fit residues: 39.8780 Evaluate side-chains 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.299 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.9980 chunk 13 optimal weight: 1.9990 chunk 28 optimal weight: 8.9990 chunk 22 optimal weight: 0.1980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.5980 chunk 29 optimal weight: 2.9990 chunk 8 optimal weight: 0.9990 chunk 11 optimal weight: 1.9990 chunk 6 optimal weight: 0.9980 chunk 19 optimal weight: 0.5980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8046 moved from start: 0.2742 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2675 Z= 0.188 Angle : 0.518 7.994 3665 Z= 0.288 Chirality : 0.039 0.146 443 Planarity : 0.004 0.038 440 Dihedral : 4.894 43.910 428 Min Nonbonded Distance : 2.292 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.10 % Allowed : 10.50 % Favored : 87.39 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.69 (0.46), residues: 329 helix: 3.07 (0.33), residues: 233 sheet: -0.08 (1.69), residues: 9 loop : -1.91 (0.52), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 PHE 0.015 0.002 PHE R 375 TYR 0.014 0.002 TYR R 256 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.308 Fit side-chains REVERT: R 123 GLU cc_start: 0.8098 (OUTLIER) cc_final: 0.7609 (tt0) outliers start: 5 outliers final: 2 residues processed: 36 average time/residue: 1.0378 time to fit residues: 38.5977 Evaluate side-chains 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.271 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 0.8980 chunk 32 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 15 optimal weight: 0.8980 chunk 2 optimal weight: 0.5980 chunk 10 optimal weight: 0.0020 chunk 17 optimal weight: 0.6980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 0.7980 chunk 18 optimal weight: 0.9990 chunk 24 optimal weight: 0.9990 overall best weight: 0.5988 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8033 moved from start: 0.2872 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 2675 Z= 0.174 Angle : 0.497 7.910 3665 Z= 0.277 Chirality : 0.038 0.144 443 Planarity : 0.004 0.040 440 Dihedral : 4.824 43.502 428 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.52 % Allowed : 10.92 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.73 (0.46), residues: 329 helix: 3.12 (0.33), residues: 233 sheet: -0.27 (1.74), residues: 9 loop : -1.91 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 PHE 0.014 0.002 PHE R 375 TYR 0.013 0.001 TYR R 256 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.254 Fit side-chains REVERT: R 123 GLU cc_start: 0.8095 (OUTLIER) cc_final: 0.7598 (tt0) outliers start: 6 outliers final: 3 residues processed: 37 average time/residue: 1.0154 time to fit residues: 38.8581 Evaluate side-chains 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.312 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 19 optimal weight: 0.5980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 6 optimal weight: 1.9990 chunk 22 optimal weight: 0.9980 chunk 16 optimal weight: 0.4980 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8053 moved from start: 0.2834 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 2675 Z= 0.190 Angle : 0.515 7.948 3665 Z= 0.286 Chirality : 0.039 0.145 443 Planarity : 0.004 0.042 440 Dihedral : 4.852 44.028 428 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.10 % Allowed : 11.76 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.61 (0.46), residues: 329 helix: 3.04 (0.33), residues: 233 sheet: -0.38 (1.77), residues: 9 loop : -1.96 (0.52), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 PHE 0.014 0.002 PHE R 375 TYR 0.014 0.002 TYR R 256 ARG 0.001 0.000 ARG D 32 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.307 Fit side-chains REVERT: R 123 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7599 (tt0) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 0.9906 time to fit residues: 37.8841 Evaluate side-chains 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.7980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.5980 chunk 31 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 chunk 30 optimal weight: 0.7980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.7980 chunk 23 optimal weight: 0.6980 chunk 9 optimal weight: 0.5980 chunk 27 optimal weight: 0.0370 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8019 moved from start: 0.2994 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.021 2675 Z= 0.160 Angle : 0.482 7.878 3665 Z= 0.267 Chirality : 0.037 0.144 443 Planarity : 0.004 0.042 440 Dihedral : 4.769 43.097 428 Min Nonbonded Distance : 2.289 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.10 % Allowed : 11.34 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.74 (0.47), residues: 329 helix: 3.14 (0.33), residues: 233 sheet: -0.48 (1.78), residues: 9 loop : -1.93 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 129 HIS 0.003 0.001 HIS R 343 PHE 0.014 0.001 PHE R 375 TYR 0.012 0.001 TYR R 256 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.229 Fit side-chains REVERT: R 123 GLU cc_start: 0.8092 (OUTLIER) cc_final: 0.7586 (tt0) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 1.0476 time to fit residues: 38.8794 Evaluate side-chains 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.307 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 128 ILE Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 8.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 22 optimal weight: 0.0980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 6.9990 chunk 26 optimal weight: 0.0770 chunk 2 optimal weight: 0.1980 overall best weight: 0.4138 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 126 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7993 moved from start: 0.3116 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.021 2675 Z= 0.146 Angle : 0.461 7.736 3665 Z= 0.256 Chirality : 0.037 0.140 443 Planarity : 0.004 0.042 440 Dihedral : 4.690 42.673 428 Min Nonbonded Distance : 2.280 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.10 % Allowed : 11.34 % Favored : 86.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.85 (0.47), residues: 329 helix: 3.23 (0.33), residues: 233 sheet: -0.54 (1.78), residues: 9 loop : -1.89 (0.54), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP R 129 HIS 0.003 0.001 HIS R 343 PHE 0.013 0.001 PHE R 375 TYR 0.012 0.001 TYR R 144 ARG 0.001 0.000 ARG R 322 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 33 time to evaluate : 0.302 Fit side-chains REVERT: R 123 GLU cc_start: 0.8093 (OUTLIER) cc_final: 0.7571 (tt0) outliers start: 5 outliers final: 3 residues processed: 36 average time/residue: 1.0359 time to fit residues: 38.5280 Evaluate side-chains 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.289 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 20 optimal weight: 1.9990 chunk 16 optimal weight: 0.8980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 5.9990 chunk 8 optimal weight: 0.6980 chunk 24 optimal weight: 0.1980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 27 optimal weight: 0.9990 chunk 11 optimal weight: 0.6980 chunk 4 optimal weight: 0.9990 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: 0.8034 moved from start: 0.2973 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.022 2675 Z= 0.176 Angle : 0.497 7.831 3665 Z= 0.275 Chirality : 0.038 0.144 443 Planarity : 0.004 0.043 440 Dihedral : 4.752 43.764 428 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.10 % Allowed : 12.18 % Favored : 85.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.73 (0.47), residues: 329 helix: 3.14 (0.33), residues: 233 sheet: -0.52 (1.79), residues: 9 loop : -1.94 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 343 PHE 0.013 0.001 PHE R 375 TYR 0.014 0.001 TYR R 256 ARG 0.001 0.000 ARG R 322 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 658 Ramachandran restraints generated. 329 Oldfield, 0 Emsley, 329 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 39 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 34 time to evaluate : 0.285 Fit side-chains REVERT: R 123 GLU cc_start: 0.8087 (OUTLIER) cc_final: 0.7573 (tt0) outliers start: 5 outliers final: 3 residues processed: 37 average time/residue: 1.0029 time to fit residues: 38.3130 Evaluate side-chains 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.296 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain R residue 110 LEU Chi-restraints excluded: chain R residue 123 GLU Chi-restraints excluded: chain R residue 124 LEU Chi-restraints excluded: chain R residue 322 ARG Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 0.6980 chunk 1 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.9980 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.8980 chunk 20 optimal weight: 1.9990 chunk 13 optimal weight: 0.7980 chunk 12 optimal weight: 0.9990 chunk 33 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 229 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3689 r_free = 0.3689 target = 0.146343 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.3438 r_free = 0.3438 target = 0.125607 restraints weight = 2948.807| |-----------------------------------------------------------------------------| r_work (start): 0.3437 rms_B_bonded: 1.40 r_work: 0.3355 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3261 rms_B_bonded: 2.97 restraints_weight: 0.2500 r_work (final): 0.3261 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8216 moved from start: 0.2879 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 2675 Z= 0.202 Angle : 0.526 8.014 3665 Z= 0.291 Chirality : 0.039 0.147 443 Planarity : 0.005 0.043 440 Dihedral : 4.828 44.273 428 Min Nonbonded Distance : 2.261 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer: Outliers : 2.10 % Allowed : 11.76 % Favored : 86.13 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % 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: 2.56 (0.46), residues: 329 helix: 3.01 (0.33), residues: 233 sheet: -0.53 (1.75), residues: 9 loop : -1.99 (0.53), residues: 87 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP R 316 HIS 0.003 0.001 HIS R 229 PHE 0.014 0.002 PHE R 375 TYR 0.015 0.002 TYR R 256 ARG 0.001 0.000 ARG D 32 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1417.23 seconds wall clock time: 25 minutes 36.79 seconds (1536.79 seconds total)