Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:06:48 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/11_2022/6wyk_21967.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/11_2022/6wyk_21967.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/11_2022/6wyk_21967.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/11_2022/6wyk_21967.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/11_2022/6wyk_21967.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/6wyk_21967/11_2022/6wyk_21967.pdb" } resolution = 4.0 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= 0.000 sd= 0.003 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Convert atoms to be neutral Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4778/modules/chem_data/mon_lib" Total number of atoms: 3083 Number of models: 1 Model: "" Number of chains: 1 Chain: "A" Number of atoms: 3083 Number of conformers: 1 Conformer: "" Number of residues, atoms: 415, 3083 Classifications: {'peptide': 415} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 18, 'TRANS': 396} Chain breaks: 1 Time building chain proxies: 2.27, per 1000 atoms: 0.74 Number of scatterers: 3083 At special positions: 0 Unit cell: (73.95, 70.992, 76.908, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 18 16.00 O 546 8.00 N 490 7.00 C 2029 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.32 Conformation dependent library (CDL) restraints added in 471.8 milliseconds 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 750 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 0 sheets defined 86.7% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.11 Creating SS restraints... Processing helix chain 'A' and resid 5 through 10 Processing helix chain 'A' and resid 13 through 29 removed outlier: 4.045A pdb=" N LEU A 17 " --> pdb=" O LEU A 13 " (cutoff:3.500A) Processing helix chain 'A' and resid 35 through 78 Proline residue: A 45 - end of helix removed outlier: 3.508A pdb=" N PHE A 50 " --> pdb=" O PHE A 46 " (cutoff:3.500A) removed outlier: 3.807A pdb=" N LEU A 57 " --> pdb=" O LEU A 53 " (cutoff:3.500A) removed outlier: 4.081A pdb=" N VAL A 58 " --> pdb=" O LEU A 54 " (cutoff:3.500A) removed outlier: 4.263A pdb=" N MET A 59 " --> pdb=" O LYS A 55 " (cutoff:3.500A) Proline residue: A 60 - end of helix removed outlier: 3.530A pdb=" N PHE A 63 " --> pdb=" O MET A 59 " (cutoff:3.500A) Proline residue: A 75 - end of helix Processing helix chain 'A' and resid 79 through 108 Processing helix chain 'A' and resid 129 through 137 removed outlier: 3.510A pdb=" N ILE A 133 " --> pdb=" O PRO A 129 " (cutoff:3.500A) removed outlier: 3.552A pdb=" N ILE A 137 " --> pdb=" O ILE A 133 " (cutoff:3.500A) Processing helix chain 'A' and resid 141 through 149 removed outlier: 3.671A pdb=" N GLY A 149 " --> pdb=" O ALA A 145 " (cutoff:3.500A) Processing helix chain 'A' and resid 151 through 170 removed outlier: 4.268A pdb=" N ASN A 170 " --> pdb=" O THR A 166 " (cutoff:3.500A) Processing helix chain 'A' and resid 173 through 221 removed outlier: 4.025A pdb=" N GLN A 203 " --> pdb=" O ASN A 199 " (cutoff:3.500A) removed outlier: 3.844A pdb=" N TYR A 204 " --> pdb=" O GLY A 200 " (cutoff:3.500A) Proline residue: A 206 - end of helix removed outlier: 3.780A pdb=" N GLN A 220 " --> pdb=" O VAL A 216 " (cutoff:3.500A) Processing helix chain 'A' and resid 223 through 255 removed outlier: 3.832A pdb=" N GLU A 227 " --> pdb=" O LYS A 223 " (cutoff:3.500A) Processing helix chain 'A' and resid 257 through 276 removed outlier: 4.420A pdb=" N ASP A 267 " --> pdb=" O LYS A 263 " (cutoff:3.500A) removed outlier: 4.621A pdb=" N ALA A 268 " --> pdb=" O LYS A 264 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N THR A 271 " --> pdb=" O ASP A 267 " (cutoff:3.500A) Processing helix chain 'A' and resid 280 through 293 removed outlier: 4.021A pdb=" N VAL A 284 " --> pdb=" O GLY A 280 " (cutoff:3.500A) Processing helix chain 'A' and resid 295 through 310 Proline residue: A 304 - end of helix Processing helix chain 'A' and resid 312 through 330 Processing helix chain 'A' and resid 334 through 352 Processing helix chain 'A' and resid 357 through 370 removed outlier: 4.388A pdb=" N ILE A 361 " --> pdb=" O GLY A 357 " (cutoff:3.500A) removed outlier: 3.662A pdb=" N MET A 362 " --> pdb=" O ALA A 358 " (cutoff:3.500A) removed outlier: 3.902A pdb=" N LEU A 363 " --> pdb=" O GLY A 359 " (cutoff:3.500A) removed outlier: 3.690A pdb=" N ALA A 364 " --> pdb=" O ALA A 360 " (cutoff:3.500A) removed outlier: 3.717A pdb=" N MET A 365 " --> pdb=" O ILE A 361 " (cutoff:3.500A) Processing helix chain 'A' and resid 376 through 416 removed outlier: 3.667A pdb=" N GLY A 388 " --> pdb=" O ALA A 384 " (cutoff:3.500A) removed outlier: 4.025A pdb=" N ILE A 389 " --> pdb=" O MET A 385 " (cutoff:3.500A) removed outlier: 4.105A pdb=" N ALA A 391 " --> pdb=" O LEU A 387 " (cutoff:3.500A) removed outlier: 4.704A pdb=" N ILE A 392 " --> pdb=" O GLY A 388 " (cutoff:3.500A) removed outlier: 3.884A pdb=" N MET A 395 " --> pdb=" O ALA A 391 " (cutoff:3.500A) removed outlier: 3.924A pdb=" N GLY A 396 " --> pdb=" O ILE A 392 " (cutoff:3.500A) removed outlier: 3.691A pdb=" N MET A 399 " --> pdb=" O MET A 395 " (cutoff:3.500A) 251 hydrogen bonds defined for protein. 753 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: 0.81 Time building geometry restraints manager: 1.42 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 946 1.34 - 1.46: 451 1.46 - 1.57: 1705 1.57 - 1.69: 0 1.69 - 1.81: 34 Bond restraints: 3136 Sorted by residual: bond pdb=" N VAL A 225 " pdb=" CA VAL A 225 " ideal model delta sigma weight residual 1.459 1.507 -0.048 1.33e-02 5.65e+03 1.29e+01 bond pdb=" N VAL A 274 " pdb=" CA VAL A 274 " ideal model delta sigma weight residual 1.460 1.497 -0.037 1.21e-02 6.83e+03 9.53e+00 bond pdb=" N LYS A 223 " pdb=" CA LYS A 223 " ideal model delta sigma weight residual 1.456 1.496 -0.040 1.31e-02 5.83e+03 9.29e+00 bond pdb=" N VAL A 224 " pdb=" CA VAL A 224 " ideal model delta sigma weight residual 1.460 1.497 -0.036 1.26e-02 6.30e+03 8.36e+00 bond pdb=" N ASN A 148 " pdb=" CA ASN A 148 " ideal model delta sigma weight residual 1.457 1.492 -0.035 1.29e-02 6.01e+03 7.37e+00 ... (remaining 3131 not shown) Histogram of bond angle deviations from ideal: 98.27 - 104.90: 65 104.90 - 111.52: 1514 111.52 - 118.15: 932 118.15 - 124.77: 1733 124.77 - 131.40: 25 Bond angle restraints: 4269 Sorted by residual: angle pdb=" CA VAL A 224 " pdb=" C VAL A 224 " pdb=" O VAL A 224 " ideal model delta sigma weight residual 120.57 115.75 4.82 1.07e+00 8.73e-01 2.03e+01 angle pdb=" CA GLN A 150 " pdb=" C GLN A 150 " pdb=" O GLN A 150 " ideal model delta sigma weight residual 120.32 115.83 4.49 1.11e+00 8.12e-01 1.64e+01 angle pdb=" CA VAL A 274 " pdb=" C VAL A 274 " pdb=" O VAL A 274 " ideal model delta sigma weight residual 120.85 116.85 4.00 1.06e+00 8.90e-01 1.43e+01 angle pdb=" CA THR A 275 " pdb=" C THR A 275 " pdb=" O THR A 275 " ideal model delta sigma weight residual 119.97 115.76 4.21 1.15e+00 7.56e-01 1.34e+01 angle pdb=" CA PHE A 273 " pdb=" C PHE A 273 " pdb=" O PHE A 273 " ideal model delta sigma weight residual 120.82 117.24 3.58 1.05e+00 9.07e-01 1.16e+01 ... (remaining 4264 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.92: 1699 15.92 - 31.83: 138 31.83 - 47.75: 26 47.75 - 63.66: 2 63.66 - 79.58: 1 Dihedral angle restraints: 1866 sinusoidal: 685 harmonic: 1181 Sorted by residual: dihedral pdb=" CA ILE A 73 " pdb=" C ILE A 73 " pdb=" N SER A 74 " pdb=" CA SER A 74 " ideal model delta harmonic sigma weight residual -180.00 -154.13 -25.87 0 5.00e+00 4.00e-02 2.68e+01 dihedral pdb=" CA PRO A 109 " pdb=" C PRO A 109 " pdb=" N GLY A 110 " pdb=" CA GLY A 110 " ideal model delta harmonic sigma weight residual -180.00 -154.97 -25.03 0 5.00e+00 4.00e-02 2.51e+01 dihedral pdb=" CA GLY A 221 " pdb=" C GLY A 221 " pdb=" N VAL A 222 " pdb=" CA VAL A 222 " ideal model delta harmonic sigma weight residual -180.00 -159.02 -20.98 0 5.00e+00 4.00e-02 1.76e+01 ... (remaining 1863 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.053: 411 0.053 - 0.106: 109 0.106 - 0.159: 13 0.159 - 0.212: 3 0.212 - 0.266: 2 Chirality restraints: 538 Sorted by residual: chirality pdb=" CB VAL A 224 " pdb=" CA VAL A 224 " pdb=" CG1 VAL A 224 " pdb=" CG2 VAL A 224 " both_signs ideal model delta sigma weight residual False -2.63 -2.36 -0.27 2.00e-01 2.50e+01 1.76e+00 chirality pdb=" CB VAL A 225 " pdb=" CA VAL A 225 " pdb=" CG1 VAL A 225 " pdb=" CG2 VAL A 225 " both_signs ideal model delta sigma weight residual False -2.63 -2.41 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA GLN A 150 " pdb=" N GLN A 150 " pdb=" C GLN A 150 " pdb=" CB GLN A 150 " both_signs ideal model delta sigma weight residual False 2.51 2.70 -0.19 2.00e-01 2.50e+01 9.45e-01 ... (remaining 535 not shown) Planarity restraints: 524 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA A 147 " 0.015 2.00e-02 2.50e+03 2.87e-02 8.23e+00 pdb=" C ALA A 147 " -0.050 2.00e-02 2.50e+03 pdb=" O ALA A 147 " 0.019 2.00e-02 2.50e+03 pdb=" N ASN A 148 " 0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 299 " 0.022 2.00e-02 2.50e+03 1.80e-02 6.46e+00 pdb=" CG TYR A 299 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 299 " 0.010 2.00e-02 2.50e+03 pdb=" CD2 TYR A 299 " 0.000 2.00e-02 2.50e+03 pdb=" CE1 TYR A 299 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 TYR A 299 " 0.006 2.00e-02 2.50e+03 pdb=" CZ TYR A 299 " 0.008 2.00e-02 2.50e+03 pdb=" OH TYR A 299 " -0.000 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA VAL A 224 " 0.010 2.00e-02 2.50e+03 2.06e-02 4.25e+00 pdb=" C VAL A 224 " -0.036 2.00e-02 2.50e+03 pdb=" O VAL A 224 " 0.013 2.00e-02 2.50e+03 pdb=" N VAL A 225 " 0.013 2.00e-02 2.50e+03 ... (remaining 521 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.76: 560 2.76 - 3.29: 3550 3.29 - 3.83: 4990 3.83 - 4.36: 5548 4.36 - 4.90: 9361 Nonbonded interactions: 24009 Sorted by model distance: nonbonded pdb=" O ALA A 71 " pdb=" OG1 THR A 166 " model vdw 2.223 2.440 nonbonded pdb=" O SER A 278 " pdb=" OG1 THR A 281 " model vdw 2.294 2.440 nonbonded pdb=" O VAL A 151 " pdb=" OG1 THR A 154 " model vdw 2.309 2.440 nonbonded pdb=" O LEU A 228 " pdb=" OG1 THR A 232 " model vdw 2.383 2.440 nonbonded pdb=" O VAL A 412 " pdb=" OG1 THR A 415 " model vdw 2.387 2.440 ... (remaining 24004 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: 4 Type Number sf(0) Gaussians S 18 5.16 5 C 2029 2.51 5 N 490 2.21 5 O 546 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=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as group one per residue Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 0.900 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 3.450 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.020 Process input model: 13.680 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.010 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.820 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.040 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7682 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 : 0.007 0.057 3136 Z= 0.471 Angle : 0.769 5.594 4269 Z= 0.463 Chirality : 0.048 0.266 538 Planarity : 0.005 0.029 524 Dihedral : 11.978 79.581 1116 Min Nonbonded Distance : 2.223 Molprobity Statistics. All-atom Clashscore : 5.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.40 % Favored : 96.60 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.28 (0.34), residues: 412 helix: -1.19 (0.24), residues: 321 sheet: None (None), residues: 0 loop : -2.03 (0.57), residues: 91 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 114 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.321 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 114 average time/residue: 0.1497 time to fit residues: 20.5210 Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.363 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5093 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 34 optimal weight: 0.4980 chunk 31 optimal weight: 0.9980 chunk 17 optimal weight: 0.3980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.5980 chunk 16 optimal weight: 0.5980 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.3980 chunk 19 optimal weight: 0.6980 chunk 23 optimal weight: 0.6980 chunk 37 optimal weight: 0.0170 overall best weight: 0.3818 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 32 HIS Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7658 moved from start: 0.2593 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3136 Z= 0.206 Angle : 0.659 6.443 4269 Z= 0.335 Chirality : 0.042 0.152 538 Planarity : 0.004 0.025 524 Dihedral : 5.344 25.291 441 Min Nonbonded Distance : 2.245 Molprobity Statistics. All-atom Clashscore : 7.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.46 % Favored : 98.54 % Rotamer Outliers : 2.45 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 0.85 (0.39), residues: 412 helix: 1.21 (0.27), residues: 329 sheet: None (None), residues: 0 loop : -1.94 (0.57), residues: 83 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 95 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 87 time to evaluate : 0.370 Fit side-chains outliers start: 8 outliers final: 6 residues processed: 89 average time/residue: 0.1205 time to fit residues: 13.5904 Evaluate side-chains 83 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 77 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 0 residues processed: 6 average time/residue: 0.0317 time to fit residues: 0.7759 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 20 optimal weight: 0.6980 chunk 11 optimal weight: 4.9990 chunk 30 optimal weight: 0.9980 chunk 25 optimal weight: 0.0370 chunk 10 optimal weight: 0.7980 chunk 37 optimal weight: 3.9990 chunk 40 optimal weight: 0.9980 chunk 33 optimal weight: 0.9980 chunk 36 optimal weight: 0.3980 chunk 12 optimal weight: 0.4980 chunk 29 optimal weight: 0.9990 overall best weight: 0.4858 ------------------------------------------------------------------------------- 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: 0.7676 moved from start: 0.3141 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3136 Z= 0.210 Angle : 0.642 8.021 4269 Z= 0.320 Chirality : 0.043 0.167 538 Planarity : 0.003 0.021 524 Dihedral : 5.196 28.296 441 Min Nonbonded Distance : 2.271 Molprobity Statistics. All-atom Clashscore : 9.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.52 (0.40), residues: 412 helix: 1.67 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.77 (0.58), residues: 82 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 85 time to evaluate : 0.351 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 86 average time/residue: 0.1168 time to fit residues: 12.7602 Evaluate side-chains 80 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 77 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0328 time to fit residues: 0.6636 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 36 optimal weight: 0.5980 chunk 28 optimal weight: 0.9990 chunk 19 optimal weight: 0.7980 chunk 4 optimal weight: 0.7980 chunk 17 optimal weight: 0.0670 chunk 25 optimal weight: 0.0970 chunk 37 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 35 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 chunk 33 optimal weight: 0.8980 overall best weight: 0.4516 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7668 moved from start: 0.3605 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.041 3136 Z= 0.204 Angle : 0.635 9.425 4269 Z= 0.311 Chirality : 0.042 0.157 538 Planarity : 0.003 0.022 524 Dihedral : 5.005 28.920 441 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.91 % Favored : 97.09 % Rotamer Outliers : 3.37 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.86 (0.41), residues: 412 helix: 1.89 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.62 (0.59), residues: 81 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 86 time to evaluate : 0.370 Fit side-chains outliers start: 11 outliers final: 7 residues processed: 91 average time/residue: 0.1214 time to fit residues: 13.9620 Evaluate side-chains 85 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 78 time to evaluate : 0.354 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0344 time to fit residues: 0.9171 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 22 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 29 optimal weight: 1.9990 chunk 16 optimal weight: 0.4980 chunk 33 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 20 optimal weight: 0.9990 chunk 35 optimal weight: 3.9990 chunk 10 optimal weight: 2.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.0470 overall best weight: 0.9084 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.3889 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.057 3136 Z= 0.271 Angle : 0.696 10.604 4269 Z= 0.344 Chirality : 0.044 0.159 538 Planarity : 0.004 0.044 524 Dihedral : 5.202 28.708 441 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 2.76 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.41), residues: 412 helix: 1.72 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.45 (0.62), residues: 82 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 81 time to evaluate : 0.356 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 7 residues processed: 84 average time/residue: 0.1143 time to fit residues: 12.2816 Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 74 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 0 residues processed: 7 average time/residue: 0.0362 time to fit residues: 0.9272 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 23 optimal weight: 0.7980 chunk 9 optimal weight: 0.6980 chunk 39 optimal weight: 1.9990 chunk 32 optimal weight: 0.9990 chunk 18 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 13 optimal weight: 0.9980 chunk 20 optimal weight: 0.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 overall best weight: 0.8380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 318 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.4147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.045 3136 Z= 0.259 Angle : 0.701 11.229 4269 Z= 0.348 Chirality : 0.044 0.161 538 Planarity : 0.003 0.025 524 Dihedral : 5.207 29.104 441 Min Nonbonded Distance : 2.238 Molprobity Statistics. All-atom Clashscore : 11.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.64 (0.41), residues: 412 helix: 1.69 (0.28), residues: 330 sheet: None (None), residues: 0 loop : -1.38 (0.63), residues: 82 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 77 time to evaluate : 0.359 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 78 average time/residue: 0.1116 time to fit residues: 11.2028 Evaluate side-chains 79 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.370 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0351 time to fit residues: 0.6238 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.6980 chunk 22 optimal weight: 2.9990 chunk 33 optimal weight: 3.9990 chunk 39 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 18 optimal weight: 0.9990 chunk 15 optimal weight: 0.9990 chunk 23 optimal weight: 0.9980 chunk 11 optimal weight: 2.9990 chunk 7 optimal weight: 0.0170 chunk 25 optimal weight: 0.8980 overall best weight: 0.7220 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7746 moved from start: 0.4380 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.042 3136 Z= 0.244 Angle : 0.708 12.172 4269 Z= 0.353 Chirality : 0.044 0.164 538 Planarity : 0.004 0.047 524 Dihedral : 5.233 28.826 441 Min Nonbonded Distance : 2.235 Molprobity Statistics. All-atom Clashscore : 11.93 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.41), residues: 412 helix: 1.65 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.34 (0.65), residues: 81 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 87 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 82 time to evaluate : 0.396 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 85 average time/residue: 0.1338 time to fit residues: 14.1299 Evaluate side-chains 79 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 77 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0323 time to fit residues: 0.5938 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 26 optimal weight: 0.6980 chunk 19 optimal weight: 0.8980 chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 0.5980 chunk 35 optimal weight: 0.3980 chunk 37 optimal weight: 0.7980 chunk 34 optimal weight: 0.5980 chunk 36 optimal weight: 0.5980 chunk 22 optimal weight: 0.9990 chunk 16 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 overall best weight: 0.5780 ------------------------------------------------------------------------------- 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: 0.7703 moved from start: 0.4707 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3136 Z= 0.221 Angle : 0.702 12.041 4269 Z= 0.346 Chirality : 0.044 0.226 538 Planarity : 0.003 0.024 524 Dihedral : 5.126 29.187 441 Min Nonbonded Distance : 2.212 Molprobity Statistics. All-atom Clashscore : 12.09 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.43 % Favored : 97.57 % Rotamer Outliers : 1.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.68 (0.41), residues: 412 helix: 1.71 (0.28), residues: 331 sheet: None (None), residues: 0 loop : -1.34 (0.65), residues: 81 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 81 time to evaluate : 0.343 Fit side-chains outliers start: 5 outliers final: 3 residues processed: 83 average time/residue: 0.1309 time to fit residues: 13.6770 Evaluate side-chains 81 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 78 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0313 time to fit residues: 0.6116 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 11 optimal weight: 4.9990 chunk 33 optimal weight: 3.9990 chunk 34 optimal weight: 0.9990 chunk 36 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 38 optimal weight: 0.7980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.9980 chunk 27 optimal weight: 3.9990 chunk 40 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 overall best weight: 0.9184 ------------------------------------------------------------------------------- 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: 0.7750 moved from start: 0.4842 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.046 3136 Z= 0.277 Angle : 0.749 12.747 4269 Z= 0.370 Chirality : 0.045 0.212 538 Planarity : 0.004 0.052 524 Dihedral : 5.328 29.434 441 Min Nonbonded Distance : 2.173 Molprobity Statistics. All-atom Clashscore : 12.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 1.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.61 (0.41), residues: 412 helix: 1.64 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.06 (0.68), residues: 87 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 85 time to evaluate : 0.351 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 86 average time/residue: 0.1348 time to fit residues: 14.3235 Evaluate side-chains 85 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 82 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0402 time to fit residues: 0.6861 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 32 optimal weight: 0.9980 chunk 3 optimal weight: 2.9990 chunk 25 optimal weight: 2.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.9980 chunk 9 optimal weight: 0.9980 chunk 29 optimal weight: 0.7980 chunk 4 optimal weight: 0.6980 chunk 13 optimal weight: 1.9990 chunk 33 optimal weight: 0.4980 chunk 6 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7717 moved from start: 0.4995 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.044 3136 Z= 0.236 Angle : 0.724 13.110 4269 Z= 0.356 Chirality : 0.044 0.222 538 Planarity : 0.004 0.049 524 Dihedral : 5.282 29.345 441 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 11.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.79 (0.41), residues: 412 helix: 1.76 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -0.99 (0.67), residues: 87 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 824 Ramachandran restraints generated. 412 Oldfield, 0 Emsley, 412 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 85 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.376 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 85 average time/residue: 0.1319 time to fit residues: 14.1015 Evaluate side-chains 85 residues out of total 326 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 85 time to evaluate : 0.355 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4854 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 41 random chunks: chunk 28 optimal weight: 0.7980 chunk 1 optimal weight: 0.6980 chunk 23 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 27 optimal weight: 1.9990 chunk 26 optimal weight: 1.9990 chunk 24 optimal weight: 2.9990 chunk 16 optimal weight: 0.9990 chunk 15 optimal weight: 0.5980 chunk 40 optimal weight: 0.7980 overall best weight: 0.7780 ------------------------------------------------------------------------------- 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 = 0.3887 r_free = 0.3887 target = 0.159820 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3519 r_free = 0.3519 target = 0.128222 restraints weight = 5653.539| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 44)----------------| | r_work = 0.3553 r_free = 0.3553 target = 0.131043 restraints weight = 3592.579| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 49)----------------| | r_work = 0.3575 r_free = 0.3575 target = 0.132932 restraints weight = 2663.771| |-----------------------------------------------------------------------------| r_work (final): 0.3563 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7834 moved from start: 0.5137 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.032 3136 Z= 0.254 Angle : 0.769 12.976 4269 Z= 0.373 Chirality : 0.045 0.222 538 Planarity : 0.004 0.041 524 Dihedral : 5.301 29.149 441 Min Nonbonded Distance : 2.158 Molprobity Statistics. All-atom Clashscore : 11.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.67 % Favored : 97.33 % Rotamer Outliers : 0.61 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.72 (0.41), residues: 412 helix: 1.72 (0.28), residues: 325 sheet: None (None), residues: 0 loop : -1.03 (0.68), residues: 87 =============================================================================== Job complete usr+sys time: 1012.84 seconds wall clock time: 18 minutes 49.37 seconds (1129.37 seconds total)