Starting phenix.real_space_refine on Thu Jul 18 21:38:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn0_32618/07_2024/7wn0_32618.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn0_32618/07_2024/7wn0_32618.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.64 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn0_32618/07_2024/7wn0_32618.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn0_32618/07_2024/7wn0_32618.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn0_32618/07_2024/7wn0_32618.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7wn0_32618/07_2024/7wn0_32618.cif" } resolution = 3.64 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= 0.001 sd= 0.028 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 26 5.16 5 C 2553 2.51 5 N 617 2.21 5 O 683 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 82": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 92": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 111": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A PHE 116": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 146": "OE1" <-> "OE2" Residue "A TYR 152": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A ASP 238": "OD1" <-> "OD2" Residue "A ASP 273": "OD1" <-> "OD2" Residue "B TYR 37": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 64": "OE1" <-> "OE2" Residue "B TYR 79": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 88": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5388/modules/chem_data/mon_lib" Total number of atoms: 3879 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2953 Number of conformers: 1 Conformer: "" Number of residues, atoms: 371, 2953 Classifications: {'peptide': 371} Link IDs: {'PTRANS': 11, 'TRANS': 359} Chain breaks: 1 Chain: "B" Number of atoms: 926 Number of conformers: 1 Conformer: "" Number of residues, atoms: 123, 926 Classifications: {'peptide': 123} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 2, 'TRANS': 120} Time building chain proxies: 3.10, per 1000 atoms: 0.80 Number of scatterers: 3879 At special positions: 0 Unit cell: (112.05, 57.27, 61.42, 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 26 16.00 O 683 8.00 N 617 7.00 C 2553 6.00 sf(0) = scattering factor at diffraction angle 0. Number of disulfides: simple=1, symmetry=0 Simple disulfide: pdb=" SG CYS B 22 " - pdb=" SG CYS B 95 " distance=2.03 Automatic linking Parameters for automatic linking Linking & cutoffs Metal : Auto - 3.50 Amino acid : False - 1.90 Carbohydrate : True - 1.99 Ligands : True - 1.99 Small molecules : False - 1.98 Amino acid - RNA/DNA : False Number of custom bonds: simple=0, symmetry=0 Time building additional restraints: 1.53 Conformation dependent library (CDL) restraints added in 673.2 milliseconds 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 920 Finding SS restraints... Secondary structure from input PDB file: 17 helices and 3 sheets defined 61.7% alpha, 15.2% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.39 Creating SS restraints... Processing helix chain 'A' and resid 31 through 59 removed outlier: 4.516A pdb=" N VAL A 52 " --> pdb=" O SER A 48 " (cutoff:3.500A) removed outlier: 4.747A pdb=" N TRP A 53 " --> pdb=" O SER A 49 " (cutoff:3.500A) Processing helix chain 'A' and resid 62 through 83 removed outlier: 3.887A pdb=" N PHE A 82 " --> pdb=" O ILE A 78 " (cutoff:3.500A) Processing helix chain 'A' and resid 89 through 111 Processing helix chain 'A' and resid 112 through 144 Processing helix chain 'A' and resid 149 through 173 removed outlier: 4.389A pdb=" N GLN A 173 " --> pdb=" O LEU A 169 " (cutoff:3.500A) Processing helix chain 'A' and resid 184 through 210 Processing helix chain 'A' and resid 231 through 239 Processing helix chain 'A' and resid 239 through 257 removed outlier: 3.802A pdb=" N ILE A 243 " --> pdb=" O SER A 239 " (cutoff:3.500A) removed outlier: 3.798A pdb=" N VAL A 249 " --> pdb=" O THR A 245 " (cutoff:3.500A) Processing helix chain 'A' and resid 262 through 270 Processing helix chain 'A' and resid 272 through 282 removed outlier: 3.752A pdb=" N ILE A 278 " --> pdb=" O TYR A 274 " (cutoff:3.500A) Processing helix chain 'A' and resid 282 through 290 removed outlier: 4.284A pdb=" N PHE A 288 " --> pdb=" O GLN A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 309 through 320 removed outlier: 3.678A pdb=" N VAL A 314 " --> pdb=" O ASN A 310 " (cutoff:3.500A) Processing helix chain 'A' and resid 321 through 329 removed outlier: 3.769A pdb=" N TRP A 325 " --> pdb=" O LEU A 321 " (cutoff:3.500A) Processing helix chain 'A' and resid 339 through 369 removed outlier: 3.519A pdb=" N LEU A 350 " --> pdb=" O CYS A 346 " (cutoff:3.500A) removed outlier: 3.645A pdb=" N GLY A 355 " --> pdb=" O ALA A 351 " (cutoff:3.500A) removed outlier: 3.500A pdb=" N PHE A 357 " --> pdb=" O THR A 353 " (cutoff:3.500A) removed outlier: 3.598A pdb=" N VAL A 360 " --> pdb=" O TRP A 356 " (cutoff:3.500A) Proline residue: A 361 - end of helix removed outlier: 5.247A pdb=" N VAL A 366 " --> pdb=" O PHE A 362 " (cutoff:3.500A) removed outlier: 5.454A pdb=" N LYS A 367 " --> pdb=" O LEU A 363 " (cutoff:3.500A) removed outlier: 3.592A pdb=" N GLU A 368 " --> pdb=" O VAL A 364 " (cutoff:3.500A) Processing helix chain 'A' and resid 374 through 399 removed outlier: 3.611A pdb=" N GLU A 379 " --> pdb=" O LYS A 375 " (cutoff:3.500A) removed outlier: 3.787A pdb=" N TRP A 398 " --> pdb=" O PHE A 394 " (cutoff:3.500A) Processing helix chain 'A' and resid 401 through 406 removed outlier: 4.005A pdb=" N LEU A 405 " --> pdb=" O TYR A 401 " (cutoff:3.500A) removed outlier: 4.063A pdb=" N PHE A 406 " --> pdb=" O ILE A 402 " (cutoff:3.500A) No H-bonds generated for 'chain 'A' and resid 401 through 406' Processing helix chain 'B' and resid 86 through 90 Processing sheet with id=AA1, first strand: chain 'B' and resid 4 through 7 Processing sheet with id=AA2, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.716A pdb=" N SER B 122 " --> pdb=" O VAL B 12 " (cutoff:3.500A) removed outlier: 3.885A pdb=" N VAL B 33 " --> pdb=" O TYR B 98 " (cutoff:3.500A) removed outlier: 5.637A pdb=" N ARG B 38 " --> pdb=" O LEU B 47 " (cutoff:3.500A) removed outlier: 5.192A pdb=" N LEU B 47 " --> pdb=" O ARG B 38 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'B' and resid 11 through 13 removed outlier: 3.716A pdb=" N SER B 122 " --> pdb=" O VAL B 12 " (cutoff:3.500A) 259 hydrogen bonds defined for protein. 753 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: 1.11 Time building geometry restraints manager: 1.65 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: 1176 1.34 - 1.46: 999 1.46 - 1.58: 1757 1.58 - 1.70: 0 1.70 - 1.82: 39 Bond restraints: 3971 Sorted by residual: bond pdb=" N TYR B 103 " pdb=" CA TYR B 103 " ideal model delta sigma weight residual 1.457 1.497 -0.040 1.35e-02 5.49e+03 8.72e+00 bond pdb=" CG PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 1.503 1.539 -0.036 3.40e-02 8.65e+02 1.11e+00 bond pdb=" CA VAL B 48 " pdb=" CB VAL B 48 " ideal model delta sigma weight residual 1.545 1.538 0.007 9.10e-03 1.21e+04 6.63e-01 bond pdb=" CB ASP A 333 " pdb=" CG ASP A 333 " ideal model delta sigma weight residual 1.516 1.535 -0.019 2.50e-02 1.60e+03 5.84e-01 bond pdb=" CB LEU A 44 " pdb=" CG LEU A 44 " ideal model delta sigma weight residual 1.530 1.515 0.015 2.00e-02 2.50e+03 5.74e-01 ... (remaining 3966 not shown) Histogram of bond angle deviations from ideal: 99.07 - 106.05: 57 106.05 - 113.03: 2172 113.03 - 120.01: 1363 120.01 - 126.99: 1761 126.99 - 133.98: 38 Bond angle restraints: 5391 Sorted by residual: angle pdb=" CA PRO A 258 " pdb=" N PRO A 258 " pdb=" CD PRO A 258 " ideal model delta sigma weight residual 112.00 107.92 4.08 1.40e+00 5.10e-01 8.51e+00 angle pdb=" CA LEU A 201 " pdb=" CB LEU A 201 " pdb=" CG LEU A 201 " ideal model delta sigma weight residual 116.30 125.86 -9.56 3.50e+00 8.16e-02 7.47e+00 angle pdb=" N TYR B 103 " pdb=" CA TYR B 103 " pdb=" C TYR B 103 " ideal model delta sigma weight residual 112.87 110.07 2.80 1.20e+00 6.94e-01 5.43e+00 angle pdb=" CB MET A 233 " pdb=" CG MET A 233 " pdb=" SD MET A 233 " ideal model delta sigma weight residual 112.70 119.59 -6.89 3.00e+00 1.11e-01 5.27e+00 angle pdb=" N SER A 308 " pdb=" CA SER A 308 " pdb=" C SER A 308 " ideal model delta sigma weight residual 107.88 110.66 -2.78 1.41e+00 5.03e-01 3.87e+00 ... (remaining 5386 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 17.13: 1943 17.13 - 34.27: 278 34.27 - 51.40: 74 51.40 - 68.54: 8 68.54 - 85.67: 2 Dihedral angle restraints: 2305 sinusoidal: 875 harmonic: 1430 Sorted by residual: dihedral pdb=" CA HIS A 334 " pdb=" C HIS A 334 " pdb=" N PRO A 335 " pdb=" CA PRO A 335 " ideal model delta harmonic sigma weight residual 180.00 -159.76 -20.24 0 5.00e+00 4.00e-02 1.64e+01 dihedral pdb=" CA ASN A 148 " pdb=" CB ASN A 148 " pdb=" CG ASN A 148 " pdb=" OD1 ASN A 148 " ideal model delta sinusoidal sigma weight residual -90.00 -163.46 73.46 2 2.00e+01 2.50e-03 1.10e+01 dihedral pdb=" CG ARG B 66 " pdb=" CD ARG B 66 " pdb=" NE ARG B 66 " pdb=" CZ ARG B 66 " ideal model delta sinusoidal sigma weight residual -180.00 -135.39 -44.61 2 1.50e+01 4.44e-03 1.05e+01 ... (remaining 2302 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.028: 354 0.028 - 0.056: 174 0.056 - 0.085: 69 0.085 - 0.113: 27 0.113 - 0.141: 4 Chirality restraints: 628 Sorted by residual: chirality pdb=" CA PRO A 335 " pdb=" N PRO A 335 " pdb=" C PRO A 335 " pdb=" CB PRO A 335 " both_signs ideal model delta sigma weight residual False 2.72 2.58 0.14 2.00e-01 2.50e+01 4.97e-01 chirality pdb=" CA TYR B 105 " pdb=" N TYR B 105 " pdb=" C TYR B 105 " pdb=" CB TYR B 105 " both_signs ideal model delta sigma weight residual False 2.51 2.38 0.13 2.00e-01 2.50e+01 4.23e-01 chirality pdb=" CA VAL A 183 " pdb=" N VAL A 183 " pdb=" C VAL A 183 " pdb=" CB VAL A 183 " both_signs ideal model delta sigma weight residual False 2.44 2.57 -0.13 2.00e-01 2.50e+01 3.92e-01 ... (remaining 625 not shown) Planarity restraints: 663 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C PHE A 257 " -0.065 5.00e-02 4.00e+02 9.76e-02 1.52e+01 pdb=" N PRO A 258 " 0.169 5.00e-02 4.00e+02 pdb=" CA PRO A 258 " -0.050 5.00e-02 4.00e+02 pdb=" CD PRO A 258 " -0.053 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C PRO A 293 " 0.035 5.00e-02 4.00e+02 5.24e-02 4.40e+00 pdb=" N PRO A 294 " -0.091 5.00e-02 4.00e+02 pdb=" CA PRO A 294 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 294 " 0.030 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CA TYR A 119 " 0.009 2.00e-02 2.50e+03 1.81e-02 3.28e+00 pdb=" C TYR A 119 " -0.031 2.00e-02 2.50e+03 pdb=" O TYR A 119 " 0.012 2.00e-02 2.50e+03 pdb=" N CYS A 120 " 0.011 2.00e-02 2.50e+03 ... (remaining 660 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1043 2.80 - 3.32: 3846 3.32 - 3.85: 6520 3.85 - 4.37: 7483 4.37 - 4.90: 13006 Nonbonded interactions: 31898 Sorted by model distance: nonbonded pdb=" N GLU B 88 " pdb=" OE1 GLU B 88 " model vdw 2.273 2.520 nonbonded pdb=" N GLU A 146 " pdb=" OE1 GLU A 146 " model vdw 2.275 2.520 nonbonded pdb=" OG1 THR A 253 " pdb=" NH2 ARG A 319 " model vdw 2.284 2.520 nonbonded pdb=" N GLN B 44 " pdb=" OE1 GLN B 44 " model vdw 2.316 2.520 nonbonded pdb=" O SER B 102 " pdb=" OG SER B 102 " model vdw 2.325 2.440 ... (remaining 31893 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 group one per residue 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: 1.490 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: 0.170 Check model and map are aligned: 0.030 Set scattering table: 0.040 Process input model: 15.810 Find NCS groups from input model: 0.040 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:2.840 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.440 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 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 0.040 3971 Z= 0.199 Angle : 0.572 9.565 5391 Z= 0.296 Chirality : 0.041 0.141 628 Planarity : 0.005 0.098 663 Dihedral : 16.818 85.672 1382 Min Nonbonded Distance : 2.273 Molprobity Statistics. All-atom Clashscore : 9.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.28 % Favored : 96.72 % Rotamer: Outliers : 0.47 % Allowed : 28.44 % Favored : 71.10 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.10 (0.39), residues: 488 helix: 1.00 (0.32), residues: 278 sheet: 1.61 (0.73), residues: 56 loop : 0.07 (0.51), residues: 154 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 356 HIS 0.010 0.001 HIS A 334 PHE 0.012 0.001 PHE A 82 TYR 0.015 0.001 TYR A 119 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 78 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 76 time to evaluate : 0.433 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 1 residues processed: 76 average time/residue: 0.1484 time to fit residues: 14.3755 Evaluate side-chains 77 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 76 time to evaluate : 0.450 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 148 ASN Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 41 optimal weight: 0.7980 chunk 37 optimal weight: 5.9990 chunk 20 optimal weight: 1.9990 chunk 12 optimal weight: 3.9990 chunk 25 optimal weight: 1.9990 chunk 19 optimal weight: 0.5980 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 3.9990 chunk 23 optimal weight: 0.7980 chunk 28 optimal weight: 2.9990 chunk 44 optimal weight: 3.9990 overall best weight: 1.2384 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 66 ASN A 135 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 255 GLN A 284 GLN A 316 ASN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7945 moved from start: 0.1167 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.035 3971 Z= 0.295 Angle : 0.611 8.078 5391 Z= 0.320 Chirality : 0.043 0.132 628 Planarity : 0.005 0.054 663 Dihedral : 5.000 55.967 521 Min Nonbonded Distance : 2.258 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.59 % Allowed : 25.17 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.39), residues: 488 helix: 1.26 (0.32), residues: 280 sheet: 1.08 (0.61), residues: 69 loop : 0.02 (0.55), residues: 139 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 356 HIS 0.007 0.002 HIS A 334 PHE 0.014 0.001 PHE A 36 TYR 0.014 0.002 TYR A 119 ARG 0.003 0.001 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 79 time to evaluate : 0.428 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6921 (OUTLIER) cc_final: 0.6483 (mt) REVERT: A 349 MET cc_start: 0.6770 (tpt) cc_final: 0.6128 (mtp) REVERT: B 55 ASP cc_start: 0.8376 (t0) cc_final: 0.8072 (t0) outliers start: 24 outliers final: 17 residues processed: 93 average time/residue: 0.1373 time to fit residues: 16.5502 Evaluate side-chains 95 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 166 VAL Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 68 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 78 VAL Chi-restraints excluded: chain B residue 117 THR Chi-restraints excluded: chain B residue 123 SER Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 24 optimal weight: 0.5980 chunk 13 optimal weight: 0.5980 chunk 37 optimal weight: 0.6980 chunk 30 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 44 optimal weight: 1.9990 chunk 48 optimal weight: 0.9990 chunk 39 optimal weight: 5.9990 chunk 15 optimal weight: 0.8980 chunk 35 optimal weight: 0.8980 chunk 33 optimal weight: 0.3980 overall best weight: 0.6380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** A 334 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.1308 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3971 Z= 0.196 Angle : 0.550 7.848 5391 Z= 0.283 Chirality : 0.041 0.123 628 Planarity : 0.004 0.052 663 Dihedral : 4.233 33.153 519 Min Nonbonded Distance : 2.272 Molprobity Statistics. All-atom Clashscore : 9.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 4.90 % Allowed : 25.87 % Favored : 69.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.41 (0.39), residues: 488 helix: 1.46 (0.31), residues: 281 sheet: 0.90 (0.58), residues: 71 loop : -0.01 (0.56), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 356 HIS 0.006 0.001 HIS A 334 PHE 0.008 0.001 PHE A 42 TYR 0.019 0.001 TYR B 37 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 84 time to evaluate : 0.413 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6764 (OUTLIER) cc_final: 0.6361 (mt) REVERT: A 349 MET cc_start: 0.6752 (tpt) cc_final: 0.6123 (mtp) REVERT: A 389 MET cc_start: 0.9051 (ttp) cc_final: 0.8832 (ttt) REVERT: B 37 TYR cc_start: 0.8907 (m-80) cc_final: 0.8704 (m-80) REVERT: B 55 ASP cc_start: 0.8448 (t0) cc_final: 0.8084 (t0) outliers start: 21 outliers final: 11 residues processed: 96 average time/residue: 0.1354 time to fit residues: 16.6201 Evaluate side-chains 92 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 80 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 THR Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.5980 chunk 4 optimal weight: 1.9990 chunk 21 optimal weight: 2.9990 chunk 29 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 47 optimal weight: 0.9980 chunk 42 optimal weight: 0.3980 chunk 12 optimal weight: 0.9980 chunk 39 optimal weight: 1.9990 chunk 26 optimal weight: 0.6980 chunk 0 optimal weight: 6.9990 overall best weight: 0.6980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1642 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3971 Z= 0.201 Angle : 0.575 7.885 5391 Z= 0.289 Chirality : 0.041 0.122 628 Planarity : 0.004 0.052 663 Dihedral : 4.180 33.061 519 Min Nonbonded Distance : 2.275 Molprobity Statistics. All-atom Clashscore : 8.83 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.36 % Allowed : 26.81 % Favored : 67.83 % 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: 1.44 (0.39), residues: 488 helix: 1.48 (0.31), residues: 281 sheet: 0.86 (0.56), residues: 71 loop : 0.06 (0.57), residues: 136 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 356 HIS 0.005 0.001 HIS A 334 PHE 0.007 0.001 PHE A 42 TYR 0.015 0.001 TYR B 37 ARG 0.003 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 108 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 85 time to evaluate : 0.439 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6784 (OUTLIER) cc_final: 0.6369 (mt) REVERT: A 250 ASN cc_start: 0.8773 (OUTLIER) cc_final: 0.8571 (t0) REVERT: A 349 MET cc_start: 0.6752 (tpt) cc_final: 0.6131 (mtp) REVERT: B 37 TYR cc_start: 0.8911 (m-80) cc_final: 0.8662 (m-80) REVERT: B 55 ASP cc_start: 0.8474 (t0) cc_final: 0.8031 (t0) REVERT: B 118 GLN cc_start: 0.8546 (tp-100) cc_final: 0.7808 (tp-100) outliers start: 23 outliers final: 15 residues processed: 99 average time/residue: 0.1305 time to fit residues: 16.6331 Evaluate side-chains 97 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 80 time to evaluate : 0.423 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 208 CYS Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 333 ASP Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 12 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 35 optimal weight: 0.9980 chunk 19 optimal weight: 0.8980 chunk 40 optimal weight: 2.9990 chunk 32 optimal weight: 0.7980 chunk 0 optimal weight: 6.9990 chunk 24 optimal weight: 1.9990 chunk 42 optimal weight: 1.9990 chunk 11 optimal weight: 3.9990 chunk 15 optimal weight: 0.6980 chunk 9 optimal weight: 0.6980 chunk 27 optimal weight: 1.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN A 148 ASN A 209 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 284 GLN ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** B 110 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.1700 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.036 3971 Z= 0.221 Angle : 0.573 7.940 5391 Z= 0.290 Chirality : 0.042 0.122 628 Planarity : 0.004 0.052 663 Dihedral : 4.153 32.731 519 Min Nonbonded Distance : 2.268 Molprobity Statistics. All-atom Clashscore : 10.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.10 % Favored : 95.90 % Rotamer: Outliers : 5.59 % Allowed : 26.34 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.38), residues: 488 helix: 1.41 (0.31), residues: 287 sheet: 0.87 (0.56), residues: 71 loop : -0.17 (0.57), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.004 0.001 HIS A 334 PHE 0.007 0.001 PHE A 365 TYR 0.014 0.001 TYR B 98 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 106 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 24 poor density : 82 time to evaluate : 0.426 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6802 (OUTLIER) cc_final: 0.6371 (mt) REVERT: A 250 ASN cc_start: 0.8813 (OUTLIER) cc_final: 0.8610 (t0) REVERT: A 349 MET cc_start: 0.6769 (tpt) cc_final: 0.6143 (mtp) REVERT: A 389 MET cc_start: 0.9051 (ttp) cc_final: 0.8776 (ttt) REVERT: B 37 TYR cc_start: 0.8908 (m-80) cc_final: 0.8658 (m-80) REVERT: B 55 ASP cc_start: 0.8437 (t0) cc_final: 0.7978 (t0) REVERT: B 118 GLN cc_start: 0.8466 (tp-100) cc_final: 0.7716 (tp-100) outliers start: 24 outliers final: 17 residues processed: 97 average time/residue: 0.1271 time to fit residues: 15.9760 Evaluate side-chains 99 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.431 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 115 GLN Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 209 ASN Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 11 optimal weight: 2.9990 chunk 47 optimal weight: 0.0060 chunk 39 optimal weight: 2.9990 chunk 21 optimal weight: 0.7980 chunk 3 optimal weight: 0.7980 chunk 15 optimal weight: 0.8980 chunk 24 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 5 optimal weight: 3.9990 chunk 27 optimal weight: 0.7980 chunk 34 optimal weight: 0.6980 overall best weight: 0.6196 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** A 209 ASN ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7915 moved from start: 0.1835 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 3971 Z= 0.190 Angle : 0.563 7.961 5391 Z= 0.286 Chirality : 0.041 0.122 628 Planarity : 0.004 0.052 663 Dihedral : 4.139 33.085 519 Min Nonbonded Distance : 2.262 Molprobity Statistics. All-atom Clashscore : 10.23 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.51 % Favored : 95.49 % Rotamer: Outliers : 5.13 % Allowed : 26.57 % Favored : 68.30 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.26 (0.38), residues: 488 helix: 1.41 (0.31), residues: 286 sheet: 0.87 (0.56), residues: 71 loop : -0.31 (0.57), residues: 131 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 251 HIS 0.003 0.001 HIS A 334 PHE 0.006 0.001 PHE A 365 TYR 0.014 0.001 TYR B 98 ARG 0.002 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 103 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 81 time to evaluate : 0.433 Fit side-chains revert: symmetry clash REVERT: A 93 LEU cc_start: 0.6762 (OUTLIER) cc_final: 0.6359 (mt) REVERT: A 250 ASN cc_start: 0.8797 (OUTLIER) cc_final: 0.8591 (t0) REVERT: A 349 MET cc_start: 0.6749 (tpt) cc_final: 0.6128 (mtp) REVERT: A 389 MET cc_start: 0.9034 (ttp) cc_final: 0.8759 (ttt) REVERT: B 37 TYR cc_start: 0.8904 (m-80) cc_final: 0.8638 (m-80) REVERT: B 55 ASP cc_start: 0.8450 (t0) cc_final: 0.7973 (t0) REVERT: B 105 TYR cc_start: 0.7488 (OUTLIER) cc_final: 0.5203 (p90) REVERT: B 118 GLN cc_start: 0.8498 (tp-100) cc_final: 0.7740 (tp-100) outliers start: 22 outliers final: 15 residues processed: 94 average time/residue: 0.1305 time to fit residues: 15.8499 Evaluate side-chains 97 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 79 time to evaluate : 0.426 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 112 THR Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 26 optimal weight: 1.9990 chunk 39 optimal weight: 1.9990 chunk 47 optimal weight: 2.9990 chunk 29 optimal weight: 0.3980 chunk 28 optimal weight: 0.4980 chunk 21 optimal weight: 0.7980 chunk 18 optimal weight: 7.9990 chunk 14 optimal weight: 0.0470 chunk 9 optimal weight: 0.9980 chunk 30 optimal weight: 0.9990 chunk 32 optimal weight: 0.7980 overall best weight: 0.5078 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7901 moved from start: 0.1895 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3971 Z= 0.177 Angle : 0.555 7.932 5391 Z= 0.281 Chirality : 0.041 0.130 628 Planarity : 0.004 0.051 663 Dihedral : 4.156 32.898 519 Min Nonbonded Distance : 2.253 Molprobity Statistics. All-atom Clashscore : 10.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.20 % Allowed : 27.27 % Favored : 68.53 % 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: 1.25 (0.39), residues: 488 helix: 1.39 (0.31), residues: 287 sheet: 0.94 (0.57), residues: 71 loop : -0.38 (0.57), residues: 130 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 251 HIS 0.008 0.001 HIS A 334 PHE 0.007 0.001 PHE A 82 TYR 0.015 0.001 TYR A 240 ARG 0.001 0.000 ARG B 19 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 82 time to evaluate : 0.465 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8043 (tpp) cc_final: 0.7696 (tpp) REVERT: A 104 PHE cc_start: 0.6809 (OUTLIER) cc_final: 0.6377 (t80) REVERT: A 250 ASN cc_start: 0.8786 (OUTLIER) cc_final: 0.8585 (t0) REVERT: A 349 MET cc_start: 0.6734 (tpt) cc_final: 0.6117 (mtp) REVERT: A 389 MET cc_start: 0.9017 (ttp) cc_final: 0.8754 (ttt) REVERT: B 37 TYR cc_start: 0.8885 (m-80) cc_final: 0.8614 (m-80) REVERT: B 55 ASP cc_start: 0.8464 (t0) cc_final: 0.7986 (t0) REVERT: B 105 TYR cc_start: 0.7465 (OUTLIER) cc_final: 0.5143 (p90) REVERT: B 118 GLN cc_start: 0.8513 (tp-100) cc_final: 0.7755 (tp-100) outliers start: 18 outliers final: 13 residues processed: 91 average time/residue: 0.1337 time to fit residues: 15.8659 Evaluate side-chains 95 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 79 time to evaluate : 0.428 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 104 PHE Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 23 optimal weight: 0.8980 chunk 4 optimal weight: 0.9980 chunk 37 optimal weight: 0.9980 chunk 42 optimal weight: 0.8980 chunk 45 optimal weight: 4.9990 chunk 41 optimal weight: 3.9990 chunk 44 optimal weight: 6.9990 chunk 26 optimal weight: 1.9990 chunk 19 optimal weight: 2.9990 chunk 34 optimal weight: 0.6980 chunk 13 optimal weight: 0.9980 overall best weight: 0.8980 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7931 moved from start: 0.2003 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3971 Z= 0.233 Angle : 0.588 8.018 5391 Z= 0.296 Chirality : 0.042 0.150 628 Planarity : 0.004 0.052 663 Dihedral : 4.246 32.698 519 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.43 % Allowed : 27.97 % Favored : 67.60 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.23 (0.38), residues: 488 helix: 1.36 (0.31), residues: 285 sheet: 1.03 (0.58), residues: 71 loop : -0.37 (0.56), residues: 132 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.007 0.001 HIS A 334 PHE 0.008 0.001 PHE A 365 TYR 0.013 0.001 TYR B 98 ARG 0.002 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 97 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 78 time to evaluate : 0.427 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8105 (tpp) cc_final: 0.7770 (tpp) REVERT: A 93 LEU cc_start: 0.6816 (OUTLIER) cc_final: 0.6389 (mt) REVERT: A 250 ASN cc_start: 0.8819 (OUTLIER) cc_final: 0.8616 (t0) REVERT: A 349 MET cc_start: 0.6773 (tpt) cc_final: 0.6146 (mtp) REVERT: A 389 MET cc_start: 0.9021 (ttp) cc_final: 0.8750 (ttt) REVERT: B 37 TYR cc_start: 0.8895 (m-80) cc_final: 0.8601 (m-80) REVERT: B 55 ASP cc_start: 0.8513 (t0) cc_final: 0.8021 (t0) REVERT: B 105 TYR cc_start: 0.7553 (OUTLIER) cc_final: 0.5182 (p90) REVERT: B 118 GLN cc_start: 0.8508 (tp-100) cc_final: 0.7743 (tp-100) outliers start: 19 outliers final: 15 residues processed: 89 average time/residue: 0.1337 time to fit residues: 15.2560 Evaluate side-chains 95 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 18 poor density : 77 time to evaluate : 0.406 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 69 ILE Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 39 optimal weight: 2.9990 chunk 41 optimal weight: 0.0030 chunk 43 optimal weight: 0.8980 chunk 28 optimal weight: 0.8980 chunk 46 optimal weight: 2.9990 chunk 22 optimal weight: 0.8980 chunk 32 optimal weight: 0.8980 chunk 48 optimal weight: 0.8980 chunk 44 optimal weight: 5.9990 chunk 38 optimal weight: 0.8980 chunk 4 optimal weight: 0.7980 overall best weight: 0.6990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7919 moved from start: 0.2072 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3971 Z= 0.202 Angle : 0.576 7.988 5391 Z= 0.291 Chirality : 0.041 0.123 628 Planarity : 0.004 0.051 663 Dihedral : 4.158 32.368 519 Min Nonbonded Distance : 2.251 Molprobity Statistics. All-atom Clashscore : 11.26 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 4.43 % Allowed : 27.04 % Favored : 68.53 % 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: 1.30 (0.39), residues: 488 helix: 1.41 (0.31), residues: 290 sheet: 1.03 (0.58), residues: 71 loop : -0.37 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.006 0.001 HIS A 334 PHE 0.007 0.001 PHE A 42 TYR 0.013 0.001 TYR B 98 ARG 0.001 0.000 ARG A 319 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 99 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 80 time to evaluate : 0.506 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8135 (tpp) cc_final: 0.7847 (tpp) REVERT: A 93 LEU cc_start: 0.6755 (OUTLIER) cc_final: 0.6347 (mt) REVERT: A 250 ASN cc_start: 0.8792 (OUTLIER) cc_final: 0.8588 (t0) REVERT: A 349 MET cc_start: 0.6746 (tpt) cc_final: 0.6128 (mtp) REVERT: A 389 MET cc_start: 0.9017 (ttp) cc_final: 0.8750 (ttt) REVERT: B 37 TYR cc_start: 0.8880 (m-80) cc_final: 0.8585 (m-80) REVERT: B 55 ASP cc_start: 0.8542 (t0) cc_final: 0.8033 (t0) REVERT: B 105 TYR cc_start: 0.7568 (OUTLIER) cc_final: 0.5335 (p90) REVERT: B 118 GLN cc_start: 0.8492 (tp-100) cc_final: 0.7718 (tp-100) outliers start: 19 outliers final: 14 residues processed: 90 average time/residue: 0.1571 time to fit residues: 17.9441 Evaluate side-chains 96 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 79 time to evaluate : 0.432 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 13 GLN Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 50 THR Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 30 optimal weight: 1.9990 chunk 23 optimal weight: 0.9990 chunk 41 optimal weight: 6.9990 chunk 11 optimal weight: 0.9980 chunk 35 optimal weight: 0.0770 chunk 5 optimal weight: 1.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 0.9980 chunk 16 optimal weight: 0.5980 chunk 39 optimal weight: 0.5980 chunk 4 optimal weight: 0.9990 overall best weight: 0.6338 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7911 moved from start: 0.2121 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.031 3971 Z= 0.193 Angle : 0.581 8.011 5391 Z= 0.291 Chirality : 0.041 0.122 628 Planarity : 0.004 0.051 663 Dihedral : 4.116 32.163 519 Min Nonbonded Distance : 2.247 Molprobity Statistics. All-atom Clashscore : 11.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.69 % Favored : 96.31 % Rotamer: Outliers : 3.96 % Allowed : 28.21 % Favored : 67.83 % 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: 1.35 (0.39), residues: 488 helix: 1.46 (0.31), residues: 290 sheet: 1.04 (0.58), residues: 71 loop : -0.39 (0.58), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.006 0.001 HIS A 334 PHE 0.008 0.001 PHE A 42 TYR 0.016 0.001 TYR A 240 ARG 0.001 0.000 ARG A 319 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 976 Ramachandran restraints generated. 488 Oldfield, 0 Emsley, 488 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 100 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 83 time to evaluate : 0.406 Fit side-chains revert: symmetry clash REVERT: A 37 MET cc_start: 0.8105 (tpp) cc_final: 0.7759 (tpp) REVERT: A 84 GLU cc_start: 0.8163 (pt0) cc_final: 0.7176 (pp20) REVERT: A 93 LEU cc_start: 0.6750 (OUTLIER) cc_final: 0.6346 (mt) REVERT: A 250 ASN cc_start: 0.8770 (OUTLIER) cc_final: 0.8568 (t0) REVERT: A 349 MET cc_start: 0.6736 (tpt) cc_final: 0.6121 (mtp) REVERT: A 389 MET cc_start: 0.9012 (ttp) cc_final: 0.8745 (ttt) REVERT: B 37 TYR cc_start: 0.8876 (m-80) cc_final: 0.8586 (m-80) REVERT: B 55 ASP cc_start: 0.8564 (t0) cc_final: 0.8055 (t0) REVERT: B 105 TYR cc_start: 0.7507 (OUTLIER) cc_final: 0.5264 (p90) REVERT: B 118 GLN cc_start: 0.8482 (tp-100) cc_final: 0.7705 (tp-100) outliers start: 17 outliers final: 13 residues processed: 93 average time/residue: 0.1367 time to fit residues: 16.3841 Evaluate side-chains 98 residues out of total 429 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 82 time to evaluate : 0.559 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 50 LEU Chi-restraints excluded: chain A residue 93 LEU Chi-restraints excluded: chain A residue 173 GLN Chi-restraints excluded: chain A residue 201 LEU Chi-restraints excluded: chain A residue 250 ASN Chi-restraints excluded: chain A residue 267 GLU Chi-restraints excluded: chain A residue 282 MET Chi-restraints excluded: chain A residue 307 PHE Chi-restraints excluded: chain A residue 314 VAL Chi-restraints excluded: chain A residue 329 ASN Chi-restraints excluded: chain A residue 341 VAL Chi-restraints excluded: chain B residue 5 VAL Chi-restraints excluded: chain B residue 31 ILE Chi-restraints excluded: chain B residue 33 VAL Chi-restraints excluded: chain B residue 105 TYR Chi-restraints excluded: chain B residue 117 THR Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 49 random chunks: chunk 7 optimal weight: 0.9980 chunk 34 optimal weight: 0.8980 chunk 2 optimal weight: 0.9980 chunk 28 optimal weight: 0.8980 chunk 44 optimal weight: 2.9990 chunk 26 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 1 optimal weight: 0.9990 chunk 31 optimal weight: 0.8980 chunk 29 optimal weight: 0.5980 chunk 19 optimal weight: 1.9990 overall best weight: 0.7780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 135 GLN ** A 148 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 209 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 250 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 358 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 32 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 110 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3367 r_free = 0.3367 target = 0.120943 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 46)----------------| | r_work = 0.3059 r_free = 0.3059 target = 0.098273 restraints weight = 5490.785| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 40)----------------| | r_work = 0.3103 r_free = 0.3103 target = 0.101275 restraints weight = 3190.020| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 36)----------------| | r_work = 0.3129 r_free = 0.3129 target = 0.103116 restraints weight = 2294.234| |-----------------------------------------------------------------------------| r_work (final): 0.3030 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8421 moved from start: 0.2150 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3971 Z= 0.215 Angle : 0.584 8.039 5391 Z= 0.294 Chirality : 0.042 0.122 628 Planarity : 0.004 0.051 663 Dihedral : 4.143 32.275 519 Min Nonbonded Distance : 2.241 Molprobity Statistics. All-atom Clashscore : 11.51 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.89 % Favored : 96.11 % Rotamer: Outliers : 4.20 % Allowed : 27.74 % Favored : 68.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.32 (0.39), residues: 488 helix: 1.42 (0.31), residues: 290 sheet: 1.06 (0.58), residues: 71 loop : -0.36 (0.59), residues: 127 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 251 HIS 0.006 0.001 HIS A 334 PHE 0.010 0.001 PHE A 42 TYR 0.014 0.001 TYR A 119 ARG 0.001 0.000 ARG A 319 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1215.68 seconds wall clock time: 22 minutes 18.64 seconds (1338.64 seconds total)