Starting phenix.real_space_refine (version: dev) on Tue Nov 29 12:23:22 2022 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/11_2022/7lck_23276_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/11_2022/7lck_23276.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.24 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/11_2022/7lck_23276.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/11_2022/7lck_23276.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/11_2022/7lck_23276_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lck_23276/11_2022/7lck_23276_updated.pdb" } resolution = 3.24 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= 0.001 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: 3258 Number of models: 1 Model: "" Number of chains: 1 Chain: "R" Number of atoms: 3258 Number of conformers: 1 Conformer: "" Number of residues, atoms: 402, 3258 Unusual residues: {'UK4': 1} Classifications: {'peptide': 390, 'undetermined': 1, 'water': 11} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 14, 'TRANS': 375, None: 12} 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 7 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: 2.47, per 1000 atoms: 0.76 Number of scatterers: 3258 At special positions: 0 Unit cell: (60.8, 115.9, 69.35, 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 565 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=2.04 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 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: 1.31 Conformation dependent library (CDL) restraints added in 454.7 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: 14 helices and 1 sheets defined 62.3% alpha, 2.1% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing helix chain 'R' and resid 32 through 52 removed outlier: 3.690A pdb=" N GLU R 41 " --> pdb=" O GLN R 37 " (cutoff:3.500A) removed outlier: 3.730A pdb=" N THR R 51 " --> pdb=" O GLN R 47 " (cutoff:3.500A) Processing helix chain 'R' and resid 137 through 168 Processing helix chain 'R' and resid 176 through 200 removed outlier: 3.923A pdb=" N PHE R 195 " --> pdb=" O ALA R 191 " (cutoff:3.500A) Processing helix chain 'R' and resid 211 through 221 removed outlier: 5.230A pdb=" N ASP R 215 " --> pdb=" O HIS R 212 " (cutoff:3.500A) removed outlier: 3.578A pdb=" N LEU R 217 " --> pdb=" O TRP R 214 " (cutoff:3.500A) removed outlier: 3.517A pdb=" N LEU R 218 " --> pdb=" O ASP R 215 " (cutoff:3.500A) removed outlier: 4.042A pdb=" N SER R 219 " --> pdb=" O GLY R 216 " (cutoff:3.500A) Processing helix chain 'R' and resid 225 through 255 removed outlier: 3.610A pdb=" N MET R 233 " --> pdb=" O VAL R 229 " (cutoff:3.500A) removed outlier: 3.776A pdb=" N ASN R 240 " --> pdb=" O CYS R 236 " (cutoff:3.500A) removed outlier: 3.607A pdb=" N TYR R 241 " --> pdb=" O VAL R 237 " (cutoff:3.500A) removed outlier: 3.744A pdb=" N LEU R 244 " --> pdb=" O ASN R 240 " (cutoff:3.500A) removed outlier: 3.886A pdb=" N GLU R 247 " --> pdb=" O TRP R 243 " (cutoff:3.500A) Processing helix chain 'R' and resid 262 through 274 Processing helix chain 'R' and resid 277 through 279 No H-bonds generated for 'chain 'R' and resid 277 through 279' Processing helix chain 'R' and resid 281 through 291 removed outlier: 3.616A pdb=" N TYR R 289 " --> pdb=" O GLY R 285 " (cutoff:3.500A) Processing helix chain 'R' and resid 305 through 336 removed outlier: 3.538A pdb=" N ILE R 308 " --> pdb=" O TYR R 305 " (cutoff:3.500A) removed outlier: 3.538A pdb=" N ARG R 310 " --> pdb=" O LEU R 307 " (cutoff:3.500A) removed outlier: 5.016A pdb=" N LEU R 311 " --> pdb=" O ILE R 308 " (cutoff:3.500A) Proline residue: R 312 - end of helix removed outlier: 4.005A pdb=" N VAL R 332 " --> pdb=" O CYS R 329 " (cutoff:3.500A) Processing helix chain 'R' and resid 342 through 360 removed outlier: 4.280A pdb=" N LYS R 346 " --> pdb=" O LYS R 342 " (cutoff:3.500A) Proline residue: R 358 - end of helix Processing helix chain 'R' and resid 362 through 369 removed outlier: 3.502A pdb=" N VAL R 365 " --> pdb=" O THR R 362 " (cutoff:3.500A) removed outlier: 3.793A pdb=" N ALA R 368 " --> pdb=" O VAL R 365 " (cutoff:3.500A) Processing helix chain 'R' and resid 378 through 390 removed outlier: 3.552A pdb=" N GLU R 387 " --> pdb=" O LYS R 383 " (cutoff:3.500A) Processing helix chain 'R' and resid 394 through 401 Processing helix chain 'R' and resid 407 through 422 removed outlier: 4.099A pdb=" N LEU R 422 " --> pdb=" O GLU R 418 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'R' and resid 80 through 84 removed outlier: 3.611A pdb=" N ARG R 102 " --> pdb=" O VAL R 81 " (cutoff:3.500A) removed outlier: 3.756A pdb=" N VAL R 83 " --> pdb=" O VAL R 100 " (cutoff:3.500A) 165 hydrogen bonds defined for protein. 408 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.78 Time building geometry restraints manager: 1.41 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: 980 1.41 - 1.54: 1857 1.54 - 1.68: 4 1.68 - 1.82: 23 Bond restraints: 3351 Sorted by residual: bond pdb=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.417 0.118 2.00e-02 2.50e+03 3.47e+01 bond pdb=" C38 UK4 R 501 " pdb=" C39 UK4 R 501 " ideal model delta sigma weight residual 1.427 1.525 -0.098 2.00e-02 2.50e+03 2.42e+01 bond pdb=" C28 UK4 R 501 " pdb=" C29 UK4 R 501 " ideal model delta sigma weight residual 1.529 1.448 0.081 2.00e-02 2.50e+03 1.65e+01 bond pdb=" CA SER R 392 " pdb=" CB SER R 392 " ideal model delta sigma weight residual 1.531 1.480 0.051 1.56e-02 4.11e+03 1.08e+01 bond pdb=" C GLU R 387 " pdb=" O GLU R 387 " ideal model delta sigma weight residual 1.236 1.199 0.037 1.15e-02 7.56e+03 1.05e+01 ... (remaining 3346 not shown) Histogram of bond angle deviations from ideal: 89.16 - 107.30: 126 107.30 - 125.44: 4348 125.44 - 143.57: 96 143.57 - 161.71: 0 161.71 - 179.85: 1 Bond angle restraints: 4571 Sorted by residual: angle pdb=" N LEU R 244 " pdb=" CA LEU R 244 " pdb=" C LEU R 244 " ideal model delta sigma weight residual 113.97 104.88 9.09 1.28e+00 6.10e-01 5.04e+01 angle pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta sigma weight residual 110.85 121.54 -10.69 1.70e+00 3.46e-01 3.95e+01 angle pdb=" N LEU R 245 " pdb=" CA LEU R 245 " pdb=" C LEU R 245 " ideal model delta sigma weight residual 112.23 104.36 7.87 1.26e+00 6.30e-01 3.90e+01 angle pdb=" N TYR R 152 " pdb=" CA TYR R 152 " pdb=" C TYR R 152 " ideal model delta sigma weight residual 113.01 106.26 6.75 1.20e+00 6.94e-01 3.16e+01 angle pdb=" C08 UK4 R 501 " pdb=" C09 UK4 R 501 " pdb=" C32 UK4 R 501 " ideal model delta sigma weight residual 110.26 93.70 16.56 3.00e+00 1.11e-01 3.05e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.60: 1694 16.60 - 33.20: 168 33.20 - 49.80: 47 49.80 - 66.40: 7 66.40 - 83.00: 2 Dihedral angle restraints: 1918 sinusoidal: 762 harmonic: 1156 Sorted by residual: 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 -144.20 21.60 0 2.50e+00 1.60e-01 7.46e+01 dihedral pdb=" N TYR R 148 " pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta harmonic sigma weight residual 122.80 141.04 -18.24 0 2.50e+00 1.60e-01 5.32e+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 -44.74 -41.26 1 1.00e+01 1.00e-02 2.38e+01 ... (remaining 1915 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.165: 480 0.165 - 0.329: 14 0.329 - 0.493: 2 0.493 - 0.658: 0 0.658 - 0.822: 1 Chirality restraints: 497 Sorted by residual: 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 1.69 0.82 2.00e-01 2.50e+01 1.69e+01 chirality pdb=" CA PHE R 385 " pdb=" N PHE R 385 " pdb=" C PHE R 385 " pdb=" CB PHE R 385 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.12e+00 chirality pdb=" CA PHE R 367 " pdb=" N PHE R 367 " pdb=" C PHE R 367 " pdb=" CB PHE R 367 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 2.98e+00 ... (remaining 494 not shown) Planarity restraints: 557 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA LEU R 144 " -0.017 2.00e-02 2.50e+03 3.49e-02 1.22e+01 pdb=" C LEU R 144 " 0.060 2.00e-02 2.50e+03 pdb=" O LEU R 144 " -0.022 2.00e-02 2.50e+03 pdb=" N TYR R 145 " -0.021 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ILE R 146 " -0.013 2.00e-02 2.50e+03 2.69e-02 7.25e+00 pdb=" C ILE R 146 " 0.047 2.00e-02 2.50e+03 pdb=" O ILE R 146 " -0.017 2.00e-02 2.50e+03 pdb=" N ILE R 147 " -0.016 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA R 368 " 0.013 2.00e-02 2.50e+03 2.64e-02 6.96e+00 pdb=" C ALA R 368 " -0.046 2.00e-02 2.50e+03 pdb=" O ALA R 368 " 0.017 2.00e-02 2.50e+03 pdb=" N PHE R 369 " 0.016 2.00e-02 2.50e+03 ... (remaining 554 not shown) Histogram of nonbonded interaction distances: 2.16 - 2.71: 89 2.71 - 3.26: 3219 3.26 - 3.80: 4981 3.80 - 4.35: 6333 4.35 - 4.90: 10748 Nonbonded interactions: 25370 Sorted by model distance: nonbonded pdb=" NE2 GLN R 112 " pdb=" O SER R 117 " model vdw 2.160 2.520 nonbonded pdb=" O LEU R 244 " pdb=" ND2 ASN R 320 " model vdw 2.204 2.520 nonbonded pdb=" O LYS R 342 " pdb=" NZ LYS R 346 " model vdw 2.278 2.520 nonbonded pdb=" OD2 ASP R 67 " pdb=" NH2 ARG R 102 " model vdw 2.315 2.520 nonbonded pdb=" OG SER R 31 " pdb=" N LEU R 32 " model vdw 2.422 2.520 ... (remaining 25365 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 565 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 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: 0.600 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 3.480 Check model and map are aligned: 0.050 Convert atoms to be neutral: 0.020 Process input model: 13.820 Find NCS groups from input model: 0.080 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.020 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:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.890 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7850 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.118 3351 Z= 0.488 Angle : 1.050 16.557 4571 Z= 0.664 Chirality : 0.075 0.822 497 Planarity : 0.006 0.040 557 Dihedral : 14.226 82.998 1158 Min Nonbonded Distance : 2.160 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.74 % Favored : 93.26 % Rotamer Outliers : 1.16 % Cbeta Deviations : 1.07 % 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: -0.93 (0.42), residues: 386 helix: -0.15 (0.32), residues: 265 sheet: 0.36 (2.04), residues: 10 loop : -1.62 (0.58), residues: 111 *********************** 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 46 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 42 time to evaluate : 0.406 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 45 average time/residue: 0.1693 time to fit residues: 9.4252 Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.392 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0417 time to fit residues: 0.7103 ------------------------------------------------------------------------------- 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: 0.7980 chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 0.8980 chunk 10 optimal weight: 1.9990 chunk 20 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 12 optimal weight: 0.5980 chunk 19 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 overall best weight: 0.7580 ------------------------------------------------------------------------------- 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: 0.7911 moved from start: 0.1951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.042 3351 Z= 0.215 Angle : 0.614 10.890 4571 Z= 0.311 Chirality : 0.039 0.156 497 Planarity : 0.005 0.041 557 Dihedral : 4.853 38.922 439 Min Nonbonded Distance : 2.302 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.66 % Favored : 95.34 % Rotamer Outliers : 0.29 % 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: -0.49 (0.44), residues: 386 helix: 0.16 (0.33), residues: 267 sheet: 0.28 (1.98), residues: 10 loop : -1.38 (0.59), residues: 109 *********************** 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 32 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 31 time to evaluate : 0.391 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 31 average time/residue: 0.1651 time to fit residues: 6.5808 Evaluate side-chains 24 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5198 ------------------------------------------------------------------------------- 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: 1.9990 chunk 24 optimal weight: 0.2980 chunk 10 optimal weight: 0.5980 chunk 36 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.9980 chunk 12 optimal weight: 0.7980 chunk 29 optimal weight: 0.9980 chunk 35 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 18 optimal weight: 0.0980 overall best weight: 0.5180 ------------------------------------------------------------------------------- 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: 0.7912 moved from start: 0.2226 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.166 Angle : 0.532 7.369 4571 Z= 0.273 Chirality : 0.037 0.122 497 Planarity : 0.005 0.047 557 Dihedral : 4.446 38.432 439 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.58 % 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: -0.09 (0.44), residues: 386 helix: 0.61 (0.33), residues: 261 sheet: 0.33 (1.86), residues: 10 loop : -1.55 (0.56), residues: 115 *********************** 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 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.382 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 26 average time/residue: 0.1419 time to fit residues: 4.9679 Evaluate side-chains 25 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.383 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0325 time to fit residues: 0.5696 ------------------------------------------------------------------------------- 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: 0.0070 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.0670 chunk 36 optimal weight: 0.0010 chunk 38 optimal weight: 0.9990 chunk 19 optimal weight: 1.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 overall best weight: 0.4144 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7904 moved from start: 0.2464 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 3351 Z= 0.156 Angle : 0.520 7.338 4571 Z= 0.267 Chirality : 0.037 0.136 497 Planarity : 0.004 0.050 557 Dihedral : 4.377 38.039 439 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.40 % Favored : 95.60 % 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: 0.15 (0.44), residues: 386 helix: 0.82 (0.34), residues: 261 sheet: 0.37 (1.71), residues: 10 loop : -1.54 (0.57), residues: 115 *********************** 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 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 25 time to evaluate : 0.389 Fit side-chains outliers start: 3 outliers final: 2 residues processed: 26 average time/residue: 0.1512 time to fit residues: 5.3358 Evaluate side-chains 24 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 22 time to evaluate : 0.391 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0533 time to fit residues: 0.6942 ------------------------------------------------------------------------------- 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: 0.7980 chunk 15 optimal weight: 0.6980 chunk 32 optimal weight: 0.0770 chunk 26 optimal weight: 0.1980 chunk 0 optimal weight: 2.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 overall best weight: 0.4938 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7912 moved from start: 0.2587 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.037 3351 Z= 0.155 Angle : 0.529 12.333 4571 Z= 0.265 Chirality : 0.036 0.121 497 Planarity : 0.005 0.051 557 Dihedral : 4.231 38.305 439 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.58 % 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: 0.34 (0.44), residues: 386 helix: 1.06 (0.34), residues: 255 sheet: 0.39 (1.55), residues: 10 loop : -1.56 (0.54), residues: 121 *********************** 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 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 27 time to evaluate : 0.394 Fit side-chains outliers start: 2 outliers final: 2 residues processed: 28 average time/residue: 0.1333 time to fit residues: 5.0848 Evaluate side-chains 25 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 23 time to evaluate : 0.389 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0447 time to fit residues: 0.6595 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 0.6980 chunk 32 optimal weight: 0.0370 chunk 17 optimal weight: 0.1980 chunk 3 optimal weight: 0.6980 chunk 12 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 37 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 22 optimal weight: 0.0770 chunk 28 optimal weight: 0.6980 overall best weight: 0.3216 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7894 moved from start: 0.2780 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.043 3351 Z= 0.145 Angle : 0.540 13.461 4571 Z= 0.268 Chirality : 0.036 0.120 497 Planarity : 0.004 0.052 557 Dihedral : 4.216 38.000 439 Min Nonbonded Distance : 2.225 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.63 % Favored : 96.37 % Rotamer Outliers : 0.29 % 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: 0.56 (0.44), residues: 386 helix: 1.22 (0.34), residues: 256 sheet: 0.41 (1.50), residues: 10 loop : -1.48 (0.54), residues: 120 *********************** 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 27 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 26 time to evaluate : 0.293 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 26 average time/residue: 0.1249 time to fit residues: 4.4652 Evaluate side-chains 22 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 22 time to evaluate : 0.368 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4911 ------------------------------------------------------------------------------- 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: 1.9990 chunk 32 optimal weight: 0.6980 chunk 38 optimal weight: 0.5980 chunk 24 optimal weight: 0.8980 chunk 23 optimal weight: 0.6980 chunk 17 optimal weight: 0.8980 chunk 15 optimal weight: 1.9990 chunk 11 optimal weight: 0.5980 chunk 7 optimal weight: 0.9990 chunk 26 optimal weight: 3.9990 chunk 19 optimal weight: 0.9990 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 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2819 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3351 Z= 0.185 Angle : 0.560 13.586 4571 Z= 0.276 Chirality : 0.037 0.122 497 Planarity : 0.005 0.052 557 Dihedral : 4.200 39.076 439 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.37 % Favored : 96.63 % Rotamer Outliers : 0.58 % 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: 0.56 (0.44), residues: 386 helix: 1.24 (0.34), residues: 255 sheet: 0.40 (1.44), residues: 10 loop : -1.49 (0.54), residues: 121 *********************** 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 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.405 Fit side-chains outliers start: 2 outliers final: 1 residues processed: 27 average time/residue: 0.1439 time to fit residues: 5.2921 Evaluate side-chains 26 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 25 time to evaluate : 0.395 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0336 time to fit residues: 0.5886 ------------------------------------------------------------------------------- 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: 1.9990 chunk 30 optimal weight: 0.9980 chunk 35 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 33 optimal weight: 0.9980 chunk 21 optimal weight: 1.9990 chunk 15 optimal weight: 0.6980 chunk 28 optimal weight: 0.9980 chunk 11 optimal weight: 0.5980 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 0.9980 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7948 moved from start: 0.2976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 3351 Z= 0.211 Angle : 0.576 13.953 4571 Z= 0.285 Chirality : 0.037 0.121 497 Planarity : 0.005 0.053 557 Dihedral : 4.354 39.443 439 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 4.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.92 % Favored : 95.08 % Rotamer Outliers : 0.29 % 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: 0.51 (0.44), residues: 386 helix: 1.17 (0.34), residues: 257 sheet: 0.64 (1.44), residues: 10 loop : -1.53 (0.55), residues: 119 *********************** 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 25 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 24 time to evaluate : 0.414 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 24 average time/residue: 0.1475 time to fit residues: 4.9294 Evaluate side-chains 23 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.401 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5068 ------------------------------------------------------------------------------- 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: 4.9990 chunk 23 optimal weight: 0.3980 chunk 18 optimal weight: 0.7980 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 2.9990 chunk 36 optimal weight: 0.6980 chunk 31 optimal weight: 0.9990 chunk 3 optimal weight: 0.9990 chunk 24 optimal weight: 0.6980 chunk 19 optimal weight: 0.7980 chunk 25 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7943 moved from start: 0.3027 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.186 Angle : 0.561 13.198 4571 Z= 0.278 Chirality : 0.037 0.122 497 Planarity : 0.005 0.053 557 Dihedral : 4.240 39.073 439 Min Nonbonded Distance : 2.215 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % 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: 0.59 (0.44), residues: 386 helix: 1.27 (0.34), residues: 256 sheet: 0.76 (1.47), residues: 10 loop : -1.57 (0.54), residues: 120 *********************** 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 25 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 25 time to evaluate : 0.369 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 25 average time/residue: 0.1537 time to fit residues: 5.1078 Evaluate side-chains 23 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 23 time to evaluate : 0.347 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5009 ------------------------------------------------------------------------------- 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: 1.9990 chunk 9 optimal weight: 0.9990 chunk 29 optimal weight: 0.6980 chunk 4 optimal weight: 0.8980 chunk 8 optimal weight: 1.9990 chunk 31 optimal weight: 0.6980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 27 optimal weight: 0.0870 chunk 1 optimal weight: 0.7980 overall best weight: 0.5958 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7936 moved from start: 0.3133 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.176 Angle : 0.566 14.182 4571 Z= 0.280 Chirality : 0.037 0.131 497 Planarity : 0.005 0.053 557 Dihedral : 4.281 38.782 439 Min Nonbonded Distance : 2.213 Molprobity Statistics. All-atom Clashscore : 4.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer Outliers : 0.29 % 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: 0.64 (0.44), residues: 386 helix: 1.31 (0.34), residues: 255 sheet: 0.90 (1.50), residues: 10 loop : -1.54 (0.54), residues: 121 ********************** 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 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 27 time to evaluate : 0.402 Fit side-chains outliers start: 1 outliers final: 0 residues processed: 27 average time/residue: 0.1288 time to fit residues: 4.7642 Evaluate side-chains 24 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 24 time to evaluate : 0.322 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4354 ------------------------------------------------------------------------------- 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: 0.0980 chunk 36 optimal weight: 0.8980 chunk 21 optimal weight: 0.9990 chunk 27 optimal weight: 0.5980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.5980 chunk 24 optimal weight: 0.9990 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 39 optimal weight: 4.9990 overall best weight: 0.5980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** R 304 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3870 r_free = 0.3870 target = 0.128371 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3566 r_free = 0.3566 target = 0.104207 restraints weight = 6039.532| |-----------------------------------------------------------------------------| r_work (start): 0.3558 rms_B_bonded: 2.99 r_work: 0.3548 rms_B_bonded: 2.81 restraints_weight: 0.5000 r_work: 0.3539 rms_B_bonded: 2.76 restraints_weight: 0.2500 r_work: 0.3529 rms_B_bonded: 2.78 restraints_weight: 0.1250 r_work: 0.3519 rms_B_bonded: 2.83 restraints_weight: 0.0625 r_work: 0.3510 rms_B_bonded: 2.90 restraints_weight: 0.0312 r_work: 0.3499 rms_B_bonded: 3.01 restraints_weight: 0.0156 r_work: 0.3489 rms_B_bonded: 3.13 restraints_weight: 0.0078 r_work: 0.3478 rms_B_bonded: 3.28 restraints_weight: 0.0039 r_work: 0.3466 rms_B_bonded: 3.45 restraints_weight: 0.0020 r_work: 0.3454 rms_B_bonded: 3.64 restraints_weight: 0.0010 r_work: 0.3441 rms_B_bonded: 3.86 restraints_weight: 0.0005 r_work: 0.3428 rms_B_bonded: 4.10 restraints_weight: 0.0002 r_work: 0.3414 rms_B_bonded: 4.37 restraints_weight: 0.0001 r_work: 0.3399 rms_B_bonded: 4.68 restraints_weight: 0.0001 r_work (final): 0.3399 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.3165 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.037 3351 Z= 0.175 Angle : 0.571 14.403 4571 Z= 0.280 Chirality : 0.038 0.206 497 Planarity : 0.005 0.053 557 Dihedral : 4.188 38.643 439 Min Nonbonded Distance : 2.228 Molprobity Statistics. All-atom Clashscore : 4.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.15 % Favored : 95.85 % Rotamer Outliers : 0.29 % 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: 0.64 (0.44), residues: 386 helix: 1.30 (0.34), residues: 256 sheet: 1.09 (1.59), residues: 10 loop : -1.57 (0.54), residues: 120 =============================================================================== Job complete usr+sys time: 1025.13 seconds wall clock time: 19 minutes 18.76 seconds (1158.76 seconds total)