Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 12:27:30 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/08_2023/7lcj_23275_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/08_2023/7lcj_23275.map 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 { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/08_2023/7lcj_23275.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/08_2023/7lcj_23275.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/08_2023/7lcj_23275_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7lcj_23275/08_2023/7lcj_23275_updated.pdb" } resolution = 2.82 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= -0.000 sd= 0.091 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 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. Process input model Symmetric amino acids flipped Residue "R TYR 101": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 102": "NH1" <-> "NH2" Residue "R GLU 107": "OE1" <-> "OE2" Residue "R ASP 114": "OD1" <-> "OD2" Residue "R ARG 121": "NH1" <-> "NH2" Residue "R PHE 169": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ASP 198": "OD1" <-> "OD2" Residue "R ASP 215": "OD1" <-> "OD2" Residue "R ASP 222": "OD1" <-> "OD2" Residue "R TYR 242": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 280": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 291": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R ARG 299": "NH1" <-> "NH2" Residue "R ARG 310": "NH1" <-> "NH2" Residue "R GLU 364": "OE1" <-> "OE2" Residue "R ASP 372": "OD1" <-> "OD2" Residue "R ARG 376": "NH1" <-> "NH2" Residue "R PHE 390": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R PHE 393": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R TYR 402": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "R GLU 418": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5044/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: {'peptide': 390, 'undetermined': 1, 'water': 17} 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: 2.29, per 1000 atoms: 0.70 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 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: 1.27 Conformation dependent library (CDL) restraints added in 446.1 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: 0.57 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: 0.73 Time building geometry restraints manager: 1.38 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=" C27 UK4 R 501 " pdb=" C28 UK4 R 501 " ideal model delta sigma weight residual 1.535 1.421 0.114 2.00e-02 2.50e+03 3.25e+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 1.447 0.082 2.00e-02 2.50e+03 1.68e+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 ... (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=" C SER R 136 " pdb=" N PRO R 137 " pdb=" CA PRO R 137 " ideal model delta sigma weight residual 119.28 126.40 -7.12 1.10e+00 8.26e-01 4.19e+01 angle pdb=" C THR R 362 " pdb=" CA THR R 362 " pdb=" CB THR R 362 " ideal model delta sigma weight residual 110.67 122.36 -11.69 1.92e+00 2.71e-01 3.71e+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 92.12 18.14 3.00e+00 1.11e-01 3.66e+01 angle pdb=" C LEU R 89 " pdb=" N PRO R 90 " pdb=" CA PRO R 90 " ideal model delta sigma weight residual 119.28 125.52 -6.24 1.10e+00 8.26e-01 3.21e+01 angle pdb=" C TYR R 148 " pdb=" CA TYR R 148 " pdb=" CB TYR R 148 " ideal model delta sigma weight residual 110.79 119.63 -8.84 1.66e+00 3.63e-01 2.83e+01 ... (remaining 4566 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.85: 1733 17.85 - 35.70: 154 35.70 - 53.55: 26 53.55 - 71.39: 3 71.39 - 89.24: 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 - 0.145: 466 0.145 - 0.290: 27 0.290 - 0.435: 2 0.435 - 0.580: 1 0.580 - 0.724: 1 Chirality restraints: 497 Sorted by residual: 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 chirality pdb=" CA TRP R 243 " pdb=" N TRP R 243 " pdb=" C TRP R 243 " pdb=" CB TRP R 243 " both_signs ideal model delta sigma weight residual False 2.51 2.16 0.35 2.00e-01 2.50e+01 3.15e+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 Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=0.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic Make a string to write initial .geo file Internal consistency checks Time: Set random seed: 0.000 Set model cs if undefined: 0.000 Decide on map wrapping: 0.000 Normalize map: mean=0, sd=1: 1.030 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 5.190 Check model and map are aligned: 0.050 Set scattering table: 0.030 Process input model: 13.480 Find NCS groups from input model: 0.090 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:13.040 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.930 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7656 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 : 0.011 0.114 3351 Z= 0.645 Angle : 1.188 18.141 4571 Z= 0.785 Chirality : 0.083 0.724 497 Planarity : 0.006 0.049 557 Dihedral : 13.355 89.243 1158 Min Nonbonded Distance : 2.216 Molprobity Statistics. All-atom Clashscore : 8.89 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 : 0.369 Fit side-chains outliers start: 4 outliers final: 2 residues processed: 36 average time/residue: 0.9977 time to fit residues: 37.4272 Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 26 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 1.0707 time to fit residues: 1.5905 ------------------------------------------------------------------------------- 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: 0.5980 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: 0.8980 chunk 23 optimal weight: 0.9990 chunk 36 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7563 moved from start: 0.1354 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= 0.187 Angle : 0.561 7.393 4571 Z= 0.304 Chirality : 0.038 0.136 497 Planarity : 0.005 0.050 557 Dihedral : 4.292 24.872 439 Min Nonbonded Distance : 2.303 Molprobity Statistics. All-atom Clashscore : 4.99 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.85 % Favored : 97.15 % 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: 1.23 (0.42), residues: 386 helix: 1.76 (0.33), residues: 248 sheet: None (None), residues: 0 loop : -0.95 (0.48), residues: 138 *********************** 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: 6 poor density : 27 time to evaluate : 0.332 Fit side-chains outliers start: 6 outliers final: 3 residues processed: 30 average time/residue: 0.8497 time to fit residues: 26.8437 Evaluate side-chains 26 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 23 time to evaluate : 0.315 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 2 residues processed: 1 average time/residue: 1.1406 time to fit residues: 1.6673 ------------------------------------------------------------------------------- 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: 2.9990 chunk 24 optimal weight: 0.0980 chunk 10 optimal weight: 2.9990 chunk 36 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 32 optimal weight: 0.6980 chunk 12 optimal weight: 0.9980 chunk 29 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 27 optimal weight: 0.7980 chunk 18 optimal weight: 0.5980 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: 0.7554 moved from start: 0.1801 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= 0.160 Angle : 0.498 8.647 4571 Z= 0.265 Chirality : 0.036 0.127 497 Planarity : 0.005 0.053 557 Dihedral : 3.963 21.764 439 Min Nonbonded Distance : 2.293 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer Outliers : 2.03 % 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: 1.33 (0.43), residues: 386 helix: 1.82 (0.33), residues: 252 sheet: None (None), residues: 0 loop : -0.97 (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 34 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.373 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 32 average time/residue: 0.8291 time to fit residues: 27.9890 Evaluate side-chains 31 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 25 time to evaluate : 0.350 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.5847 time to fit residues: 1.7390 ------------------------------------------------------------------------------- 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: 6.9990 chunk 17 optimal weight: 1.9990 chunk 24 optimal weight: 0.5980 chunk 36 optimal weight: 0.9990 chunk 38 optimal weight: 3.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 0.9980 chunk 10 optimal weight: 0.0870 chunk 32 optimal weight: 0.9980 chunk 21 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 overall best weight: 0.6758 ------------------------------------------------------------------------------- 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: 0.7566 moved from start: 0.2033 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 : 0.483 7.066 4571 Z= 0.256 Chirality : 0.036 0.121 497 Planarity : 0.005 0.056 557 Dihedral : 3.893 20.445 439 Min Nonbonded Distance : 2.276 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 2.03 % 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: 1.35 (0.43), residues: 386 helix: 1.82 (0.34), residues: 252 sheet: None (None), residues: 0 loop : -0.92 (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 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.354 Fit side-chains outliers start: 7 outliers final: 5 residues processed: 32 average time/residue: 0.7892 time to fit residues: 26.6566 Evaluate side-chains 31 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 26 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 4 residues processed: 1 average time/residue: 1.1253 time to fit residues: 1.6565 ------------------------------------------------------------------------------- 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: 0.8980 chunk 15 optimal weight: 1.9990 chunk 32 optimal weight: 0.5980 chunk 26 optimal weight: 5.9990 chunk 0 optimal weight: 4.9990 chunk 19 optimal weight: 0.6980 chunk 34 optimal weight: 1.9990 chunk 9 optimal weight: 40.0000 chunk 13 optimal weight: 3.9990 chunk 7 optimal weight: 7.9990 chunk 22 optimal weight: 0.0060 overall best weight: 0.8398 ------------------------------------------------------------------------------- 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: 0.7588 moved from start: 0.2064 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3351 Z= 0.178 Angle : 0.486 7.028 4571 Z= 0.257 Chirality : 0.036 0.122 497 Planarity : 0.005 0.056 557 Dihedral : 3.921 19.291 439 Min Nonbonded Distance : 2.265 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 2.91 % 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: 1.76 (0.33), residues: 252 sheet: None (None), residues: 0 loop : -0.89 (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 37 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 27 time to evaluate : 0.354 Fit side-chains outliers start: 10 outliers final: 7 residues processed: 34 average time/residue: 0.7716 time to fit residues: 27.7470 Evaluate side-chains 34 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.328 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.5626 time to fit residues: 1.6302 ------------------------------------------------------------------------------- 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: 40.0000 chunk 38 optimal weight: 0.7980 chunk 32 optimal weight: 0.8980 chunk 17 optimal weight: 4.9990 chunk 3 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 chunk 20 optimal weight: 0.7980 chunk 37 optimal weight: 0.9990 chunk 4 optimal weight: 7.9990 chunk 22 optimal weight: 0.0980 chunk 28 optimal weight: 0.9990 overall best weight: 0.7180 ------------------------------------------------------------------------------- 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: 0.7576 moved from start: 0.2174 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= 0.160 Angle : 0.472 7.076 4571 Z= 0.250 Chirality : 0.035 0.117 497 Planarity : 0.005 0.056 557 Dihedral : 3.842 19.396 439 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 2.03 % 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: 1.33 (0.43), residues: 386 helix: 1.78 (0.33), residues: 252 sheet: None (None), residues: 0 loop : -0.86 (0.50), residues: 134 *********************** 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 34 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 27 time to evaluate : 0.358 Fit side-chains outliers start: 7 outliers final: 6 residues processed: 33 average time/residue: 0.8642 time to fit residues: 29.9818 Evaluate side-chains 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 27 time to evaluate : 0.351 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 6 residues processed: 0 time to fit residues: 0.4964 ------------------------------------------------------------------------------- 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: 1.9990 chunk 38 optimal weight: 0.8980 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.9980 chunk 17 optimal weight: 4.9990 chunk 15 optimal weight: 0.8980 chunk 11 optimal weight: 0.8980 chunk 7 optimal weight: 2.9990 chunk 26 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 overall best weight: 0.8580 ------------------------------------------------------------------------------- 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: 0.7595 moved from start: 0.2210 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= 0.179 Angle : 0.482 7.030 4571 Z= 0.254 Chirality : 0.036 0.121 497 Planarity : 0.005 0.056 557 Dihedral : 3.877 19.007 439 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % Rotamer Outliers : 2.91 % 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: 1.26 (0.43), residues: 386 helix: 1.66 (0.33), residues: 254 sheet: None (None), residues: 0 loop : -0.79 (0.51), 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 36 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 26 time to evaluate : 0.365 Fit side-chains outliers start: 10 outliers final: 6 residues processed: 34 average time/residue: 0.7996 time to fit residues: 28.6876 Evaluate side-chains 32 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 26 time to evaluate : 0.357 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 2 average time/residue: 0.6148 time to fit residues: 1.7806 ------------------------------------------------------------------------------- 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: 5.9990 chunk 30 optimal weight: 5.9990 chunk 35 optimal weight: 0.9980 chunk 36 optimal weight: 0.5980 chunk 33 optimal weight: 0.7980 chunk 21 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 28 optimal weight: 1.9990 chunk 11 optimal weight: 0.7980 chunk 32 optimal weight: 0.9990 chunk 23 optimal weight: 1.9990 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: 0.7591 moved from start: 0.2299 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.030 3351 Z= 0.173 Angle : 0.476 7.021 4571 Z= 0.252 Chirality : 0.036 0.121 497 Planarity : 0.005 0.056 557 Dihedral : 3.859 19.147 439 Min Nonbonded Distance : 2.257 Molprobity Statistics. All-atom Clashscore : 4.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % Rotamer Outliers : 2.03 % 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: 1.27 (0.43), residues: 386 helix: 1.69 (0.33), residues: 254 sheet: None (None), residues: 0 loop : -0.82 (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 33 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 26 time to evaluate : 0.352 Fit side-chains outliers start: 7 outliers final: 4 residues processed: 32 average time/residue: 0.8278 time to fit residues: 27.9096 Evaluate side-chains 29 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 25 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4579 ------------------------------------------------------------------------------- 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: 0.7980 chunk 23 optimal weight: 0.9990 chunk 18 optimal weight: 1.9990 chunk 26 optimal weight: 5.9990 chunk 39 optimal weight: 5.9990 chunk 36 optimal weight: 0.7980 chunk 31 optimal weight: 2.9990 chunk 3 optimal weight: 8.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 1.9990 chunk 25 optimal weight: 0.0570 overall best weight: 0.7100 ------------------------------------------------------------------------------- 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: 0.7581 moved from start: 0.2376 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= 0.160 Angle : 0.464 6.896 4571 Z= 0.246 Chirality : 0.035 0.118 497 Planarity : 0.005 0.056 557 Dihedral : 3.811 19.166 439 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % 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: 1.33 (0.43), residues: 386 helix: 1.72 (0.34), residues: 254 sheet: None (None), residues: 0 loop : -0.77 (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 30 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 25 time to evaluate : 0.357 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 29 average time/residue: 0.8823 time to fit residues: 26.9652 Evaluate side-chains 27 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 23 time to evaluate : 0.358 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.5027 ------------------------------------------------------------------------------- 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: 0.0770 chunk 9 optimal weight: 9.9990 chunk 29 optimal weight: 1.9990 chunk 4 optimal weight: 7.9990 chunk 8 optimal weight: 2.9990 chunk 31 optimal weight: 0.4980 chunk 13 optimal weight: 3.9990 chunk 32 optimal weight: 0.9990 chunk 5 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 2.9990 overall best weight: 0.9142 ------------------------------------------------------------------------------- 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: 0.7604 moved from start: 0.2351 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= 0.187 Angle : 0.485 6.902 4571 Z= 0.256 Chirality : 0.036 0.124 497 Planarity : 0.005 0.055 557 Dihedral : 3.900 19.143 439 Min Nonbonded Distance : 2.252 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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 (0.43), residues: 386 helix: 1.63 (0.33), residues: 254 sheet: None (None), residues: 0 loop : -0.77 (0.51), residues: 132 ********************** 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: 5 poor density : 24 time to evaluate : 0.384 Fit side-chains outliers start: 5 outliers final: 4 residues processed: 28 average time/residue: 0.7332 time to fit residues: 21.8931 Evaluate side-chains 28 residues out of total 350 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 24 time to evaluate : 0.334 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.4874 ------------------------------------------------------------------------------- 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: 0.0270 chunk 36 optimal weight: 0.7980 chunk 21 optimal weight: 0.5980 chunk 27 optimal weight: 0.9980 chunk 1 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 24 optimal weight: 0.9980 chunk 23 optimal weight: 0.8980 chunk 15 optimal weight: 0.9980 chunk 14 optimal weight: 1.9990 chunk 39 optimal weight: 5.9990 overall best weight: 0.4796 ------------------------------------------------------------------------------- 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 = 0.4205 r_free = 0.4205 target = 0.202130 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 57)----------------| | r_work = 0.3522 r_free = 0.3522 target = 0.132139 restraints weight = 3280.115| |-----------------------------------------------------------------------------| r_work (start): 0.3472 rms_B_bonded: 2.11 r_work: 0.3352 rms_B_bonded: 2.79 restraints_weight: 0.5000 r_work: 0.3228 rms_B_bonded: 4.34 restraints_weight: 0.2500 r_work (final): 0.3228 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7865 moved from start: 0.2525 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.024 3351 Z= 0.134 Angle : 0.451 6.865 4571 Z= 0.240 Chirality : 0.035 0.115 497 Planarity : 0.005 0.056 557 Dihedral : 3.735 19.875 439 Min Nonbonded Distance : 2.255 Molprobity Statistics. All-atom Clashscore : 4.21 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.07 % Favored : 97.93 % 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: 1.42 (0.44), residues: 386 helix: 1.80 (0.34), residues: 254 sheet: None (None), residues: 0 loop : -0.75 (0.51), residues: 132 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1353.89 seconds wall clock time: 24 minutes 46.52 seconds (1486.52 seconds total)