Starting phenix.real_space_refine (version: dev) on Fri Feb 17 10:26:16 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/02_2023/7ul2_26589_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/02_2023/7ul2_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_26589/02_2023/7ul2_26589.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/02_2023/7ul2_26589.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/02_2023/7ul2_26589_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ul2_26589/02_2023/7ul2_26589_updated.pdb" } resolution = 2.4 write_initial_geo_file = False refinement { macro_cycles = 10 } 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 ------------------------------------------------------------------------------- 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 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-4877/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: 2.20, per 1000 atoms: 0.84 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: 1.16 Conformation dependent library (CDL) restraints added in 428.9 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: 0.34 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: 0.69 Time building geometry restraints manager: 1.25 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: 1409 17.86 - 35.72: 60 35.72 - 53.58: 22 53.58 - 71.45: 3 71.45 - 89.31: 2 Dihedral angle restraints: 1496 sinusoidal: 479 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 1493 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 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. 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: 2.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.020 Construct map_model_manager: 0.010 Extract box with map and model: 7.470 Check model and map are aligned: 0.030 Process input model: 12.350 Find NCS groups from input model: 0.070 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:12.560 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 34.900 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8411 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 : 12.803 89.306 833 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 % 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 *********************** 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 : 0.306 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 50 average time/residue: 1.0816 time to fit residues: 55.6039 Evaluate side-chains 40 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 38 time to evaluate : 0.270 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 2 residues processed: 0 time to fit residues: 0.3642 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.8303 moved from start: 0.2121 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= 0.183 Angle : 0.563 8.660 3665 Z= 0.316 Chirality : 0.041 0.175 443 Planarity : 0.004 0.028 440 Dihedral : 4.328 19.180 373 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Rotamer Outliers : 2.10 % 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: 2.87 (0.44), residues: 329 helix: 3.20 (0.31), residues: 226 sheet: 1.19 (1.53), residues: 9 loop : -1.52 (0.51), residues: 94 *********************** 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 40 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 35 time to evaluate : 0.312 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 39 average time/residue: 1.1084 time to fit residues: 44.6174 Evaluate side-chains 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 2 average time/residue: 0.1568 time to fit residues: 0.8212 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 17 optimal weight: 0.0980 chunk 9 optimal weight: 1.9990 chunk 25 optimal weight: 0.9980 chunk 21 optimal weight: 0.5980 chunk 8 optimal weight: 0.6980 chunk 30 optimal weight: 6.9990 chunk 33 optimal weight: 0.3980 chunk 27 optimal weight: 2.9990 chunk 10 optimal weight: 1.9990 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 overall best weight: 0.4780 ------------------------------------------------------------------------------- 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: 0.8285 moved from start: 0.2571 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= 0.164 Angle : 0.498 7.854 3665 Z= 0.279 Chirality : 0.038 0.142 443 Planarity : 0.004 0.031 440 Dihedral : 4.107 20.333 373 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 2.52 % 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: 3.06 (0.45), residues: 329 helix: 3.40 (0.32), residues: 227 sheet: 0.96 (1.75), residues: 9 loop : -1.66 (0.51), residues: 93 *********************** 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 40 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.280 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 1.1052 time to fit residues: 42.2100 Evaluate side-chains 34 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 32 time to evaluate : 0.313 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0960 time to fit residues: 0.5259 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 16 optimal weight: 0.9990 chunk 3 optimal weight: 0.9980 chunk 14 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 6.9990 chunk 32 optimal weight: 1.9990 chunk 29 optimal weight: 0.9980 chunk 8 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.8366 moved from start: 0.2431 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.030 2675 Z= 0.235 Angle : 0.576 8.143 3665 Z= 0.319 Chirality : 0.041 0.149 443 Planarity : 0.005 0.035 440 Dihedral : 4.261 20.672 373 Min Nonbonded Distance : 2.317 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.61 % Favored : 99.39 % Rotamer Outliers : 2.52 % 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 (0.45), residues: 329 helix: 2.96 (0.32), residues: 233 sheet: 0.51 (1.73), residues: 9 loop : -1.95 (0.51), residues: 87 *********************** 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 42 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 36 time to evaluate : 0.373 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 38 average time/residue: 0.9794 time to fit residues: 38.5278 Evaluate side-chains 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 35 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 0.0524 time to fit residues: 0.5031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 24 optimal weight: 0.3980 chunk 13 optimal weight: 2.9990 chunk 28 optimal weight: 7.9990 chunk 22 optimal weight: 0.5980 chunk 0 optimal weight: 3.9990 chunk 16 optimal weight: 0.7980 chunk 29 optimal weight: 0.0270 chunk 8 optimal weight: 0.5980 chunk 11 optimal weight: 0.5980 chunk 6 optimal weight: 0.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.4438 ------------------------------------------------------------------------------- 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: 0.8277 moved from start: 0.2906 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 2675 Z= 0.151 Angle : 0.472 7.885 3665 Z= 0.264 Chirality : 0.037 0.144 443 Planarity : 0.004 0.036 440 Dihedral : 4.013 20.160 373 Min Nonbonded Distance : 2.309 Molprobity Statistics. All-atom Clashscore : 2.81 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer Outliers : 2.52 % 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: 2.91 (0.46), residues: 329 helix: 3.36 (0.32), residues: 227 sheet: -0.15 (1.68), residues: 9 loop : -1.77 (0.52), residues: 93 *********************** 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 40 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 34 time to evaluate : 0.290 Fit side-chains outliers start: 6 outliers final: 2 residues processed: 37 average time/residue: 1.1185 time to fit residues: 42.6141 Evaluate side-chains 36 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 34 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0824 time to fit residues: 0.5031 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 8 optimal weight: 4.9990 chunk 32 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 15 optimal weight: 0.0870 chunk 2 optimal weight: 0.7980 chunk 10 optimal weight: 0.4980 chunk 17 optimal weight: 1.9990 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.4980 chunk 18 optimal weight: 0.7980 chunk 24 optimal weight: 0.0970 overall best weight: 0.3956 ------------------------------------------------------------------------------- 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: 0.8267 moved from start: 0.3019 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.020 2675 Z= 0.144 Angle : 0.462 7.659 3665 Z= 0.256 Chirality : 0.037 0.139 443 Planarity : 0.004 0.037 440 Dihedral : 3.883 19.950 373 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 : 1.68 % 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: 3.04 (0.46), residues: 329 helix: 3.48 (0.33), residues: 227 sheet: -0.42 (1.72), residues: 9 loop : -1.76 (0.52), residues: 93 *********************** 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 38 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 34 time to evaluate : 0.306 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 37 average time/residue: 1.0863 time to fit residues: 41.5341 Evaluate side-chains 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.267 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.0779 time to fit residues: 0.4571 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 18 optimal weight: 3.9990 chunk 27 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 20 optimal weight: 0.0030 chunk 19 optimal weight: 0.6980 chunk 15 optimal weight: 3.9990 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 0.9980 chunk 6 optimal weight: 5.9990 chunk 22 optimal weight: 0.6980 chunk 16 optimal weight: 0.6980 overall best weight: 0.5990 ------------------------------------------------------------------------------- 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: 0.8318 moved from start: 0.2886 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 : 0.500 7.813 3665 Z= 0.277 Chirality : 0.038 0.141 443 Planarity : 0.004 0.040 440 Dihedral : 3.966 20.604 373 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer Outliers : 1.68 % 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: 2.80 (0.46), residues: 329 helix: 3.18 (0.33), residues: 233 sheet: -0.54 (1.76), residues: 9 loop : -1.87 (0.53), residues: 87 *********************** 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: 4 poor density : 35 time to evaluate : 0.283 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 38 average time/residue: 1.1400 time to fit residues: 44.7373 Evaluate side-chains 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.279 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0813 time to fit residues: 0.5673 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 0.5980 chunk 29 optimal weight: 0.9980 chunk 31 optimal weight: 0.8980 chunk 28 optimal weight: 0.0000 chunk 30 optimal weight: 0.5980 chunk 18 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 23 optimal weight: 0.5980 chunk 9 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 overall best weight: 0.5384 ------------------------------------------------------------------------------- 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: 0.8300 moved from start: 0.2982 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= 0.164 Angle : 0.483 7.795 3665 Z= 0.268 Chirality : 0.038 0.140 443 Planarity : 0.004 0.041 440 Dihedral : 3.933 20.246 373 Min Nonbonded Distance : 2.290 Molprobity Statistics. All-atom Clashscore : 2.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer Outliers : 1.68 % 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: 2.81 (0.46), residues: 329 helix: 3.19 (0.33), residues: 233 sheet: -0.54 (1.77), residues: 9 loop : -1.88 (0.53), residues: 87 *********************** 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 39 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 35 time to evaluate : 0.303 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 37 average time/residue: 1.1352 time to fit residues: 43.3385 Evaluate side-chains 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.273 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.0902 time to fit residues: 0.4971 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 28 optimal weight: 6.9990 chunk 30 optimal weight: 5.9990 chunk 20 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 chunk 19 optimal weight: 0.4980 chunk 15 optimal weight: 0.5980 chunk 22 optimal weight: 0.0870 chunk 33 optimal weight: 1.9990 chunk 31 optimal weight: 5.9990 chunk 26 optimal weight: 0.7980 chunk 2 optimal weight: 0.9980 overall best weight: 0.5958 ------------------------------------------------------------------------------- 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: 0.8317 moved from start: 0.2942 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 : 0.500 7.846 3665 Z= 0.276 Chirality : 0.038 0.143 443 Planarity : 0.004 0.042 440 Dihedral : 3.957 20.477 373 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer Outliers : 1.26 % 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: 3.13 (0.33), residues: 233 sheet: -0.54 (1.80), residues: 9 loop : -1.91 (0.53), residues: 87 *********************** 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: 3 poor density : 35 time to evaluate : 0.320 Fit side-chains outliers start: 3 outliers final: 1 residues processed: 37 average time/residue: 1.1566 time to fit residues: 44.0912 Evaluate side-chains 36 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.265 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4195 ------------------------------------------------------------------------------- Set rotamer restraints ********************** 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: 0.6980 chunk 21 optimal weight: 0.5980 chunk 28 optimal weight: 6.9990 chunk 8 optimal weight: 0.5980 chunk 24 optimal weight: 0.2980 chunk 3 optimal weight: 1.9990 chunk 7 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 11 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 overall best weight: 0.5580 ------------------------------------------------------------------------------- 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: 0.8307 moved from start: 0.2997 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= 0.168 Angle : 0.490 7.824 3665 Z= 0.271 Chirality : 0.038 0.142 443 Planarity : 0.004 0.042 440 Dihedral : 3.937 20.324 373 Min Nonbonded Distance : 2.279 Molprobity Statistics. All-atom Clashscore : 2.41 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer Outliers : 0.84 % 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: 2.75 (0.47), residues: 329 helix: 3.15 (0.33), residues: 233 sheet: -0.60 (1.81), residues: 9 loop : -1.92 (0.54), residues: 87 ********************** 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 37 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 35 time to evaluate : 0.319 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 37 average time/residue: 1.1093 time to fit residues: 42.4291 Evaluate side-chains 36 residues out of total 300 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 35 time to evaluate : 0.323 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 1 residues processed: 0 time to fit residues: 0.4077 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 34 random chunks: chunk 23 optimal weight: 0.5980 chunk 1 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 5.9990 chunk 18 optimal weight: 0.9990 chunk 0 optimal weight: 2.9990 chunk 21 optimal weight: 0.5980 chunk 20 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 12 optimal weight: 0.8980 chunk 33 optimal weight: 2.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- 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 = 0.3688 r_free = 0.3688 target = 0.145979 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 38)----------------| | r_work = 0.3437 r_free = 0.3437 target = 0.125416 restraints weight = 2954.311| |-----------------------------------------------------------------------------| r_work (start): 0.3434 rms_B_bonded: 1.39 r_work: 0.3351 rms_B_bonded: 1.75 restraints_weight: 0.5000 r_work: 0.3257 rms_B_bonded: 2.99 restraints_weight: 0.2500 r_work (final): 0.3257 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8402 moved from start: 0.2844 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 2675 Z= 0.209 Angle : 0.536 8.087 3665 Z= 0.295 Chirality : 0.039 0.148 443 Planarity : 0.005 0.043 440 Dihedral : 4.041 20.427 373 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 2.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.30 % Favored : 99.70 % Rotamer Outliers : 0.84 % 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: 2.55 (0.46), residues: 329 helix: 3.00 (0.33), residues: 233 sheet: -0.61 (1.80), residues: 9 loop : -2.00 (0.53), residues: 87 =============================================================================== Job complete usr+sys time: 1438.82 seconds wall clock time: 26 minutes 20.39 seconds (1580.39 seconds total)