Starting phenix.real_space_refine (version: 1.21rc1) on Wed Aug 9 14:43:58 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/08_2023/8ore_17121.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/08_2023/8ore_17121.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=2.5 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/08_2023/8ore_17121.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/08_2023/8ore_17121.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/08_2023/8ore_17121.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ore_17121/08_2023/8ore_17121.pdb" } resolution = 2.5 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= 0.004 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 3 5.16 5 C 1110 2.51 5 N 327 2.21 5 O 330 1.98 5 H 1845 0.53 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 342": "OE1" <-> "OE2" Residue "A GLU 380": "OE1" <-> "OE2" Residue "B GLU 342": "OE1" <-> "OE2" Residue "B GLU 380": "OE1" <-> "OE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "C GLU 380": "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: 3615 Number of models: 1 Model: "" Number of chains: 3 Chain: "A" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "B" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Chain: "C" Number of atoms: 1205 Number of conformers: 1 Conformer: "" Number of residues, atoms: 77, 1205 Classifications: {'peptide': 77} Link IDs: {'PTRANS': 3, 'TRANS': 73} Time building chain proxies: 1.97, per 1000 atoms: 0.54 Number of scatterers: 3615 At special positions: 0 Unit cell: (82.84, 81.75, 37.06, 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 3 16.00 O 330 8.00 N 327 7.00 C 1110 6.00 H 1845 1.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 2.89 Conformation dependent library (CDL) restraints added in 318.0 milliseconds 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 402 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 49.4% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.31 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 306 through 310 Processing sheet with id=AA2, first strand: chain 'A' and resid 313 through 314 Processing sheet with id=AA3, first strand: chain 'A' and resid 317 through 322 Processing sheet with id=AA4, first strand: chain 'A' and resid 327 through 330 removed outlier: 6.612A pdb=" N ILE A 328 " --> pdb=" O HIS B 329 " (cutoff:3.500A) removed outlier: 6.660A pdb=" N ILE B 328 " --> pdb=" O HIS C 329 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'A' and resid 336 through 340 Processing sheet with id=AA6, first strand: chain 'A' and resid 343 through 346 Processing sheet with id=AA7, first strand: chain 'A' and resid 351 through 361 removed outlier: 6.938A pdb=" N SER B 352 " --> pdb=" O GLN A 351 " (cutoff:3.500A) removed outlier: 6.859A pdb=" N LYS A 353 " --> pdb=" O SER B 352 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N ILE B 354 " --> pdb=" O LYS A 353 " (cutoff:3.500A) removed outlier: 6.884A pdb=" N GLY A 355 " --> pdb=" O ILE B 354 " (cutoff:3.500A) removed outlier: 6.853A pdb=" N SER C 352 " --> pdb=" O GLN B 351 " (cutoff:3.500A) removed outlier: 6.877A pdb=" N LYS B 353 " --> pdb=" O SER C 352 " (cutoff:3.500A) removed outlier: 6.882A pdb=" N ILE C 354 " --> pdb=" O LYS B 353 " (cutoff:3.500A) removed outlier: 6.894A pdb=" N GLY B 355 " --> pdb=" O ILE C 354 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 369 through 377 62 hydrogen bonds defined for protein. 186 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: 1.12 Time building geometry restraints manager: 3.01 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 0.94 - 1.11: 1842 1.11 - 1.29: 297 1.29 - 1.46: 490 1.46 - 1.63: 1010 1.63 - 1.81: 3 Bond restraints: 3642 Sorted by residual: bond pdb=" N GLY A 366 " pdb=" H GLY A 366 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.71e+01 bond pdb=" CE1 HIS A 362 " pdb=" HE1 HIS A 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" CE1 HIS B 362 " pdb=" HE1 HIS B 362 " ideal model delta sigma weight residual 0.930 1.081 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU C 315 " pdb=" H LEU C 315 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 bond pdb=" N LEU B 315 " pdb=" H LEU B 315 " ideal model delta sigma weight residual 0.860 1.011 -0.151 2.00e-02 2.50e+03 5.69e+01 ... (remaining 3637 not shown) Histogram of bond angle deviations from ideal: 97.13 - 103.45: 34 103.45 - 109.78: 3111 109.78 - 116.11: 1610 116.11 - 122.43: 1520 122.43 - 128.76: 367 Bond angle restraints: 6642 Sorted by residual: angle pdb=" C LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta sigma weight residual 111.14 119.05 -7.91 1.39e+00 5.18e-01 3.24e+01 angle pdb=" C LEU B 325 " pdb=" CA LEU B 325 " pdb=" CB LEU B 325 " ideal model delta sigma weight residual 111.40 118.42 -7.02 1.29e+00 6.01e-01 2.96e+01 angle pdb=" N PRO B 364 " pdb=" CA PRO B 364 " pdb=" C PRO B 364 " ideal model delta sigma weight residual 113.57 120.57 -7.00 1.31e+00 5.83e-01 2.86e+01 angle pdb=" CB HIS B 362 " pdb=" CG HIS B 362 " pdb=" CD2 HIS B 362 " ideal model delta sigma weight residual 131.20 124.91 6.29 1.30e+00 5.92e-01 2.34e+01 angle pdb=" CA PHE B 346 " pdb=" CB PHE B 346 " pdb=" CG PHE B 346 " ideal model delta sigma weight residual 113.80 118.61 -4.81 1.00e+00 1.00e+00 2.31e+01 ... (remaining 6637 not shown) Histogram of dihedral angle deviations from ideal: 0.01 - 13.53: 1236 13.53 - 27.06: 98 27.06 - 40.59: 21 40.59 - 54.12: 7 54.12 - 67.65: 36 Dihedral angle restraints: 1398 sinusoidal: 687 harmonic: 711 Sorted by residual: dihedral pdb=" C LEU A 325 " pdb=" N LEU A 325 " pdb=" CA LEU A 325 " pdb=" CB LEU A 325 " ideal model delta harmonic sigma weight residual -122.60 -138.99 16.39 0 2.50e+00 1.60e-01 4.30e+01 dihedral pdb=" C VAL B 363 " pdb=" N VAL B 363 " pdb=" CA VAL B 363 " pdb=" CB VAL B 363 " ideal model delta harmonic sigma weight residual -122.00 -137.70 15.70 0 2.50e+00 1.60e-01 3.94e+01 dihedral pdb=" C VAL A 363 " pdb=" N VAL A 363 " pdb=" CA VAL A 363 " pdb=" CB VAL A 363 " ideal model delta harmonic sigma weight residual -122.00 -136.54 14.54 0 2.50e+00 1.60e-01 3.38e+01 ... (remaining 1395 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.120: 200 0.120 - 0.240: 40 0.240 - 0.360: 16 0.360 - 0.479: 9 0.479 - 0.599: 2 Chirality restraints: 267 Sorted by residual: chirality pdb=" CA LEU A 325 " pdb=" N LEU A 325 " pdb=" C LEU A 325 " pdb=" CB LEU A 325 " both_signs ideal model delta sigma weight residual False 2.51 1.91 0.60 2.00e-01 2.50e+01 8.97e+00 chirality pdb=" CA PRO B 364 " pdb=" N PRO B 364 " pdb=" C PRO B 364 " pdb=" CB PRO B 364 " both_signs ideal model delta sigma weight residual False 2.72 2.23 0.49 2.00e-01 2.50e+01 5.94e+00 chirality pdb=" CA VAL B 363 " pdb=" N VAL B 363 " pdb=" C VAL B 363 " pdb=" CB VAL B 363 " both_signs ideal model delta sigma weight residual False 2.44 1.98 0.46 2.00e-01 2.50e+01 5.21e+00 ... (remaining 264 not shown) Planarity restraints: 525 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CB PHE A 346 " 0.099 2.00e-02 2.50e+03 4.00e-02 4.80e+01 pdb=" CG PHE A 346 " 0.000 2.00e-02 2.50e+03 pdb=" CD1 PHE A 346 " -0.022 2.00e-02 2.50e+03 pdb=" CD2 PHE A 346 " -0.041 2.00e-02 2.50e+03 pdb=" CE1 PHE A 346 " -0.004 2.00e-02 2.50e+03 pdb=" CE2 PHE A 346 " -0.020 2.00e-02 2.50e+03 pdb=" CZ PHE A 346 " 0.013 2.00e-02 2.50e+03 pdb=" HD1 PHE A 346 " -0.050 2.00e-02 2.50e+03 pdb=" HD2 PHE A 346 " -0.037 2.00e-02 2.50e+03 pdb=" HE1 PHE A 346 " 0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE A 346 " 0.008 2.00e-02 2.50e+03 pdb=" HZ PHE A 346 " 0.052 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CB PHE B 346 " 0.076 2.00e-02 2.50e+03 3.28e-02 3.23e+01 pdb=" CG PHE B 346 " 0.010 2.00e-02 2.50e+03 pdb=" CD1 PHE B 346 " -0.012 2.00e-02 2.50e+03 pdb=" CD2 PHE B 346 " -0.035 2.00e-02 2.50e+03 pdb=" CE1 PHE B 346 " -0.001 2.00e-02 2.50e+03 pdb=" CE2 PHE B 346 " -0.024 2.00e-02 2.50e+03 pdb=" CZ PHE B 346 " 0.006 2.00e-02 2.50e+03 pdb=" HD1 PHE B 346 " -0.043 2.00e-02 2.50e+03 pdb=" HD2 PHE B 346 " -0.032 2.00e-02 2.50e+03 pdb=" HE1 PHE B 346 " -0.001 2.00e-02 2.50e+03 pdb=" HE2 PHE B 346 " 0.012 2.00e-02 2.50e+03 pdb=" HZ PHE B 346 " 0.044 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C SER B 341 " -0.030 2.00e-02 2.50e+03 5.52e-02 3.05e+01 pdb=" N GLU B 342 " 0.095 2.00e-02 2.50e+03 pdb=" CA GLU B 342 " -0.027 2.00e-02 2.50e+03 pdb=" H GLU B 342 " -0.038 2.00e-02 2.50e+03 ... (remaining 522 not shown) Histogram of nonbonded interaction distances: 1.61 - 2.21: 317 2.21 - 2.81: 6754 2.81 - 3.40: 9317 3.40 - 4.00: 12465 4.00 - 4.60: 17899 Nonbonded interactions: 46752 Sorted by model distance: nonbonded pdb=" OD1 ASP A 314 " pdb=" HG SER A 316 " model vdw 1.611 1.850 nonbonded pdb=" OD1 ASP B 314 " pdb=" HG SER B 316 " model vdw 1.636 1.850 nonbonded pdb=" HG1 THR A 377 " pdb=" OE1 GLU A 380 " model vdw 1.650 1.850 nonbonded pdb=" HG1 THR C 377 " pdb=" OE2 GLU C 380 " model vdw 1.662 1.850 nonbonded pdb=" OD1 ASP C 314 " pdb=" HG SER C 316 " model vdw 1.675 1.850 ... (remaining 46747 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' } 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=1.00 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: 0.700 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: 0.060 Extract box with map and model: 3.690 Check model and map are aligned: 0.060 Set scattering table: 0.030 Process input model: 16.650 Find NCS groups from input model: 0.170 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:11.500 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 32.870 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7361 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 0.052 1797 Z= 0.718 Angle : 2.085 10.566 2400 Z= 1.353 Chirality : 0.140 0.599 267 Planarity : 0.011 0.065 306 Dihedral : 10.934 54.560 696 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 0.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.00 % Favored : 92.00 % Rotamer Outliers : 0.00 % Cbeta Deviations : 3.48 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.10 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.59 (0.36), residues: 225 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 82 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 82 time to evaluate : 0.318 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 82 average time/residue: 2.5873 time to fit residues: 215.1878 Evaluate side-chains 46 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 46 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4004 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 17 optimal weight: 5.9990 chunk 15 optimal weight: 5.9990 chunk 8 optimal weight: 2.9990 chunk 5 optimal weight: 2.9990 chunk 10 optimal weight: 5.9990 chunk 16 optimal weight: 1.9990 chunk 6 optimal weight: 0.8980 chunk 12 optimal weight: 1.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 1.9990 chunk 18 optimal weight: 1.9990 overall best weight: 1.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 327 ASN A 336 GLN A 374 HIS B 307 GLN B 336 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7612 moved from start: 0.4711 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 1797 Z= 0.231 Angle : 0.734 5.051 2400 Z= 0.378 Chirality : 0.055 0.143 267 Planarity : 0.005 0.047 306 Dihedral : 7.374 23.009 237 Min Nonbonded Distance : 2.051 Molprobity Statistics. All-atom Clashscore : 4.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 4.98 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.11 (0.47), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.60 (0.36), residues: 225 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 57 time to evaluate : 0.328 Fit side-chains revert: symmetry clash outliers start: 10 outliers final: 4 residues processed: 63 average time/residue: 2.1470 time to fit residues: 138.2448 Evaluate side-chains 49 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 45 time to evaluate : 0.520 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 4 residues processed: 0 time to fit residues: 0.7394 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 6 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 4.9990 chunk 14 optimal weight: 3.9990 chunk 9 optimal weight: 2.9990 chunk 2 optimal weight: 0.9980 chunk 12 optimal weight: 3.9990 chunk 19 optimal weight: 1.9990 chunk 20 optimal weight: 0.4980 chunk 10 optimal weight: 1.9990 chunk 5 optimal weight: 1.9990 overall best weight: 1.4986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 307 GLN B 307 GLN C 374 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.5423 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.019 1797 Z= 0.176 Angle : 0.634 4.932 2400 Z= 0.326 Chirality : 0.053 0.145 267 Planarity : 0.004 0.042 306 Dihedral : 6.384 20.552 237 Min Nonbonded Distance : 2.231 Molprobity Statistics. All-atom Clashscore : 2.49 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 5.47 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.04 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.55 (0.37), residues: 225 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 58 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 47 time to evaluate : 0.362 Fit side-chains outliers start: 11 outliers final: 6 residues processed: 54 average time/residue: 1.8077 time to fit residues: 99.7907 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 1.2835 time to fit residues: 4.3402 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 16 optimal weight: 0.7980 chunk 11 optimal weight: 7.9990 chunk 0 optimal weight: 3.9990 chunk 15 optimal weight: 6.9990 chunk 8 optimal weight: 0.6980 chunk 17 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 chunk 10 optimal weight: 0.9980 chunk 18 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 6 optimal weight: 0.5980 overall best weight: 1.0182 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 336 GLN B 374 HIS Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7609 moved from start: 0.5771 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.034 1797 Z= 0.160 Angle : 0.581 4.039 2400 Z= 0.292 Chirality : 0.052 0.132 267 Planarity : 0.004 0.036 306 Dihedral : 5.896 18.125 237 Min Nonbonded Distance : 2.166 Molprobity Statistics. All-atom Clashscore : 2.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 4.48 % 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: -1.96 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.48 (0.37), residues: 225 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.364 Fit side-chains revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 2.0994 time to fit residues: 111.3415 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.333 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 4 residues processed: 3 average time/residue: 0.7843 time to fit residues: 2.8658 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 18 optimal weight: 0.9980 chunk 4 optimal weight: 5.9990 chunk 11 optimal weight: 2.9990 chunk 5 optimal weight: 4.9990 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 4.9990 chunk 9 optimal weight: 0.6980 chunk 1 optimal weight: 4.9990 chunk 6 optimal weight: 0.6980 chunk 10 optimal weight: 4.9990 chunk 19 optimal weight: 1.9990 overall best weight: 1.0784 ------------------------------------------------------------------------------- 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: 0.7616 moved from start: 0.6077 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.022 1797 Z= 0.148 Angle : 0.574 4.215 2400 Z= 0.288 Chirality : 0.052 0.136 267 Planarity : 0.004 0.036 306 Dihedral : 5.661 17.827 237 Min Nonbonded Distance : 2.168 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 3.98 % 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: -1.89 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 225 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 44 time to evaluate : 0.331 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 8 outliers final: 7 residues processed: 49 average time/residue: 2.0864 time to fit residues: 104.4716 Evaluate side-chains 51 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 44 time to evaluate : 0.294 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 4 residues processed: 3 average time/residue: 1.3476 time to fit residues: 4.5454 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 3.9990 chunk 11 optimal weight: 6.9990 chunk 14 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 20 optimal weight: 0.9980 chunk 12 optimal weight: 4.9990 chunk 9 optimal weight: 0.9980 chunk 8 optimal weight: 4.9990 chunk 6 optimal weight: 0.5980 chunk 3 optimal weight: 5.9990 chunk 13 optimal weight: 0.6980 overall best weight: 1.2582 ------------------------------------------------------------------------------- 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: 0.7629 moved from start: 0.6268 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.029 1797 Z= 0.182 Angle : 0.597 4.066 2400 Z= 0.298 Chirality : 0.052 0.139 267 Planarity : 0.004 0.037 306 Dihedral : 5.601 19.217 237 Min Nonbonded Distance : 2.179 Molprobity Statistics. All-atom Clashscore : 1.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.11 % Favored : 92.89 % Rotamer Outliers : 4.48 % 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: -1.91 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 225 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 57 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 48 time to evaluate : 0.325 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 9 outliers final: 6 residues processed: 52 average time/residue: 2.0954 time to fit residues: 111.0432 Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 46 time to evaluate : 0.300 Switching outliers to nearest non-outliers outliers start: 6 outliers final: 3 residues processed: 3 average time/residue: 0.7060 time to fit residues: 2.6051 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 10 optimal weight: 6.9990 chunk 1 optimal weight: 2.9990 chunk 15 optimal weight: 4.9990 chunk 18 optimal weight: 3.9990 chunk 19 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 11 optimal weight: 0.9980 chunk 8 optimal weight: 3.9990 chunk 14 optimal weight: 2.9990 chunk 5 optimal weight: 3.9990 chunk 12 optimal weight: 0.9980 overall best weight: 2.1986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 327 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7676 moved from start: 0.6370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.026 1797 Z= 0.259 Angle : 0.651 5.584 2400 Z= 0.329 Chirality : 0.054 0.162 267 Planarity : 0.005 0.045 306 Dihedral : 5.871 21.899 237 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.56 % Favored : 92.44 % Rotamer Outliers : 2.49 % 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: -1.89 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.43 (0.37), residues: 225 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 51 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.326 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 5 outliers final: 5 residues processed: 49 average time/residue: 1.9757 time to fit residues: 98.8470 Evaluate side-chains 51 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 46 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 5 outliers final: 3 residues processed: 2 average time/residue: 0.0859 time to fit residues: 0.6357 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 5.9990 chunk 12 optimal weight: 1.9990 chunk 9 optimal weight: 1.9990 chunk 13 optimal weight: 0.6980 chunk 20 optimal weight: 0.9990 chunk 16 optimal weight: 0.5980 chunk 1 optimal weight: 0.9980 chunk 10 optimal weight: 3.9990 chunk 17 optimal weight: 2.9990 chunk 5 optimal weight: 0.6980 chunk 15 optimal weight: 1.9990 overall best weight: 0.7982 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7606 moved from start: 0.6479 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.033 1797 Z= 0.166 Angle : 0.594 4.334 2400 Z= 0.296 Chirality : 0.051 0.128 267 Planarity : 0.003 0.036 306 Dihedral : 5.419 20.178 237 Min Nonbonded Distance : 2.174 Molprobity Statistics. All-atom Clashscore : 3.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 3.48 % 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: -1.91 (0.48), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.45 (0.37), residues: 225 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 55 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.323 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 7 outliers final: 3 residues processed: 50 average time/residue: 2.0242 time to fit residues: 103.2567 Evaluate side-chains 50 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 47 time to evaluate : 0.320 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 1 residues processed: 2 average time/residue: 2.0388 time to fit residues: 4.5344 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 2 optimal weight: 2.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 3.9990 chunk 6 optimal weight: 0.8980 chunk 17 optimal weight: 1.9990 chunk 3 optimal weight: 0.8980 chunk 14 optimal weight: 0.9990 chunk 0 optimal weight: 3.9990 chunk 12 optimal weight: 5.9990 chunk 19 optimal weight: 0.9980 chunk 11 optimal weight: 0.8980 overall best weight: 0.9382 ------------------------------------------------------------------------------- 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: 0.7615 moved from start: 0.6558 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.030 1797 Z= 0.169 Angle : 0.591 3.953 2400 Z= 0.296 Chirality : 0.052 0.131 267 Planarity : 0.004 0.036 306 Dihedral : 5.272 18.478 237 Min Nonbonded Distance : 2.185 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.22 % Favored : 93.78 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.40 (0.38), residues: 225 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 50 time to evaluate : 0.263 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 51 average time/residue: 2.1199 time to fit residues: 110.2199 Evaluate side-chains 50 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1449 time to fit residues: 0.5770 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 14 optimal weight: 0.0070 chunk 0 optimal weight: 3.9990 chunk 13 optimal weight: 4.9990 chunk 12 optimal weight: 5.9990 chunk 8 optimal weight: 4.9990 chunk 7 optimal weight: 0.6980 chunk 20 optimal weight: 2.9990 chunk 3 optimal weight: 2.9990 chunk 2 optimal weight: 1.9990 chunk 4 optimal weight: 4.9990 chunk 16 optimal weight: 0.6980 overall best weight: 1.2802 ------------------------------------------------------------------------------- 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: 0.7627 moved from start: 0.6626 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.034 1797 Z= 0.194 Angle : 0.610 4.273 2400 Z= 0.307 Chirality : 0.052 0.138 267 Planarity : 0.004 0.037 306 Dihedral : 5.316 18.218 237 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 3.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.49), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 225 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 450 Ramachandran restraints generated. 225 Oldfield, 0 Emsley, 225 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 50 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.415 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 49 average time/residue: 1.9654 time to fit residues: 98.3261 Evaluate side-chains 50 residues out of total 201 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 48 time to evaluate : 0.327 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 1 residues processed: 1 average time/residue: 0.1288 time to fit residues: 0.5608 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 21 random chunks: chunk 19 optimal weight: 3.9990 chunk 0 optimal weight: 3.9990 chunk 8 optimal weight: 5.9990 chunk 2 optimal weight: 1.9990 chunk 5 optimal weight: 3.9990 chunk 4 optimal weight: 4.9990 chunk 13 optimal weight: 1.9990 chunk 7 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 10 optimal weight: 2.9990 chunk 20 optimal weight: 0.9990 overall best weight: 1.7588 ------------------------------------------------------------------------------- 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 = 0.4173 r_free = 0.4173 target = 0.142526 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3953 r_free = 0.3953 target = 0.123192 restraints weight = 6403.154| |-----------------------------------------------------------------------------| r_work (start): 0.3974 rms_B_bonded: 2.03 r_work: 0.3899 rms_B_bonded: 1.95 restraints_weight: 0.5000 r_work: 0.3812 rms_B_bonded: 3.32 restraints_weight: 0.2500 r_work (final): 0.3812 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8070 moved from start: 0.6620 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.028 1797 Z= 0.222 Angle : 0.626 4.932 2400 Z= 0.315 Chirality : 0.052 0.152 267 Planarity : 0.004 0.040 306 Dihedral : 5.479 19.752 237 Min Nonbonded Distance : 2.218 Molprobity Statistics. All-atom Clashscore : 3.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.67 % Favored : 93.33 % Rotamer Outliers : 1.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.84 (0.50), residues: 225 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -1.39 (0.38), residues: 225 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 3139.28 seconds wall clock time: 55 minutes 39.42 seconds (3339.42 seconds total)