Starting phenix.real_space_refine (version: dev) on Fri Feb 17 00:21:42 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/02_2023/7ypg_33999.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/02_2023/7ypg_33999.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/7ypg_33999/02_2023/7ypg_33999.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/02_2023/7ypg_33999.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/02_2023/7ypg_33999.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ypg_33999/02_2023/7ypg_33999.pdb" } resolution = 2.5 write_initial_geo_file = False refinement { macro_cycles = 10 } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.001 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 Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-4877/modules/chem_data/mon_lib" Total number of atoms: 2676 Number of models: 1 Model: "" Number of chains: 6 Chain: "B" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "D" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "E" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "F" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "A" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Chain: "C" Number of atoms: 446 Number of conformers: 1 Conformer: "" Number of residues, atoms: 59, 446 Classifications: {'peptide': 59} Link IDs: {'PTRANS': 2, 'TRANS': 56} Time building chain proxies: 2.01, per 1000 atoms: 0.75 Number of scatterers: 2676 At special positions: 0 Unit cell: (99.6, 110.39, 34.86, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 6 16.00 O 516 8.00 N 486 7.00 C 1668 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=0, symmetry=0 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 0.99 Conformation dependent library (CDL) restraints added in 442.0 milliseconds 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 624 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 18.6% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.16 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'B' and resid 308 through 310 removed outlier: 6.673A pdb=" N VAL B 309 " --> pdb=" O TYR D 310 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL D 309 " --> pdb=" O TYR E 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'B' and resid 316 through 320 Processing sheet with id=AA3, first strand: chain 'B' and resid 328 through 330 removed outlier: 6.409A pdb=" N HIS B 329 " --> pdb=" O HIS D 330 " (cutoff:3.500A) removed outlier: 6.402A pdb=" N HIS D 329 " --> pdb=" O HIS E 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA3 Processing sheet with id=AA4, first strand: chain 'B' and resid 338 through 340 removed outlier: 6.652A pdb=" N GLU B 338 " --> pdb=" O VAL D 339 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU D 338 " --> pdb=" O VAL E 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA4 Processing sheet with id=AA5, first strand: chain 'B' and resid 349 through 350 Processing sheet with id=AA6, first strand: chain 'F' and resid 308 through 310 removed outlier: 6.673A pdb=" N VAL F 309 " --> pdb=" O TYR A 310 " (cutoff:3.500A) removed outlier: 6.673A pdb=" N VAL A 309 " --> pdb=" O TYR C 310 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA6 Processing sheet with id=AA7, first strand: chain 'F' and resid 316 through 320 Processing sheet with id=AA8, first strand: chain 'F' and resid 328 through 330 removed outlier: 6.410A pdb=" N HIS F 329 " --> pdb=" O HIS A 330 " (cutoff:3.500A) removed outlier: 6.403A pdb=" N HIS A 329 " --> pdb=" O HIS C 330 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA8 Processing sheet with id=AA9, first strand: chain 'F' and resid 338 through 340 removed outlier: 6.651A pdb=" N GLU F 338 " --> pdb=" O VAL A 339 " (cutoff:3.500A) removed outlier: 6.649A pdb=" N GLU A 338 " --> pdb=" O VAL C 339 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA9 Processing sheet with id=AB1, first strand: chain 'F' and resid 349 through 350 20 hydrogen bonds defined for protein. 60 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: 0.48 Time building geometry restraints manager: 1.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.33: 881 1.33 - 1.45: 217 1.45 - 1.56: 1608 1.56 - 1.67: 0 1.67 - 1.79: 6 Bond restraints: 2712 Sorted by residual: bond pdb=" CB VAL D 306 " pdb=" CG2 VAL D 306 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.68e+00 bond pdb=" CB VAL A 306 " pdb=" CG2 VAL A 306 " ideal model delta sigma weight residual 1.521 1.478 0.043 3.30e-02 9.18e+02 1.66e+00 bond pdb=" CB VAL E 306 " pdb=" CG2 VAL E 306 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB VAL C 306 " pdb=" CG2 VAL C 306 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.65e+00 bond pdb=" CB VAL F 306 " pdb=" CG2 VAL F 306 " ideal model delta sigma weight residual 1.521 1.479 0.042 3.30e-02 9.18e+02 1.64e+00 ... (remaining 2707 not shown) Histogram of bond angle deviations from ideal: 102.01 - 107.85: 174 107.85 - 113.69: 1532 113.69 - 119.53: 627 119.53 - 125.37: 1266 125.37 - 131.21: 31 Bond angle restraints: 3630 Sorted by residual: angle pdb=" N THR A 361 " pdb=" CA THR A 361 " pdb=" C THR A 361 " ideal model delta sigma weight residual 111.17 114.75 -3.58 1.41e+00 5.03e-01 6.44e+00 angle pdb=" N THR F 361 " pdb=" CA THR F 361 " pdb=" C THR F 361 " ideal model delta sigma weight residual 111.17 114.72 -3.55 1.41e+00 5.03e-01 6.35e+00 angle pdb=" N THR D 361 " pdb=" CA THR D 361 " pdb=" C THR D 361 " ideal model delta sigma weight residual 111.17 114.71 -3.54 1.41e+00 5.03e-01 6.31e+00 angle pdb=" N THR C 361 " pdb=" CA THR C 361 " pdb=" C THR C 361 " ideal model delta sigma weight residual 111.17 114.71 -3.54 1.41e+00 5.03e-01 6.31e+00 angle pdb=" N THR E 361 " pdb=" CA THR E 361 " pdb=" C THR E 361 " ideal model delta sigma weight residual 111.17 114.70 -3.53 1.41e+00 5.03e-01 6.26e+00 ... (remaining 3625 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.74: 1506 17.74 - 35.47: 114 35.47 - 53.21: 30 53.21 - 70.95: 0 70.95 - 88.68: 6 Dihedral angle restraints: 1656 sinusoidal: 678 harmonic: 978 Sorted by residual: dihedral pdb=" CB GLU B 338 " pdb=" CG GLU B 338 " pdb=" CD GLU B 338 " pdb=" OE1 GLU B 338 " ideal model delta sinusoidal sigma weight residual 0.00 88.68 -88.68 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU D 338 " pdb=" CG GLU D 338 " pdb=" CD GLU D 338 " pdb=" OE1 GLU D 338 " ideal model delta sinusoidal sigma weight residual 0.00 88.66 -88.66 1 3.00e+01 1.11e-03 1.04e+01 dihedral pdb=" CB GLU F 338 " pdb=" CG GLU F 338 " pdb=" CD GLU F 338 " pdb=" OE1 GLU F 338 " ideal model delta sinusoidal sigma weight residual 0.00 88.65 -88.65 1 3.00e+01 1.11e-03 1.04e+01 ... (remaining 1653 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.048: 296 0.048 - 0.095: 64 0.095 - 0.143: 36 0.143 - 0.190: 6 0.190 - 0.238: 12 Chirality restraints: 414 Sorted by residual: chirality pdb=" CB THR D 361 " pdb=" CA THR D 361 " pdb=" OG1 THR D 361 " pdb=" CG2 THR D 361 " both_signs ideal model delta sigma weight residual False 2.55 2.31 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CB THR E 361 " pdb=" CA THR E 361 " pdb=" OG1 THR E 361 " pdb=" CG2 THR E 361 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.40e+00 chirality pdb=" CB THR A 361 " pdb=" CA THR A 361 " pdb=" OG1 THR A 361 " pdb=" CG2 THR A 361 " both_signs ideal model delta sigma weight residual False 2.55 2.32 0.24 2.00e-01 2.50e+01 1.39e+00 ... (remaining 411 not shown) Planarity restraints: 462 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA SER E 341 " -0.004 2.00e-02 2.50e+03 7.23e-03 5.22e-01 pdb=" C SER E 341 " 0.013 2.00e-02 2.50e+03 pdb=" O SER E 341 " -0.005 2.00e-02 2.50e+03 pdb=" N GLU E 342 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER B 341 " -0.004 2.00e-02 2.50e+03 7.11e-03 5.06e-01 pdb=" C SER B 341 " 0.012 2.00e-02 2.50e+03 pdb=" O SER B 341 " -0.005 2.00e-02 2.50e+03 pdb=" N GLU B 342 " -0.004 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA SER D 341 " -0.003 2.00e-02 2.50e+03 6.96e-03 4.84e-01 pdb=" C SER D 341 " 0.012 2.00e-02 2.50e+03 pdb=" O SER D 341 " -0.005 2.00e-02 2.50e+03 pdb=" N GLU D 342 " -0.004 2.00e-02 2.50e+03 ... (remaining 459 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.84: 799 2.84 - 3.36: 2167 3.36 - 3.87: 4389 3.87 - 4.39: 4578 4.39 - 4.90: 9317 Nonbonded interactions: 21250 Sorted by model distance: nonbonded pdb=" NE2 GLN D 336 " pdb=" O GLN A 336 " model vdw 2.331 2.520 nonbonded pdb=" O GLN B 336 " pdb=" NE2 GLN A 336 " model vdw 2.343 2.520 nonbonded pdb=" O GLN D 336 " pdb=" NE2 GLN C 336 " model vdw 2.346 2.520 nonbonded pdb=" NE2 GLN B 336 " pdb=" O GLN F 336 " model vdw 2.355 2.520 nonbonded pdb=" NE2 GLN E 336 " pdb=" O GLN C 336 " model vdw 2.356 2.520 ... (remaining 21245 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' selection = chain 'D' selection = chain 'E' selection = chain 'F' } Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 6 5.16 5 C 1668 2.51 5 N 486 2.21 5 O 516 1.98 5 sf(0) = scattering factor at diffraction angle 0. Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as 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: 1.520 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 5.320 Check model and map are aligned: 0.040 Process input model: 12.690 Find NCS groups from input model: 0.170 Set up NCS constraints: 0.010 Set refine NCS operators: 0.000 Set scattering table: 0.030 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:13.490 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 33.270 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8191 moved from start: 0.0000 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.008 0.047 2712 Z= 0.563 Angle : 0.796 4.443 3630 Z= 0.430 Chirality : 0.064 0.238 414 Planarity : 0.003 0.007 462 Dihedral : 14.504 88.683 1032 Min Nonbonded Distance : 2.331 Molprobity Statistics. All-atom Clashscore : 9.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.28 % Favored : 87.72 % Rotamer Outliers : 0.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.97 (0.30), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.55 (0.23), residues: 342 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 81 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 81 time to evaluate : 0.364 Fit side-chains outliers start: 0 outliers final: 0 residues processed: 81 average time/residue: 1.4282 time to fit residues: 117.9263 Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.340 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.4604 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 25 optimal weight: 0.9990 chunk 22 optimal weight: 0.8980 chunk 12 optimal weight: 4.9990 chunk 7 optimal weight: 1.9990 chunk 15 optimal weight: 2.9990 chunk 23 optimal weight: 4.9990 chunk 9 optimal weight: 6.9990 chunk 14 optimal weight: 7.9990 chunk 17 optimal weight: 0.9990 chunk 27 optimal weight: 0.9980 chunk 8 optimal weight: 5.9990 overall best weight: 1.1786 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 307 GLN B 329 HIS B 330 HIS ** B 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 307 GLN D 329 HIS D 330 HIS E 307 GLN E 329 HIS F 307 GLN F 329 HIS F 330 HIS A 307 GLN A 329 HIS A 330 HIS C 307 GLN C 329 HIS Total number of N/Q/H flips: 16 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8103 moved from start: 0.2324 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.015 2712 Z= 0.176 Angle : 0.577 4.572 3630 Z= 0.284 Chirality : 0.053 0.146 414 Planarity : 0.002 0.021 462 Dihedral : 4.172 11.433 360 Min Nonbonded Distance : 2.260 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.73 % Favored : 93.27 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.49 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.18 (0.24), residues: 342 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 80 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 69 time to evaluate : 0.350 Fit side-chains outliers start: 11 outliers final: 4 residues processed: 72 average time/residue: 1.4824 time to fit residues: 108.7738 Evaluate side-chains 53 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 49 time to evaluate : 0.336 Switching outliers to nearest non-outliers outliers start: 4 outliers final: 1 residues processed: 3 average time/residue: 0.1431 time to fit residues: 0.9522 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 22 optimal weight: 3.9990 chunk 18 optimal weight: 0.1980 chunk 7 optimal weight: 5.9990 chunk 27 optimal weight: 1.9990 chunk 29 optimal weight: 8.9990 chunk 24 optimal weight: 3.9990 chunk 9 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 26 optimal weight: 4.9990 chunk 20 optimal weight: 5.9990 chunk 14 optimal weight: 5.9990 overall best weight: 2.6388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 351 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8108 moved from start: 0.2555 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.029 2712 Z= 0.268 Angle : 0.615 5.184 3630 Z= 0.300 Chirality : 0.052 0.149 414 Planarity : 0.002 0.013 462 Dihedral : 4.415 12.392 360 Min Nonbonded Distance : 2.250 Molprobity Statistics. All-atom Clashscore : 11.97 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 4.49 % 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: -5.53 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.21 (0.24), residues: 342 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 67 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 53 time to evaluate : 0.365 Fit side-chains outliers start: 14 outliers final: 7 residues processed: 63 average time/residue: 1.4438 time to fit residues: 92.8847 Evaluate side-chains 55 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 7 poor density : 48 time to evaluate : 0.352 Switching outliers to nearest non-outliers outliers start: 7 outliers final: 5 residues processed: 2 average time/residue: 0.1103 time to fit residues: 0.7373 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 3 optimal weight: 10.0000 chunk 13 optimal weight: 0.0010 chunk 18 optimal weight: 2.9990 chunk 27 optimal weight: 7.9990 chunk 28 optimal weight: 1.9990 chunk 14 optimal weight: 3.9990 chunk 25 optimal weight: 7.9990 chunk 7 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 16 optimal weight: 4.9990 chunk 0 optimal weight: 7.9990 overall best weight: 2.5994 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.2874 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.038 2712 Z= 0.270 Angle : 0.617 5.137 3630 Z= 0.305 Chirality : 0.052 0.148 414 Planarity : 0.003 0.019 462 Dihedral : 4.474 12.276 360 Min Nonbonded Distance : 2.244 Molprobity Statistics. All-atom Clashscore : 12.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.89 % Favored : 92.11 % Rotamer Outliers : 6.41 % 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: -5.42 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.12 (0.24), residues: 342 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 71 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 51 time to evaluate : 0.318 Fit side-chains outliers start: 20 outliers final: 13 residues processed: 64 average time/residue: 1.3339 time to fit residues: 87.3402 Evaluate side-chains 60 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 47 time to evaluate : 0.317 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 8 residues processed: 5 average time/residue: 0.3863 time to fit residues: 2.5096 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 21 optimal weight: 20.0000 chunk 11 optimal weight: 3.9990 chunk 24 optimal weight: 9.9990 chunk 20 optimal weight: 5.9990 chunk 0 optimal weight: 8.9990 chunk 14 optimal weight: 10.0000 chunk 26 optimal weight: 6.9990 chunk 7 optimal weight: 5.9990 chunk 9 optimal weight: 6.9990 chunk 5 optimal weight: 1.9990 chunk 17 optimal weight: 0.0570 overall best weight: 3.6106 ------------------------------------------------------------------------------- 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: 0.8083 moved from start: 0.3053 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.035 2712 Z= 0.337 Angle : 0.664 6.038 3630 Z= 0.327 Chirality : 0.053 0.147 414 Planarity : 0.003 0.021 462 Dihedral : 4.754 13.521 360 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 11.70 % Favored : 88.30 % Rotamer Outliers : 8.33 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.46 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.24), residues: 342 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 26 poor density : 47 time to evaluate : 0.319 Fit side-chains outliers start: 26 outliers final: 17 residues processed: 64 average time/residue: 1.2548 time to fit residues: 82.1844 Evaluate side-chains 65 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 48 time to evaluate : 0.348 Switching outliers to nearest non-outliers outliers start: 17 outliers final: 12 residues processed: 5 average time/residue: 0.1393 time to fit residues: 1.2709 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 0.7980 chunk 29 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 13 optimal weight: 3.9990 chunk 2 optimal weight: 0.9980 chunk 9 optimal weight: 0.8980 chunk 15 optimal weight: 7.9990 chunk 27 optimal weight: 0.9980 chunk 3 optimal weight: 0.8980 chunk 16 optimal weight: 0.9990 chunk 21 optimal weight: 5.9990 overall best weight: 0.9180 ------------------------------------------------------------------------------- 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: 0.8018 moved from start: 0.3405 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.002 0.019 2712 Z= 0.153 Angle : 0.536 4.638 3630 Z= 0.260 Chirality : 0.050 0.137 414 Planarity : 0.002 0.015 462 Dihedral : 3.913 11.222 360 Min Nonbonded Distance : 2.284 Molprobity Statistics. All-atom Clashscore : 10.31 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.97 % Favored : 95.03 % Rotamer Outliers : 6.41 % 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: -5.10 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.88 (0.25), residues: 342 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 74 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 54 time to evaluate : 0.317 Fit side-chains outliers start: 20 outliers final: 12 residues processed: 68 average time/residue: 1.1803 time to fit residues: 82.2103 Evaluate side-chains 60 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 48 time to evaluate : 0.343 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 8 residues processed: 4 average time/residue: 0.9353 time to fit residues: 4.2946 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 16 optimal weight: 5.9990 chunk 24 optimal weight: 9.9990 chunk 28 optimal weight: 1.9990 chunk 18 optimal weight: 9.9990 chunk 17 optimal weight: 3.9990 chunk 13 optimal weight: 6.9990 chunk 11 optimal weight: 9.9990 chunk 8 optimal weight: 10.0000 chunk 5 optimal weight: 0.5980 chunk 19 optimal weight: 5.9990 chunk 14 optimal weight: 3.9990 overall best weight: 3.3188 ------------------------------------------------------------------------------- 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: 0.8074 moved from start: 0.3194 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.005 0.033 2712 Z= 0.315 Angle : 0.642 6.118 3630 Z= 0.314 Chirality : 0.052 0.145 414 Planarity : 0.003 0.014 462 Dihedral : 4.554 13.169 360 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 14.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 12.57 % Favored : 87.43 % Rotamer Outliers : 5.45 % 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: -5.28 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.25), residues: 342 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 44 time to evaluate : 0.316 Fit side-chains outliers start: 17 outliers final: 12 residues processed: 59 average time/residue: 1.2871 time to fit residues: 77.6638 Evaluate side-chains 56 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 44 time to evaluate : 0.305 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 12 residues processed: 0 time to fit residues: 0.4034 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 2 optimal weight: 5.9990 chunk 22 optimal weight: 0.7980 chunk 26 optimal weight: 6.9990 chunk 27 optimal weight: 6.9990 chunk 25 optimal weight: 0.1980 chunk 16 optimal weight: 0.9980 chunk 11 optimal weight: 8.9990 chunk 21 optimal weight: 6.9990 chunk 8 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 17 optimal weight: 5.9990 overall best weight: 2.7984 ------------------------------------------------------------------------------- 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: 0.8071 moved from start: 0.3227 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.004 0.028 2712 Z= 0.275 Angle : 0.621 5.911 3630 Z= 0.302 Chirality : 0.052 0.144 414 Planarity : 0.003 0.014 462 Dihedral : 4.530 13.245 360 Min Nonbonded Distance : 2.256 Molprobity Statistics. All-atom Clashscore : 14.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.77 % Favored : 91.23 % Rotamer Outliers : 6.09 % 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: -5.28 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.02 (0.25), residues: 342 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 65 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 46 time to evaluate : 0.328 Fit side-chains outliers start: 19 outliers final: 13 residues processed: 60 average time/residue: 1.2512 time to fit residues: 76.8169 Evaluate side-chains 59 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 46 time to evaluate : 0.321 Switching outliers to nearest non-outliers outliers start: 13 outliers final: 10 residues processed: 3 average time/residue: 0.1263 time to fit residues: 0.8907 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 28 optimal weight: 9.9990 chunk 17 optimal weight: 2.9990 chunk 13 optimal weight: 6.9990 chunk 19 optimal weight: 6.9990 chunk 29 optimal weight: 7.9990 chunk 27 optimal weight: 9.9990 chunk 23 optimal weight: 9.9990 chunk 2 optimal weight: 0.0670 chunk 18 optimal weight: 1.9990 chunk 14 optimal weight: 4.9990 chunk 25 optimal weight: 0.0770 overall best weight: 2.0282 ------------------------------------------------------------------------------- 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: 0.8058 moved from start: 0.3314 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.022 2712 Z= 0.220 Angle : 0.591 6.278 3630 Z= 0.284 Chirality : 0.051 0.141 414 Planarity : 0.002 0.016 462 Dihedral : 4.282 12.731 360 Min Nonbonded Distance : 2.264 Molprobity Statistics. All-atom Clashscore : 12.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.48 % Favored : 91.52 % Rotamer Outliers : 3.53 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -5.21 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.25), residues: 342 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 56 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 45 time to evaluate : 0.345 Fit side-chains outliers start: 11 outliers final: 10 residues processed: 55 average time/residue: 1.3280 time to fit residues: 74.7606 Evaluate side-chains 52 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 42 time to evaluate : 0.356 Switching outliers to nearest non-outliers outliers start: 10 outliers final: 10 residues processed: 1 average time/residue: 0.0808 time to fit residues: 0.5887 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 7 optimal weight: 8.9990 chunk 21 optimal weight: 20.0000 chunk 3 optimal weight: 10.0000 chunk 6 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 9 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 4 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 1 optimal weight: 4.9990 chunk 17 optimal weight: 0.6980 overall best weight: 5.3388 ------------------------------------------------------------------------------- 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: 0.8093 moved from start: 0.3166 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.007 0.045 2712 Z= 0.459 Angle : 0.755 7.291 3630 Z= 0.371 Chirality : 0.055 0.148 414 Planarity : 0.004 0.031 462 Dihedral : 5.163 15.694 360 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 12.71 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.20 % Favored : 84.80 % Rotamer Outliers : 4.49 % 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: -5.47 (0.32), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.16 (0.24), residues: 342 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 684 Ramachandran restraints generated. 342 Oldfield, 0 Emsley, 342 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 61 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 14 poor density : 47 time to evaluate : 0.340 Fit side-chains outliers start: 14 outliers final: 12 residues processed: 58 average time/residue: 1.2900 time to fit residues: 76.6237 Evaluate side-chains 59 residues out of total 312 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 47 time to evaluate : 0.345 Switching outliers to nearest non-outliers outliers start: 12 outliers final: 10 residues processed: 2 average time/residue: 0.1892 time to fit residues: 0.8850 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 30 random chunks: chunk 27 optimal weight: 5.9990 chunk 16 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 0 optimal weight: 5.9990 chunk 19 optimal weight: 2.9990 chunk 18 optimal weight: 3.9990 chunk 17 optimal weight: 0.9990 chunk 11 optimal weight: 2.9990 chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 0.9980 chunk 28 optimal weight: 7.9990 overall best weight: 1.3384 ------------------------------------------------------------------------------- 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 = 0.4252 r_free = 0.4252 target = 0.141357 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 35)----------------| | r_work = 0.3941 r_free = 0.3941 target = 0.114148 restraints weight = 3368.550| |-----------------------------------------------------------------------------| r_work (start): 0.3954 rms_B_bonded: 2.03 r_work: 0.3863 rms_B_bonded: 2.15 restraints_weight: 0.5000 r_work: 0.3763 rms_B_bonded: 3.60 restraints_weight: 0.2500 r_work (final): 0.3763 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8174 moved from start: 0.3387 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd. rmsZ for bonds and angles. Bond : 0.003 0.020 2712 Z= 0.173 Angle : 0.569 6.450 3630 Z= 0.275 Chirality : 0.051 0.139 414 Planarity : 0.003 0.019 462 Dihedral : 4.221 12.762 360 Min Nonbonded Distance : 2.259 Molprobity Statistics. All-atom Clashscore : 10.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.56 % Favored : 94.44 % Rotamer Outliers : 3.21 % 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: -5.21 (0.33), residues: 342 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.96 (0.25), residues: 342 =============================================================================== Job complete usr+sys time: 1820.69 seconds wall clock time: 33 minutes 10.84 seconds (1990.84 seconds total)