Starting phenix.real_space_refine on Fri Apr 5 16:31:45 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoo_33354/04_2024/7xoo_33354.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoo_33354/04_2024/7xoo_33354.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.0 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoo_33354/04_2024/7xoo_33354.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoo_33354/04_2024/7xoo_33354.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoo_33354/04_2024/7xoo_33354.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7xoo_33354/04_2024/7xoo_33354.pdb" } resolution = 3.0 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= 0.006 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: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2397 2.51 5 N 665 2.21 5 O 773 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "B PHE 44": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B PHE 204": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 434": "OE1" <-> "OE2" Residue "B TYR 476": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5288/modules/chem_data/mon_lib" Total number of atoms: 3855 Number of models: 1 Model: "" Number of chains: 1 Chain: "B" Number of atoms: 3855 Number of conformers: 1 Conformer: "" Number of residues, atoms: 524, 3855 Classifications: {'peptide': 524} Link IDs: {'PTRANS': 14, 'TRANS': 509} Time building chain proxies: 2.67, per 1000 atoms: 0.69 Number of scatterers: 3855 At special positions: 0 Unit cell: (69.6, 73.95, 85.26, 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 20 16.00 O 773 8.00 N 665 7.00 C 2397 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: 1.46 Conformation dependent library (CDL) restraints added in 778.6 milliseconds 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 948 Finding SS restraints... Secondary structure from input PDB file: 19 helices and 7 sheets defined 59.4% alpha, 14.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.44 Creating SS restraints... Processing helix chain 'B' and resid 9 through 29 removed outlier: 4.116A pdb=" N VAL B 29 " --> pdb=" O ASP B 25 " (cutoff:3.500A) Processing helix chain 'B' and resid 52 through 60 Processing helix chain 'B' and resid 64 through 86 Processing helix chain 'B' and resid 88 through 109 Processing helix chain 'B' and resid 112 through 135 Processing helix chain 'B' and resid 140 through 152 Processing helix chain 'B' and resid 155 through 170 removed outlier: 3.598A pdb=" N GLY B 159 " --> pdb=" O ASP B 155 " (cutoff:3.500A) Processing helix chain 'B' and resid 201 through 205 Processing helix chain 'B' and resid 233 through 244 Processing helix chain 'B' and resid 256 through 268 Processing helix chain 'B' and resid 282 through 297 Processing helix chain 'B' and resid 338 through 355 removed outlier: 3.812A pdb=" N ILE B 342 " --> pdb=" O GLU B 338 " (cutoff:3.500A) Processing helix chain 'B' and resid 358 through 375 removed outlier: 4.218A pdb=" N GLY B 375 " --> pdb=" O LYS B 371 " (cutoff:3.500A) Processing helix chain 'B' and resid 385 through 409 Processing helix chain 'B' and resid 416 through 427 Processing helix chain 'B' and resid 433 through 459 Proline residue: B 450 - end of helix Processing helix chain 'B' and resid 461 through 472 Processing helix chain 'B' and resid 488 through 492 Processing helix chain 'B' and resid 497 through 516 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 8 Processing sheet with id=AA2, first strand: chain 'B' and resid 38 through 40 Processing sheet with id=AA3, first strand: chain 'B' and resid 174 through 179 removed outlier: 6.423A pdb=" N VAL B 174 " --> pdb=" O ALA B 377 " (cutoff:3.500A) removed outlier: 7.549A pdb=" N ILE B 379 " --> pdb=" O VAL B 174 " (cutoff:3.500A) removed outlier: 6.485A pdb=" N THR B 176 " --> pdb=" O ILE B 379 " (cutoff:3.500A) removed outlier: 7.356A pdb=" N VAL B 381 " --> pdb=" O THR B 176 " (cutoff:3.500A) removed outlier: 6.742A pdb=" N GLU B 178 " --> pdb=" O VAL B 381 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.373A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 3.720A pdb=" N VAL B 323 " --> pdb=" O LEU B 215 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'B' and resid 193 through 195 removed outlier: 6.373A pdb=" N GLY B 335 " --> pdb=" O ALA B 320 " (cutoff:3.500A) removed outlier: 6.527A pdb=" N ALA B 320 " --> pdb=" O GLY B 335 " (cutoff:3.500A) removed outlier: 6.093A pdb=" N PHE B 219 " --> pdb=" O LEU B 248 " (cutoff:3.500A) removed outlier: 7.205A pdb=" N ILE B 250 " --> pdb=" O PHE B 219 " (cutoff:3.500A) removed outlier: 6.258A pdb=" N LEU B 221 " --> pdb=" O ILE B 250 " (cutoff:3.500A) removed outlier: 6.372A pdb=" N LEU B 247 " --> pdb=" O ALA B 274 " (cutoff:3.500A) removed outlier: 7.843A pdb=" N VAL B 276 " --> pdb=" O LEU B 247 " (cutoff:3.500A) removed outlier: 5.927A pdb=" N ILE B 249 " --> pdb=" O VAL B 276 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 411 through 413 Processing sheet with id=AA7, first strand: chain 'B' and resid 476 through 479 270 hydrogen bonds defined for protein. 771 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: 1.14 Time building geometry restraints manager: 1.57 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1339 1.34 - 1.46: 414 1.46 - 1.57: 2093 1.57 - 1.69: 0 1.69 - 1.80: 37 Bond restraints: 3883 Sorted by residual: bond pdb=" CB THR B 522 " pdb=" CG2 THR B 522 " ideal model delta sigma weight residual 1.521 1.480 0.041 3.30e-02 9.18e+02 1.54e+00 bond pdb=" CB MET B 16 " pdb=" CG MET B 16 " ideal model delta sigma weight residual 1.520 1.495 0.025 3.00e-02 1.11e+03 6.87e-01 bond pdb=" CB MET B 520 " pdb=" CG MET B 520 " ideal model delta sigma weight residual 1.520 1.496 0.024 3.00e-02 1.11e+03 6.52e-01 bond pdb=" CA ALA B 449 " pdb=" C ALA B 449 " ideal model delta sigma weight residual 1.520 1.530 -0.010 1.23e-02 6.61e+03 6.46e-01 bond pdb=" C GLY B 70 " pdb=" O GLY B 70 " ideal model delta sigma weight residual 1.234 1.243 -0.010 1.21e-02 6.83e+03 6.31e-01 ... (remaining 3878 not shown) Histogram of bond angle deviations from ideal: 98.35 - 104.90: 55 104.90 - 111.45: 1814 111.45 - 118.00: 1196 118.00 - 124.56: 2159 124.56 - 131.11: 19 Bond angle restraints: 5243 Sorted by residual: angle pdb=" N GLY B 306 " pdb=" CA GLY B 306 " pdb=" C GLY B 306 " ideal model delta sigma weight residual 113.18 119.04 -5.86 2.37e+00 1.78e-01 6.12e+00 angle pdb=" N SER B 228 " pdb=" CA SER B 228 " pdb=" C SER B 228 " ideal model delta sigma weight residual 113.18 110.26 2.92 1.33e+00 5.65e-01 4.83e+00 angle pdb=" N ALA B 449 " pdb=" CA ALA B 449 " pdb=" C ALA B 449 " ideal model delta sigma weight residual 112.75 115.46 -2.71 1.36e+00 5.41e-01 3.98e+00 angle pdb=" N GLN B 351 " pdb=" CA GLN B 351 " pdb=" CB GLN B 351 " ideal model delta sigma weight residual 110.12 112.90 -2.78 1.47e+00 4.63e-01 3.58e+00 angle pdb=" CB MET B 69 " pdb=" CG MET B 69 " pdb=" SD MET B 69 " ideal model delta sigma weight residual 112.70 107.32 5.38 3.00e+00 1.11e-01 3.21e+00 ... (remaining 5238 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.66: 2218 15.66 - 31.31: 151 31.31 - 46.97: 35 46.97 - 62.62: 3 62.62 - 78.28: 5 Dihedral angle restraints: 2412 sinusoidal: 934 harmonic: 1478 Sorted by residual: dihedral pdb=" CA GLU B 338 " pdb=" C GLU B 338 " pdb=" N GLU B 339 " pdb=" CA GLU B 339 " ideal model delta harmonic sigma weight residual 180.00 -164.71 -15.29 0 5.00e+00 4.00e-02 9.35e+00 dihedral pdb=" CG ARG B 421 " pdb=" CD ARG B 421 " pdb=" NE ARG B 421 " pdb=" CZ ARG B 421 " ideal model delta sinusoidal sigma weight residual 180.00 -138.97 -41.03 2 1.50e+01 4.44e-03 9.19e+00 dihedral pdb=" CG LYS B 132 " pdb=" CD LYS B 132 " pdb=" CE LYS B 132 " pdb=" NZ LYS B 132 " ideal model delta sinusoidal sigma weight residual -60.00 -107.83 47.83 3 1.50e+01 4.44e-03 8.55e+00 ... (remaining 2409 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 395 0.028 - 0.057: 154 0.057 - 0.085: 50 0.085 - 0.114: 34 0.114 - 0.142: 5 Chirality restraints: 638 Sorted by residual: chirality pdb=" CA GLU B 102 " pdb=" N GLU B 102 " pdb=" C GLU B 102 " pdb=" CB GLU B 102 " both_signs ideal model delta sigma weight residual False 2.51 2.37 0.14 2.00e-01 2.50e+01 5.04e-01 chirality pdb=" CA ILE B 332 " pdb=" N ILE B 332 " pdb=" C ILE B 332 " pdb=" CB ILE B 332 " both_signs ideal model delta sigma weight residual False 2.43 2.55 -0.12 2.00e-01 2.50e+01 3.65e-01 chirality pdb=" CA PRO B 462 " pdb=" N PRO B 462 " pdb=" C PRO B 462 " pdb=" CB PRO B 462 " both_signs ideal model delta sigma weight residual False 2.72 2.60 0.12 2.00e-01 2.50e+01 3.54e-01 ... (remaining 635 not shown) Planarity restraints: 687 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA B 98 " -0.009 2.00e-02 2.50e+03 1.89e-02 3.56e+00 pdb=" C ALA B 98 " 0.033 2.00e-02 2.50e+03 pdb=" O ALA B 98 " -0.012 2.00e-02 2.50e+03 pdb=" N ILE B 99 " -0.011 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA MET B 233 " 0.005 2.00e-02 2.50e+03 1.09e-02 1.19e+00 pdb=" C MET B 233 " -0.019 2.00e-02 2.50e+03 pdb=" O MET B 233 " 0.007 2.00e-02 2.50e+03 pdb=" N LEU B 234 " 0.006 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C ALA B 449 " -0.015 5.00e-02 4.00e+02 2.26e-02 8.20e-01 pdb=" N PRO B 450 " 0.039 5.00e-02 4.00e+02 pdb=" CA PRO B 450 " -0.011 5.00e-02 4.00e+02 pdb=" CD PRO B 450 " -0.013 5.00e-02 4.00e+02 ... (remaining 684 not shown) Histogram of nonbonded interaction distances: 2.33 - 2.85: 1284 2.85 - 3.36: 4021 3.36 - 3.87: 6325 3.87 - 4.39: 6853 4.39 - 4.90: 12172 Nonbonded interactions: 30655 Sorted by model distance: nonbonded pdb=" OD1 ASN B 479 " pdb=" OG1 THR B 482 " model vdw 2.333 2.440 nonbonded pdb=" OG SER B 135 " pdb=" OG1 THR B 497 " model vdw 2.339 2.440 nonbonded pdb=" OE2 GLU B 339 " pdb=" NE2 GLN B 343 " model vdw 2.374 2.520 nonbonded pdb=" O PHE B 219 " pdb=" N LEU B 248 " model vdw 2.407 2.520 nonbonded pdb=" OD1 ASN B 229 " pdb=" N ILE B 230 " model vdw 2.431 2.520 ... (remaining 30650 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=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: 1.270 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: 5.650 Check model and map are aligned: 0.070 Set scattering table: 0.040 Process input model: 15.270 Find NCS groups from input model: 0.110 Set up NCS constraints: 0.020 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:12.650 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 35.080 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8614 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 : 0.003 0.041 3883 Z= 0.214 Angle : 0.461 5.862 5243 Z= 0.255 Chirality : 0.039 0.142 638 Planarity : 0.002 0.023 687 Dihedral : 11.952 78.277 1464 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 7.79 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.00 % Allowed : 0.25 % Favored : 99.75 % 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: 2.57 (0.36), residues: 522 helix: 2.86 (0.29), residues: 297 sheet: 0.25 (0.54), residues: 88 loop : 0.10 (0.51), residues: 137 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.007 0.001 PHE B 195 TYR 0.008 0.001 TYR B 199 ARG 0.003 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 27 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 27 time to evaluate : 0.459 Fit side-chains revert: symmetry clash REVERT: B 288 MET cc_start: 0.8613 (mtt) cc_final: 0.8396 (mtt) outliers start: 0 outliers final: 0 residues processed: 27 average time/residue: 1.7153 time to fit residues: 47.8678 Evaluate side-chains 20 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 43 optimal weight: 0.9990 chunk 39 optimal weight: 4.9990 chunk 21 optimal weight: 0.0030 chunk 13 optimal weight: 3.9990 chunk 26 optimal weight: 1.9990 chunk 40 optimal weight: 9.9990 chunk 15 optimal weight: 5.9990 chunk 24 optimal weight: 8.9990 chunk 30 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 14 optimal weight: 8.9990 overall best weight: 2.1998 ------------------------------------------------------------------------------- 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: 0.8628 moved from start: 0.1037 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3883 Z= 0.187 Angle : 0.449 6.068 5243 Z= 0.244 Chirality : 0.040 0.153 638 Planarity : 0.002 0.022 687 Dihedral : 3.534 13.955 552 Min Nonbonded Distance : 2.360 Molprobity Statistics. All-atom Clashscore : 8.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.99 % Allowed : 5.20 % Favored : 93.81 % 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: 2.60 (0.36), residues: 522 helix: 2.99 (0.29), residues: 301 sheet: 0.14 (0.55), residues: 88 loop : -0.15 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.015 0.001 PHE B 195 TYR 0.006 0.001 TYR B 360 ARG 0.002 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 21 time to evaluate : 0.473 Fit side-chains REVERT: B 518 GLU cc_start: 0.6389 (pt0) cc_final: 0.5989 (pt0) outliers start: 4 outliers final: 1 residues processed: 22 average time/residue: 1.5958 time to fit residues: 36.5249 Evaluate side-chains 20 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 19 time to evaluate : 0.446 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 522 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 39 optimal weight: 4.9990 chunk 32 optimal weight: 0.8980 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 5.9990 chunk 51 optimal weight: 0.9990 chunk 42 optimal weight: 4.9990 chunk 46 optimal weight: 0.8980 chunk 16 optimal weight: 5.9990 chunk 37 optimal weight: 8.9990 chunk 35 optimal weight: 0.0470 chunk 24 optimal weight: 20.0000 overall best weight: 1.3682 ------------------------------------------------------------------------------- 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: 0.8607 moved from start: 0.1295 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3883 Z= 0.141 Angle : 0.430 6.781 5243 Z= 0.232 Chirality : 0.039 0.141 638 Planarity : 0.002 0.021 687 Dihedral : 3.485 15.686 552 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 0.25 % Allowed : 7.92 % Favored : 91.83 % 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: 2.63 (0.37), residues: 522 helix: 2.98 (0.28), residues: 304 sheet: 0.21 (0.57), residues: 88 loop : -0.19 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.013 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.003 0.000 ARG B 362 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 21 time to evaluate : 0.467 Fit side-chains revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 22 average time/residue: 1.4416 time to fit residues: 33.0583 Evaluate side-chains 19 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 19 time to evaluate : 0.479 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 4.9990 chunk 22 optimal weight: 20.0000 chunk 31 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 50 optimal weight: 6.9990 chunk 24 optimal weight: 20.0000 chunk 44 optimal weight: 0.0870 chunk 13 optimal weight: 0.9990 chunk 41 optimal weight: 7.9990 chunk 28 optimal weight: 4.9990 chunk 0 optimal weight: 8.9990 overall best weight: 3.6166 ------------------------------------------------------------------------------- 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: 0.8667 moved from start: 0.1545 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3883 Z= 0.266 Angle : 0.467 7.006 5243 Z= 0.248 Chirality : 0.040 0.138 638 Planarity : 0.002 0.022 687 Dihedral : 3.583 16.403 552 Min Nonbonded Distance : 2.304 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Rotamer: Outliers : 0.74 % Allowed : 9.41 % Favored : 89.85 % 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: 2.65 (0.37), residues: 522 helix: 3.00 (0.29), residues: 301 sheet: 0.30 (0.57), residues: 88 loop : -0.17 (0.50), residues: 133 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.001 0.000 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.006 0.001 TYR B 360 ARG 0.002 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 24 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 21 time to evaluate : 0.396 Fit side-chains revert: symmetry clash REVERT: B 518 GLU cc_start: 0.6587 (pt0) cc_final: 0.5917 (pt0) outliers start: 3 outliers final: 0 residues processed: 23 average time/residue: 1.5653 time to fit residues: 37.4179 Evaluate side-chains 20 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 20 time to evaluate : 0.449 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 37 optimal weight: 9.9990 chunk 20 optimal weight: 7.9990 chunk 42 optimal weight: 6.9990 chunk 34 optimal weight: 6.9990 chunk 0 optimal weight: 7.9990 chunk 25 optimal weight: 8.9990 chunk 45 optimal weight: 0.6980 chunk 12 optimal weight: 2.9990 chunk 16 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 29 optimal weight: 4.9990 overall best weight: 2.2986 ------------------------------------------------------------------------------- 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: 0.8647 moved from start: 0.1668 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3883 Z= 0.185 Angle : 0.435 8.339 5243 Z= 0.229 Chirality : 0.039 0.137 638 Planarity : 0.002 0.022 687 Dihedral : 3.525 14.394 552 Min Nonbonded Distance : 2.323 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.50 % Allowed : 11.39 % Favored : 88.12 % 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: 2.69 (0.37), residues: 522 helix: 3.05 (0.29), residues: 302 sheet: 0.29 (0.57), residues: 88 loop : -0.21 (0.50), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.013 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 20 time to evaluate : 0.401 Fit side-chains revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 22 average time/residue: 1.4487 time to fit residues: 33.2741 Evaluate side-chains 21 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 20 time to evaluate : 0.447 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 12 optimal weight: 1.9990 chunk 50 optimal weight: 0.9990 chunk 41 optimal weight: 9.9990 chunk 23 optimal weight: 8.9990 chunk 4 optimal weight: 0.0870 chunk 16 optimal weight: 7.9990 chunk 26 optimal weight: 9.9990 chunk 48 optimal weight: 10.0000 chunk 5 optimal weight: 0.8980 chunk 28 optimal weight: 10.0000 chunk 36 optimal weight: 2.9990 overall best weight: 1.3964 ------------------------------------------------------------------------------- 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: 0.8623 moved from start: 0.1752 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.022 3883 Z= 0.140 Angle : 0.427 8.832 5243 Z= 0.225 Chirality : 0.038 0.136 638 Planarity : 0.002 0.020 687 Dihedral : 3.471 14.239 552 Min Nonbonded Distance : 2.333 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.57 % Favored : 99.43 % Rotamer: Outliers : 1.24 % Allowed : 11.14 % Favored : 87.62 % 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: 2.77 (0.37), residues: 522 helix: 3.09 (0.29), residues: 304 sheet: 0.31 (0.57), residues: 88 loop : -0.16 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.013 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 25 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 5 poor density : 20 time to evaluate : 0.447 Fit side-chains revert: symmetry clash outliers start: 5 outliers final: 3 residues processed: 25 average time/residue: 1.2908 time to fit residues: 33.8023 Evaluate side-chains 23 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.437 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 169 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 28 optimal weight: 8.9990 chunk 42 optimal weight: 0.9980 chunk 50 optimal weight: 0.9980 chunk 31 optimal weight: 30.0000 chunk 30 optimal weight: 6.9990 chunk 23 optimal weight: 5.9990 chunk 20 optimal weight: 5.9990 chunk 29 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 6.9990 overall best weight: 2.9384 ------------------------------------------------------------------------------- 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: 0.8658 moved from start: 0.1789 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3883 Z= 0.221 Angle : 0.455 9.929 5243 Z= 0.238 Chirality : 0.039 0.137 638 Planarity : 0.002 0.022 687 Dihedral : 3.516 13.651 552 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.96 % Favored : 99.04 % Rotamer: Outliers : 0.74 % Allowed : 11.88 % Favored : 87.38 % 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: 2.73 (0.37), residues: 522 helix: 3.07 (0.29), residues: 302 sheet: 0.37 (0.57), residues: 88 loop : -0.24 (0.49), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.010 0.001 PHE B 195 TYR 0.005 0.001 TYR B 476 ARG 0.001 0.000 ARG B 368 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 23 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 20 time to evaluate : 0.431 Fit side-chains REVERT: B 193 MET cc_start: 0.9119 (ptp) cc_final: 0.8807 (ptt) outliers start: 3 outliers final: 3 residues processed: 23 average time/residue: 1.2379 time to fit residues: 29.9233 Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.477 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 27 VAL Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 169 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 24 optimal weight: 10.0000 chunk 4 optimal weight: 8.9990 chunk 39 optimal weight: 0.9990 chunk 45 optimal weight: 2.9990 chunk 48 optimal weight: 0.7980 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.7980 chunk 28 optimal weight: 6.9990 chunk 20 optimal weight: 5.9990 chunk 36 optimal weight: 1.9990 chunk 14 optimal weight: 9.9990 overall best weight: 1.5186 ------------------------------------------------------------------------------- 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: 0.8626 moved from start: 0.1868 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.023 3883 Z= 0.146 Angle : 0.453 10.933 5243 Z= 0.237 Chirality : 0.038 0.136 638 Planarity : 0.002 0.020 687 Dihedral : 3.460 13.181 552 Min Nonbonded Distance : 2.339 Molprobity Statistics. All-atom Clashscore : 6.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.74 % Allowed : 12.62 % Favored : 86.63 % 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: 2.77 (0.37), residues: 522 helix: 3.07 (0.29), residues: 304 sheet: 0.40 (0.58), residues: 88 loop : -0.19 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.477 Fit side-chains revert: symmetry clash REVERT: B 193 MET cc_start: 0.9093 (ptp) cc_final: 0.8774 (ptt) outliers start: 3 outliers final: 2 residues processed: 22 average time/residue: 1.4080 time to fit residues: 32.3931 Evaluate side-chains 21 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 19 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 42 optimal weight: 5.9990 chunk 44 optimal weight: 0.9980 chunk 46 optimal weight: 3.9990 chunk 30 optimal weight: 3.9990 chunk 49 optimal weight: 0.9990 chunk 23 optimal weight: 6.9990 chunk 34 optimal weight: 10.0000 chunk 51 optimal weight: 6.9990 chunk 47 optimal weight: 3.9990 chunk 41 optimal weight: 0.8980 chunk 4 optimal weight: 0.0670 overall best weight: 1.3922 ------------------------------------------------------------------------------- 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: 0.8619 moved from start: 0.1893 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3883 Z= 0.143 Angle : 0.459 11.980 5243 Z= 0.240 Chirality : 0.038 0.135 638 Planarity : 0.002 0.021 687 Dihedral : 3.426 12.809 552 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 7.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Rotamer: Outliers : 0.74 % Allowed : 12.62 % Favored : 86.63 % 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: 2.75 (0.37), residues: 522 helix: 3.06 (0.28), residues: 304 sheet: 0.40 (0.58), residues: 88 loop : -0.20 (0.50), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 404 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.402 Fit side-chains revert: symmetry clash outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 1.3257 time to fit residues: 30.6384 Evaluate side-chains 21 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.353 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 20.0000 chunk 32 optimal weight: 0.9990 chunk 43 optimal weight: 3.9990 chunk 12 optimal weight: 0.9990 chunk 38 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 11 optimal weight: 0.9990 chunk 41 optimal weight: 8.9990 chunk 17 optimal weight: 1.9990 chunk 42 optimal weight: 0.9980 overall best weight: 1.1988 ------------------------------------------------------------------------------- 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: 0.8609 moved from start: 0.1976 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.026 3883 Z= 0.135 Angle : 0.466 12.713 5243 Z= 0.241 Chirality : 0.038 0.135 638 Planarity : 0.002 0.021 687 Dihedral : 3.394 12.850 552 Min Nonbonded Distance : 2.338 Molprobity Statistics. All-atom Clashscore : 6.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Rotamer: Outliers : 0.74 % Allowed : 12.62 % Favored : 86.63 % 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: 2.82 (0.37), residues: 522 helix: 3.10 (0.28), residues: 304 sheet: 0.46 (0.59), residues: 88 loop : -0.16 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.011 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 345 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1044 Ramachandran restraints generated. 522 Oldfield, 0 Emsley, 522 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 22 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 19 time to evaluate : 0.442 Fit side-chains revert: symmetry clash REVERT: B 193 MET cc_start: 0.9148 (ptp) cc_final: 0.8787 (ptt) outliers start: 3 outliers final: 3 residues processed: 22 average time/residue: 1.3286 time to fit residues: 30.6111 Evaluate side-chains 21 residues out of total 404 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 18 time to evaluate : 0.440 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain B residue 54 VAL Chi-restraints excluded: chain B residue 169 VAL Chi-restraints excluded: chain B residue 351 GLN Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 52 random chunks: chunk 5 optimal weight: 6.9990 chunk 7 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 2 optimal weight: 4.9990 chunk 29 optimal weight: 0.1980 chunk 47 optimal weight: 10.0000 chunk 27 optimal weight: 5.9990 chunk 35 optimal weight: 6.9990 chunk 1 optimal weight: 0.8980 chunk 33 optimal weight: 0.9990 chunk 31 optimal weight: 8.9990 overall best weight: 2.4186 ------------------------------------------------------------------------------- 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 = 0.3437 r_free = 0.3437 target = 0.078933 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 41)----------------| | r_work = 0.2916 r_free = 0.2916 target = 0.054310 restraints weight = 9355.357| |-----------------------------------------------------------------------------| r_work (start): 0.2870 rms_B_bonded: 2.79 r_work: 0.2717 rms_B_bonded: 3.12 restraints_weight: 0.5000 r_work (final): 0.2717 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8774 moved from start: 0.1993 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.065 3883 Z= 0.198 Angle : 0.500 12.787 5243 Z= 0.259 Chirality : 0.039 0.136 638 Planarity : 0.002 0.021 687 Dihedral : 3.445 13.393 552 Min Nonbonded Distance : 2.327 Molprobity Statistics. All-atom Clashscore : 6.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.34 % Favored : 98.66 % Rotamer: Outliers : 0.74 % Allowed : 13.12 % Favored : 86.14 % 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: 2.75 (0.37), residues: 522 helix: 3.09 (0.28), residues: 304 sheet: 0.26 (0.57), residues: 88 loop : -0.18 (0.51), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.000 0.000 HIS B 401 PHE 0.010 0.001 PHE B 195 TYR 0.006 0.001 TYR B 476 ARG 0.001 0.000 ARG B 404 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1364.04 seconds wall clock time: 25 minutes 21.30 seconds (1521.30 seconds total)