Starting phenix.real_space_refine (version: 1.20rc4) on Wed Dec 1 13:29:48 2021 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275.map Found restraint, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275_ligands.cif Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.82 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { restraint_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275_ligands.cif" default_restraint = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275_ligands.cif" real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/12_2021/7lcj_23275_updated.pdb" } resolution = 2.82 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= 0.091 Set stop_for_unknowns flag Set to: True Assert model is a single copy model 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 Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.20rc4-4434/modules/chem_data/mon_lib" Total number of atoms: 3264 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 3264 Number of conformers: 1 Conformer: "" Number of residues, atoms: 408, 3264 Unusual residues: {'UK4': 1} Classifications: {'undetermined': 1, 'water': 17, 'peptide': 390} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375, None: 18} Not linked: pdbres="GLU R 423 " pdbres="UK4 R 501 " Not linked: pdbres="UK4 R 501 " pdbres="HOH R 601 " Not linked: pdbres="HOH R 601 " pdbres="HOH R 602 " Not linked: pdbres="HOH R 602 " pdbres="HOH R 603 " Not linked: pdbres="HOH R 603 " pdbres="HOH R 604 " ... (remaining 13 not shown) Chain breaks: 1 Unresolved non-hydrogen bonds: 16 Unresolved non-hydrogen angles: 19 Unresolved non-hydrogen dihedrals: 13 Unresolved non-hydrogen chiralities: 2 Planarities with less than four sites: {'ASN:plan1': 1} Unresolved non-hydrogen planarities: 3 Time building chain proxies: 2.19, per 1000 atoms: 0.67 Number of scatterers: 3264 At special positions: 0 Unit cell: (60.079, 116.866, 69.955, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 18 16.00 F 1 9.00 O 571 8.00 N 526 7.00 C 2148 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=4, symmetry=0 Simple disulfide: pdb=" SG CYS R 46 " - pdb=" SG CYS R 71 " distance=2.02 Simple disulfide: pdb=" SG CYS R 62 " - pdb=" SG CYS R 104 " distance=2.03 Simple disulfide: pdb=" SG CYS R 85 " - pdb=" SG CYS R 126 " distance=2.03 Simple disulfide: pdb=" SG CYS R 226 " - pdb=" SG CYS R 296 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amimo 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: 1.38 Conformation dependent library (CDL) restraints added in 479.4 milliseconds 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 748 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 12 helices and 0 sheets defined 63.3% alpha, 0.0% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.32 Creating SS restraints... Processing helix chain 'R' and resid 32 through 52 removed outlier: 3.918A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 Processing helix chain 'R' and resid 176 through 200 Processing helix chain 'R' and resid 211 through 221 removed outlier: 3.944A pdb=" N ASP R 215 " --> pdb=" O GLN R 211 " (cutoff:3.500A) removed outlier: 4.411A pdb=" N GLY R 216 " --> pdb=" O HIS R 212 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 256 Processing helix chain 'R' and resid 264 through 275 removed outlier: 3.705A pdb=" N LEU R 268 " --> pdb=" O TRP R 264 " (cutoff:3.500A) Processing helix chain 'R' and resid 277 through 290 removed outlier: 4.031A pdb=" N VAL R 281 " --> pdb=" O LEU R 278 " (cutoff:3.500A) removed outlier: 5.762A pdb=" N VAL R 282 " --> pdb=" O LEU R 279 " (cutoff:3.500A) Proline residue: R 283 - end of helix removed outlier: 4.061A pdb=" N LYS R 288 " --> pdb=" O GLY R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 306 through 337 removed outlier: 3.608A pdb=" N ARG R 310 " --> pdb=" O LEU R 307 " (cutoff:3.500A) removed outlier: 5.020A pdb=" N LEU R 311 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 3.960A pdb=" N ALA R 337 " --> pdb=" O LYS R 334 " (cutoff:3.500A) Processing helix chain 'R' and resid 344 through 360 Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 370 removed outlier: 3.903A pdb=" N PHE R 367 " --> pdb=" O GLU R 364 " (cutoff:3.500A) removed outlier: 3.543A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) removed outlier: 3.900A pdb=" N VAL R 370 " --> pdb=" O PHE R 367 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 403 removed outlier: 4.917A pdb=" N PHE R 393 " --> pdb=" O SER R 389 " (cutoff:3.500A) removed outlier: 4.760A pdb=" N GLN R 394 " --> pdb=" O PHE R 390 " (cutoff:3.500A) removed outlier: 5.093A pdb=" N GLY R 395 " --> pdb=" O THR R 391 " (cutoff:3.500A) removed outlier: 5.137A pdb=" N LEU R 396 " --> pdb=" O SER R 392 " (cutoff:3.500A) Processing helix chain 'R' and resid 407 through 422 removed outlier: 3.547A pdb=" N TRP R 420 " --> pdb=" O SER R 416 " (cutoff:3.500A) 175 hydrogen bonds defined for protein. 432 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: 0.80 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: 1.13 - 1.27: 487 1.27 - 1.41: 974 1.41 - 1.54: 1861 1.54 - 1.68: 6 1.68 - 1.82: 23 Bond restraints: 3351 Sorted by residual: bond pdb=" C29 UK4 R 501 " pdb=" O30 UK4 R 501 " ideal model delta sigma weight residual 1.499 1.425 0.074 2.00e-02 2.50e+03 1.38e+01 bond pdb=" C LEU R 89 " pdb=" N PRO R 90 " ideal model delta sigma weight residual 1.335 1.380 -0.045 1.28e-02 6.10e+03 1.24e+01 bond pdb=" C TRP R 72 " pdb=" N PRO R 73 " ideal model delta sigma weight residual 1.326 1.375 -0.049 1.44e-02 4.82e+03 1.17e+01 bond pdb=" N LEU R 356 " pdb=" CA LEU R 356 " ideal model delta sigma weight residual 1.456 1.500 -0.045 1.35e-02 5.49e+03 1.09e+01 bond pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " ideal model delta sigma weight residual 1.587 1.525 0.062 2.00e-02 2.50e+03 9.67e+00 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 89.13 - 107.18: 108 107.18 - 125.23: 4368 125.23 - 143.28: 94 143.28 - 161.33: 0 161.33 - 179.39: 1 Bond angle restraints: 4571 Sorted by residual: angle pdb=" C14 UK4 R 501 " pdb=" N25 UK4 R 501 " pdb=" C26 UK4 R 501 " ideal model delta sigma weight residual 93.53 125.83 -32.30 3.00e+00 1.11e-01 1.16e+02 angle pdb=" C13 UK4 R 501 " pdb=" C14 UK4 R 501 " pdb=" N15 UK4 R 501 " ideal model delta sigma weight residual 93.41 124.83 -31.42 3.00e+00 1.11e-01 1.10e+02 angle pdb=" C18 UK4 R 501 " pdb=" C19 UK4 R 501 " pdb=" C20 UK4 R 501 " ideal model delta sigma weight residual 90.14 119.52 -29.38 3.00e+00 1.11e-01 9.59e+01 angle pdb=" C20 UK4 R 501 " pdb=" C19 UK4 R 501 " pdb=" C23 UK4 R 501 " ideal model delta sigma weight residual 142.61 120.28 22.33 3.00e+00 1.11e-01 5.54e+01 angle pdb=" C24 UK4 R 501 " pdb=" N25 UK4 R 501 " pdb=" C26 UK4 R 501 " ideal model delta sigma weight residual 147.63 125.80 21.83 3.00e+00 1.11e-01 5.29e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 34.39: 1877 34.39 - 68.78: 36 68.78 - 103.17: 3 103.17 - 137.56: 0 137.56 - 171.95: 2 Dihedral angle restraints: 1918 sinusoidal: 762 harmonic: 1156 Sorted by residual: dihedral pdb=" C THR R 362 " pdb=" N THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta harmonic sigma weight residual -122.00 -143.04 21.04 0 2.50e+00 1.60e-01 7.08e+01 dihedral pdb=" CB CYS R 46 " pdb=" SG CYS R 46 " pdb=" SG CYS R 71 " pdb=" CB CYS R 71 " ideal model delta sinusoidal sigma weight residual -86.00 -142.72 56.72 1 1.00e+01 1.00e-02 4.33e+01 dihedral pdb=" C TYR R 148 " pdb=" N TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual -122.60 -138.17 15.57 0 2.50e+00 1.60e-01 3.88e+01 ... (remaining 1915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 1.025: 496 1.025 - 2.050: 0 2.050 - 3.076: 0 3.076 - 4.101: 0 4.101 - 5.126: 1 Chirality restraints: 497 Sorted by residual: chirality pdb=" C09 UK4 R 501 " pdb=" C08 UK4 R 501 " pdb=" C10 UK4 R 501 " pdb=" C32 UK4 R 501 " both_signs ideal model delta sigma weight residual False 2.70 -2.43 5.13 2.00e-01 2.50e+01 6.57e+02 chirality pdb=" CA THR R 362 " pdb=" N THR R 362 " pdb=" C THR R 362 " pdb=" CB THR R 362 " both_signs ideal model delta sigma weight residual False 2.53 1.80 0.72 2.00e-01 2.50e+01 1.31e+01 chirality pdb=" CA TYR R 148 " pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CB TYR R 148 " both_signs ideal model delta sigma weight residual False 2.51 1.98 0.53 2.00e-01 2.50e+01 7.02e+00 ... (remaining 494 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA THR R 355 " 0.013 2.00e-02 2.50e+03 2.58e-02 6.66e+00 pdb=" C THR R 355 " -0.045 2.00e-02 2.50e+03 pdb=" O THR R 355 " 0.016 2.00e-02 2.50e+03 pdb=" N LEU R 356 " 0.015 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 146 " -0.010 2.00e-02 2.50e+03 2.12e-02 4.47e+00 pdb=" C ILE R 146 " 0.037 2.00e-02 2.50e+03 pdb=" O ILE R 146 " -0.014 2.00e-02 2.50e+03 pdb=" N ILE R 147 " -0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C VAL R 276 " 0.033 5.00e-02 4.00e+02 4.89e-02 3.82e+00 pdb=" N PRO R 277 " -0.084 5.00e-02 4.00e+02 pdb=" CA PRO R 277 " 0.025 5.00e-02 4.00e+02 pdb=" CD PRO R 277 " 0.027 5.00e-02 4.00e+02 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.22 - 2.75: 439 2.75 - 3.29: 3232 3.29 - 3.83: 5209 3.83 - 4.36: 6382 4.36 - 4.90: 10621 Nonbonded interactions: 25883 Sorted by model distance: nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.216 2.520 nonbonded pdb=" O GLY R 98 " pdb=" ND1 HIS R 99 " model vdw 2.335 2.520 nonbonded pdb=" O GLU R 408 " pdb=" OE1 GLU R 412 " model vdw 2.335 3.040 nonbonded pdb=" OE2 GLU R 76 " pdb=" OG SER R 79 " model vdw 2.342 2.440 nonbonded pdb=" OD1 ASN R 300 " pdb=" N SER R 301 " model vdw 2.383 2.520 ... (remaining 25878 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: 5 Type Number sf(0) Gaussians S 18 5.16 5 C 2148 2.51 5 N 526 2.21 5 O 571 1.98 5 F 1 1.80 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 Write .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: 0.850 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.070 Check model and map are aligned: 0.060 Convert atoms to be neutral: 0.030 Process input model: 13.030 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Set scattering table: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.890 Set ADP refinement strategy: 0.000 Write .geo file: 0.000 Internal consistency checks: 0.000 Total: 33.030 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8016 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 : 0.010 0.074 3351 Z= 0.635 Angle : 1.506 32.300 4571 Z= 0.844 Chirality : 0.245 5.126 497 Planarity : 0.006 0.049 557 Dihedral : 15.137 171.952 1158 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.57 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 1.16 % Cbeta Deviations : 0.80 % 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: 0.54 (0.41), residues: 386 helix: 1.08 (0.32), residues: 247 sheet: None (None), residues: 0 loop : -0.90 (0.50), residues: 139 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 33 time to evaluate : 0.341 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.9244 time to fit residues: 34.8371 Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.367 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.1380 time to fit residues: 1.6902 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 30 optimal weight: 0.9980 chunk 16 optimal weight: 0.6980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.6980 chunk 31 optimal weight: 2.9990 chunk 12 optimal weight: 0.8980 chunk 19 optimal weight: 0.5980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.6980 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 45 GLN R 212 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7935 moved from start: 0.1327 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.027 3351 Z= 0.186 Angle : 0.623 8.358 4571 Z= 0.317 Chirality : 0.038 0.132 497 Planarity : 0.005 0.050 557 Dihedral : 12.715 177.989 439 Min Nonbonded Distance : 2.299 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 1.45 % 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: 1.23 (0.42), residues: 386 helix: 1.76 (0.33), residues: 247 sheet: None (None), residues: 0 loop : -0.93 (0.48), residues: 139 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 28 time to evaluate : 0.350 Fit side-chains outliers start: 5 outliers final: 2 residues processed: 30 average time/residue: 0.8555 time to fit residues: 27.0727 Evaluate side-chains 25 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.390 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.2615 time to fit residues: 1.8429 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 30 optimal weight: 0.9980 chunk 24 optimal weight: 0.0670 chunk 10 optimal weight: 0.7980 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.5980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 0.8980 chunk 35 optimal weight: 1.9990 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 0.6318 ------------------------------------------------------------------------------- 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: 0.7921 moved from start: 0.1726 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 3351 Z= 0.161 Angle : 0.554 7.957 4571 Z= 0.278 Chirality : 0.036 0.122 497 Planarity : 0.005 0.053 557 Dihedral : 12.326 172.176 439 Min Nonbonded Distance : 2.294 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.16 % 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: 1.32 (0.43), residues: 386 helix: 1.82 (0.33), residues: 252 sheet: None (None), residues: 0 loop : -0.98 (0.49), residues: 134 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.378 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 28 average time/residue: 0.8921 time to fit residues: 26.3199 Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 0.9926 time to fit residues: 1.5437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 4 optimal weight: 4.9990 chunk 17 optimal weight: 2.9990 chunk 24 optimal weight: 0.0170 chunk 36 optimal weight: 0.0570 chunk 38 optimal weight: 6.9990 chunk 19 optimal weight: 0.9990 chunk 34 optimal weight: 2.9990 chunk 10 optimal weight: 0.9990 chunk 32 optimal weight: 0.9990 chunk 21 optimal weight: 0.6980 chunk 0 optimal weight: 4.9990 overall best weight: 0.5540 ------------------------------------------------------------------------------- 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: 0.7907 moved from start: 0.1931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.025 3351 Z= 0.142 Angle : 0.526 7.862 4571 Z= 0.263 Chirality : 0.035 0.114 497 Planarity : 0.005 0.056 557 Dihedral : 12.159 169.037 439 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % Rotamer Outliers : 2.33 % 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: 1.37 (0.43), residues: 386 helix: 1.86 (0.33), residues: 252 sheet: None (None), residues: 0 loop : -0.96 (0.50), residues: 134 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 34 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 26 time to evaluate : 0.383 Fit side-chains outliers start: 8 outliers final: 4 residues processed: 32 average time/residue: 0.7704 time to fit residues: 26.1224 Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 26 time to evaluate : 0.378 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 3 residues processed: 1 average time/residue: 0.0333 time to fit residues: 0.5949 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 28 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 chunk 9 optimal weight: 40.0000 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 2.9990 chunk 22 optimal weight: 0.0370 overall best weight: 0.6058 ------------------------------------------------------------------------------- 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: 0.7917 moved from start: 0.2089 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.026 3351 Z= 0.147 Angle : 0.530 8.128 4571 Z= 0.261 Chirality : 0.035 0.117 497 Planarity : 0.005 0.055 557 Dihedral : 12.236 170.988 439 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.74 % 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: 1.40 (0.43), residues: 386 helix: 1.87 (0.34), residues: 252 sheet: None (None), residues: 0 loop : -0.92 (0.50), residues: 134 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 32 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.440 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 31 average time/residue: 0.7849 time to fit residues: 25.7773 Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.374 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5139 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 9 optimal weight: 5.9990 chunk 38 optimal weight: 0.9980 chunk 32 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 0.9980 chunk 12 optimal weight: 0.6980 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.8980 chunk 4 optimal weight: 5.9990 chunk 22 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.9180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: R 177 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7954 moved from start: 0.2111 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.031 3351 Z= 0.185 Angle : 0.549 8.203 4571 Z= 0.271 Chirality : 0.036 0.123 497 Planarity : 0.005 0.056 557 Dihedral : 12.532 176.506 439 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 2.33 % 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: 1.31 (0.43), residues: 386 helix: 1.77 (0.33), residues: 251 sheet: None (None), residues: 0 loop : -0.86 (0.49), residues: 135 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 35 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 27 time to evaluate : 0.392 Fit side-chains outliers start: 8 outliers final: 5 residues processed: 34 average time/residue: 0.7146 time to fit residues: 25.7720 Evaluate side-chains 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.360 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 0.0325 time to fit residues: 0.5691 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 21 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 38 optimal weight: 0.9980 chunk 24 optimal weight: 0.0770 chunk 23 optimal weight: 1.9990 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 1.9990 chunk 26 optimal weight: 4.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.6138 ------------------------------------------------------------------------------- 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: 0.7924 moved from start: 0.2260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3351 Z= 0.145 Angle : 0.518 8.005 4571 Z= 0.256 Chirality : 0.035 0.114 497 Planarity : 0.005 0.056 557 Dihedral : 12.270 172.273 439 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 1.74 % 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: 1.39 (0.43), residues: 386 helix: 1.80 (0.34), residues: 254 sheet: None (None), residues: 0 loop : -0.83 (0.50), residues: 132 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.360 Fit side-chains outliers start: 6 outliers final: 4 residues processed: 31 average time/residue: 0.7685 time to fit residues: 25.2188 Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4968 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 3 optimal weight: 7.9990 chunk 30 optimal weight: 0.4980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.9990 chunk 33 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 15 optimal weight: 1.9990 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 0.4980 chunk 23 optimal weight: 0.9980 overall best weight: 0.6380 ------------------------------------------------------------------------------- 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: 0.7926 moved from start: 0.2336 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.027 3351 Z= 0.151 Angle : 0.519 7.990 4571 Z= 0.257 Chirality : 0.035 0.116 497 Planarity : 0.005 0.055 557 Dihedral : 12.270 172.082 439 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 1.16 % 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: 1.39 (0.43), residues: 386 helix: 1.78 (0.34), residues: 254 sheet: None (None), residues: 0 loop : -0.78 (0.51), residues: 132 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.386 Fit side-chains outliers start: 4 outliers final: 4 residues processed: 29 average time/residue: 0.8344 time to fit residues: 25.5519 Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.385 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4776 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 37 optimal weight: 0.9990 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 0.6980 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 0.9980 chunk 31 optimal weight: 4.9990 chunk 3 optimal weight: 7.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.8980 overall best weight: 0.8180 ------------------------------------------------------------------------------- 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: 0.7946 moved from start: 0.2330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 3351 Z= 0.171 Angle : 0.534 8.183 4571 Z= 0.263 Chirality : 0.036 0.121 497 Planarity : 0.005 0.055 557 Dihedral : 12.455 175.523 439 Min Nonbonded Distance : 2.254 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 1.16 % 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: 1.34 (0.43), residues: 386 helix: 1.72 (0.33), residues: 254 sheet: None (None), residues: 0 loop : -0.74 (0.51), residues: 132 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 31 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 27 time to evaluate : 0.341 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 31 average time/residue: 0.8603 time to fit residues: 28.1138 Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5233 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 33 optimal weight: 2.9990 chunk 9 optimal weight: 20.0000 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 9.9990 chunk 31 optimal weight: 0.0030 chunk 13 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 chunk 5 optimal weight: 6.9990 chunk 27 optimal weight: 1.9990 chunk 1 optimal weight: 1.9990 overall best weight: 1.1596 ------------------------------------------------------------------------------- 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: 0.7979 moved from start: 0.2286 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.035 3351 Z= 0.221 Angle : 0.568 8.432 4571 Z= 0.279 Chirality : 0.037 0.123 497 Planarity : 0.005 0.054 557 Dihedral : 12.708 179.213 439 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 0.87 % 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: 1.19 (0.43), residues: 386 helix: 1.59 (0.33), residues: 253 sheet: None (None), residues: 0 loop : -0.73 (0.51), residues: 133 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 772 Ramachandran restraints generated. 386 Oldfield, 0 Emsley, 386 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 26 time to evaluate : 0.389 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 29 average time/residue: 0.8259 time to fit residues: 25.3309 Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.366 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 3 residues processed: 0 time to fit residues: 0.5179 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 40 random chunks: chunk 22 optimal weight: 0.9980 chunk 36 optimal weight: 1.9990 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.7980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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 = 0.4224 r_free = 0.4224 target = 0.202405 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 53)----------------| | r_work = 0.3469 r_free = 0.3469 target = 0.126160 restraints weight = 3233.458| |-----------------------------------------------------------------------------| r_work (start): 0.3442 rms_B_bonded: 2.32 r_work: 0.3418 rms_B_bonded: 2.11 restraints_weight: 0.5000 r_work: 0.3399 rms_B_bonded: 2.12 restraints_weight: 0.2500 r_work: 0.3379 rms_B_bonded: 2.23 restraints_weight: 0.1250 r_work: 0.3356 rms_B_bonded: 2.42 restraints_weight: 0.0625 r_work: 0.3329 rms_B_bonded: 2.72 restraints_weight: 0.0312 r_work: 0.3297 rms_B_bonded: 3.15 restraints_weight: 0.0156 r_work: 0.3258 rms_B_bonded: 3.74 restraints_weight: 0.0078 r_work: 0.3208 rms_B_bonded: 4.59 restraints_weight: 0.0039 r_work (final): 0.3208 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8240 moved from start: 0.2405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.107 3351 Z= 0.240 Angle : 0.569 8.285 4571 Z= 0.286 Chirality : 0.036 0.118 497 Planarity : 0.005 0.055 557 Dihedral : 12.451 175.535 439 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.81 % Favored : 98.19 % Rotamer Outliers : 1.16 % 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: 1.29 (0.43), residues: 386 helix: 1.68 (0.34), residues: 254 sheet: None (None), residues: 0 loop : -0.77 (0.51), residues: 132 =============================================================================== Job complete usr+sys time: 1224.35 seconds wall clock time: 22 minutes 30.72 seconds (1350.72 seconds total)