Starting phenix.real_space_refine on Sun Mar 10 17:49:43 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/03_2024/8qxa_18716.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/03_2024/8qxa_18716.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.05 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/03_2024/8qxa_18716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/03_2024/8qxa_18716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/03_2024/8qxa_18716.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/03_2024/8qxa_18716.pdb" } resolution = 4.05 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= 0.002 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 84 5.16 5 C 2232 2.51 5 N 660 2.21 5 O 720 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped None Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5265/modules/chem_data/mon_lib" Total number of atoms: 3696 Number of models: 1 Model: "" Number of chains: 12 Chain: "A" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "B" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "C" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "D" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "E" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "F" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "G" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "H" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "I" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "J" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "K" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Chain: "L" Number of atoms: 308 Number of conformers: 1 Conformer: "" Number of residues, atoms: 45, 308 Classifications: {'peptide': 45} Link IDs: {'PTRANS': 1, 'TRANS': 43} Time building chain proxies: 2.07, per 1000 atoms: 0.56 Number of scatterers: 3696 At special positions: 0 Unit cell: (107.12, 71.76, 48.88, 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 84 16.00 O 720 8.00 N 660 7.00 C 2232 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: 1.47 Conformation dependent library (CDL) restraints added in 752.4 milliseconds 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 888 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 6 sheets defined 0.0% alpha, 13.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.42 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'A' and resid 317 through 318 removed outlier: 6.301A pdb=" N SER A 317 " --> pdb=" O ILE C 318 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER C 317 " --> pdb=" O ILE E 318 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER E 317 " --> pdb=" O ILE G 318 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER G 317 " --> pdb=" O ILE I 318 " (cutoff:3.500A) removed outlier: 6.301A pdb=" N SER I 317 " --> pdb=" O ILE K 318 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA1 Processing sheet with id=AA2, first strand: chain 'A' and resid 323 through 324 removed outlier: 7.079A pdb=" N MET A 323 " --> pdb=" O ALA C 324 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N MET C 323 " --> pdb=" O ALA E 324 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET E 323 " --> pdb=" O ALA G 324 " (cutoff:3.500A) removed outlier: 7.079A pdb=" N MET G 323 " --> pdb=" O ALA I 324 " (cutoff:3.500A) removed outlier: 7.078A pdb=" N MET I 323 " --> pdb=" O ALA K 324 " (cutoff:3.500A) No H-bonds generated for sheet with id=AA2 Processing sheet with id=AA3, first strand: chain 'A' and resid 329 through 331 Processing sheet with id=AA4, first strand: chain 'A' and resid 339 through 340 Processing sheet with id=AA5, first strand: chain 'B' and resid 326 through 332 removed outlier: 6.812A pdb=" N GLN D 327 " --> pdb=" O ALA B 326 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN F 327 " --> pdb=" O ALA D 326 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN H 327 " --> pdb=" O ALA F 326 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN J 327 " --> pdb=" O ALA H 326 " (cutoff:3.500A) removed outlier: 6.812A pdb=" N GLN L 327 " --> pdb=" O ALA J 326 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'B' and resid 337 through 338 45 hydrogen bonds defined for protein. 135 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.76 Time building geometry restraints manager: 1.35 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.21 - 1.33: 881 1.33 - 1.46: 745 1.46 - 1.58: 1950 1.58 - 1.71: 0 1.71 - 1.84: 168 Bond restraints: 3744 Sorted by residual: bond pdb=" N GLY I 308 " pdb=" CA GLY I 308 " ideal model delta sigma weight residual 1.444 1.476 -0.032 9.60e-03 1.09e+04 1.11e+01 bond pdb=" N GLY K 308 " pdb=" CA GLY K 308 " ideal model delta sigma weight residual 1.444 1.476 -0.031 9.60e-03 1.09e+04 1.07e+01 bond pdb=" N GLY G 308 " pdb=" CA GLY G 308 " ideal model delta sigma weight residual 1.444 1.476 -0.031 9.60e-03 1.09e+04 1.05e+01 bond pdb=" N GLY A 308 " pdb=" CA GLY A 308 " ideal model delta sigma weight residual 1.444 1.475 -0.031 9.60e-03 1.09e+04 1.04e+01 bond pdb=" N GLY E 308 " pdb=" CA GLY E 308 " ideal model delta sigma weight residual 1.444 1.475 -0.031 9.60e-03 1.09e+04 1.02e+01 ... (remaining 3739 not shown) Histogram of bond angle deviations from ideal: 99.08 - 106.16: 206 106.16 - 113.23: 1646 113.23 - 120.31: 1652 120.31 - 127.38: 1452 127.38 - 134.46: 24 Bond angle restraints: 4980 Sorted by residual: angle pdb=" N GLN K 327 " pdb=" CA GLN K 327 " pdb=" C GLN K 327 " ideal model delta sigma weight residual 112.23 100.17 12.06 1.26e+00 6.30e-01 9.17e+01 angle pdb=" N GLN I 327 " pdb=" CA GLN I 327 " pdb=" C GLN I 327 " ideal model delta sigma weight residual 112.23 100.18 12.05 1.26e+00 6.30e-01 9.15e+01 angle pdb=" N GLN A 327 " pdb=" CA GLN A 327 " pdb=" C GLN A 327 " ideal model delta sigma weight residual 112.23 100.18 12.05 1.26e+00 6.30e-01 9.15e+01 angle pdb=" N GLN G 327 " pdb=" CA GLN G 327 " pdb=" C GLN G 327 " ideal model delta sigma weight residual 112.23 100.19 12.04 1.26e+00 6.30e-01 9.13e+01 angle pdb=" N GLN C 327 " pdb=" CA GLN C 327 " pdb=" C GLN C 327 " ideal model delta sigma weight residual 112.23 100.20 12.03 1.26e+00 6.30e-01 9.12e+01 ... (remaining 4975 not shown) Histogram of dihedral angle deviations from ideal: 0.02 - 17.06: 1896 17.06 - 34.10: 216 34.10 - 51.14: 42 51.14 - 68.18: 12 68.18 - 85.22: 30 Dihedral angle restraints: 2196 sinusoidal: 780 harmonic: 1416 Sorted by residual: dihedral pdb=" N MET L 307 " pdb=" CA MET L 307 " pdb=" CB MET L 307 " pdb=" CG MET L 307 " ideal model delta sinusoidal sigma weight residual -60.00 -111.07 51.07 3 1.50e+01 4.44e-03 8.97e+00 dihedral pdb=" N MET D 307 " pdb=" CA MET D 307 " pdb=" CB MET D 307 " pdb=" CG MET D 307 " ideal model delta sinusoidal sigma weight residual -60.00 -111.06 51.06 3 1.50e+01 4.44e-03 8.97e+00 dihedral pdb=" N MET H 307 " pdb=" CA MET H 307 " pdb=" CB MET H 307 " pdb=" CG MET H 307 " ideal model delta sinusoidal sigma weight residual -60.00 -111.05 51.05 3 1.50e+01 4.44e-03 8.97e+00 ... (remaining 2193 not shown) Histogram of chiral volume deviations from ideal: 0.001 - 0.049: 150 0.049 - 0.097: 127 0.097 - 0.144: 125 0.144 - 0.192: 54 0.192 - 0.240: 24 Chirality restraints: 480 Sorted by residual: chirality pdb=" CA TRP B 334 " pdb=" N TRP B 334 " pdb=" C TRP B 334 " pdb=" CB TRP B 334 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.44e+00 chirality pdb=" CA TRP J 334 " pdb=" N TRP J 334 " pdb=" C TRP J 334 " pdb=" CB TRP J 334 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 chirality pdb=" CA TRP H 334 " pdb=" N TRP H 334 " pdb=" C TRP H 334 " pdb=" CB TRP H 334 " both_signs ideal model delta sigma weight residual False 2.51 2.27 0.24 2.00e-01 2.50e+01 1.42e+00 ... (remaining 477 not shown) Planarity restraints: 684 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ALA J 326 " 0.015 2.00e-02 2.50e+03 2.96e-02 8.74e+00 pdb=" C ALA J 326 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA J 326 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN J 327 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA F 326 " 0.015 2.00e-02 2.50e+03 2.95e-02 8.70e+00 pdb=" C ALA F 326 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA F 326 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN F 327 " 0.018 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" CA ALA D 326 " 0.014 2.00e-02 2.50e+03 2.95e-02 8.69e+00 pdb=" C ALA D 326 " -0.051 2.00e-02 2.50e+03 pdb=" O ALA D 326 " 0.019 2.00e-02 2.50e+03 pdb=" N GLN D 327 " 0.018 2.00e-02 2.50e+03 ... (remaining 681 not shown) Histogram of nonbonded interaction distances: 2.42 - 2.92: 1399 2.92 - 3.41: 3236 3.41 - 3.91: 6325 3.91 - 4.40: 6764 4.40 - 4.90: 13333 Nonbonded interactions: 31057 Sorted by model distance: nonbonded pdb=" N ALA I 325 " pdb=" O ALA I 325 " model vdw 2.420 2.496 nonbonded pdb=" N ALA A 325 " pdb=" O ALA A 325 " model vdw 2.421 2.496 nonbonded pdb=" N ALA C 325 " pdb=" O ALA C 325 " model vdw 2.421 2.496 nonbonded pdb=" N ALA K 325 " pdb=" O ALA K 325 " model vdw 2.421 2.496 nonbonded pdb=" N ALA G 325 " pdb=" O ALA G 325 " model vdw 2.421 2.496 ... (remaining 31052 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' selection = chain 'G' selection = chain 'H' selection = chain 'I' selection = chain 'J' selection = chain 'K' selection = chain 'L' } 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: 0.560 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: 2.590 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.310 Find NCS groups from input model: 0.280 Set up NCS constraints: 0.030 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:2.920 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 20.780 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7378 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 : 0.014 0.044 3744 Z= 0.923 Angle : 2.245 12.063 4980 Z= 1.658 Chirality : 0.104 0.240 480 Planarity : 0.009 0.030 684 Dihedral : 18.942 85.216 1308 Min Nonbonded Distance : 2.420 Molprobity Statistics. All-atom Clashscore : 4.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 3.49 % Favored : 96.51 % Rotamer: Outliers : 0.00 % Allowed : 27.59 % Favored : 72.41 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.36 (0.17), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.13), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.046 0.009 TRP L 334 PHE 0.017 0.003 PHE E 316 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 240 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 240 time to evaluate : 0.361 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 PHE cc_start: 0.7321 (m-80) cc_final: 0.5662 (p90) REVERT: A 334 TRP cc_start: 0.8104 (p90) cc_final: 0.4302 (m100) REVERT: B 311 MET cc_start: 0.7816 (ptt) cc_final: 0.7133 (tpt) REVERT: B 322 MET cc_start: 0.7750 (mtt) cc_final: 0.7470 (mtt) REVERT: B 334 TRP cc_start: 0.7730 (p90) cc_final: 0.4643 (m100) REVERT: C 313 PHE cc_start: 0.8056 (m-10) cc_final: 0.7200 (m-80) REVERT: D 334 TRP cc_start: 0.7983 (p90) cc_final: 0.7649 (p90) REVERT: E 313 PHE cc_start: 0.8164 (m-10) cc_final: 0.7912 (m-80) REVERT: G 307 MET cc_start: 0.6436 (ttt) cc_final: 0.6001 (ttt) REVERT: G 313 PHE cc_start: 0.8053 (m-10) cc_final: 0.7852 (m-80) REVERT: H 313 PHE cc_start: 0.8675 (m-10) cc_final: 0.8426 (m-10) REVERT: H 339 MET cc_start: 0.8103 (mtp) cc_final: 0.7756 (mtp) REVERT: I 334 TRP cc_start: 0.7956 (p90) cc_final: 0.7736 (p90) REVERT: J 313 PHE cc_start: 0.8531 (m-10) cc_final: 0.8224 (m-10) REVERT: J 339 MET cc_start: 0.8341 (mtp) cc_final: 0.8085 (mtt) REVERT: L 313 PHE cc_start: 0.8757 (m-10) cc_final: 0.6526 (p90) REVERT: L 337 MET cc_start: 0.8084 (mtp) cc_final: 0.7336 (mtp) outliers start: 0 outliers final: 0 residues processed: 240 average time/residue: 0.1121 time to fit residues: 34.3412 Evaluate side-chains 157 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.386 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 40 optimal weight: 0.9990 chunk 36 optimal weight: 2.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 0.9990 chunk 24 optimal weight: 0.8980 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.9990 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9990 chunk 28 optimal weight: 0.9990 chunk 43 optimal weight: 0.7980 overall best weight: 0.8782 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 346 GLN D 319 ASN D 345 ASN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** L 319 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7422 moved from start: 0.4478 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.027 3744 Z= 0.235 Angle : 0.716 5.372 4980 Z= 0.390 Chirality : 0.038 0.132 480 Planarity : 0.005 0.044 684 Dihedral : 6.605 32.651 528 Min Nonbonded Distance : 2.351 Molprobity Statistics. All-atom Clashscore : 18.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.33 % Favored : 97.67 % Rotamer: Outliers : 0.00 % Allowed : 2.30 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.97 % 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: -4.40 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP D 334 PHE 0.024 0.003 PHE I 313 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 187 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 187 time to evaluate : 0.367 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: A 316 PHE cc_start: 0.7695 (m-80) cc_final: 0.5635 (p90) REVERT: B 311 MET cc_start: 0.7629 (ptp) cc_final: 0.6645 (mmt) REVERT: B 334 TRP cc_start: 0.7896 (p90) cc_final: 0.4474 (m100) REVERT: D 307 MET cc_start: 0.8842 (ttt) cc_final: 0.8622 (ttm) REVERT: D 337 MET cc_start: 0.8729 (mtp) cc_final: 0.8002 (mtp) REVERT: E 336 MET cc_start: 0.6131 (tmm) cc_final: 0.5745 (tmm) REVERT: G 317 SER cc_start: 0.8442 (t) cc_final: 0.7981 (m) REVERT: I 313 PHE cc_start: 0.8270 (m-10) cc_final: 0.7824 (m-80) REVERT: J 337 MET cc_start: 0.8464 (mtt) cc_final: 0.8183 (mtp) REVERT: K 323 MET cc_start: 0.7112 (mtt) cc_final: 0.6882 (mtt) outliers start: 0 outliers final: 0 residues processed: 187 average time/residue: 0.1135 time to fit residues: 27.2709 Evaluate side-chains 147 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.424 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 24 optimal weight: 9.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 0.4980 chunk 29 optimal weight: 1.9990 chunk 12 optimal weight: 8.9990 chunk 43 optimal weight: 0.0050 chunk 47 optimal weight: 4.9990 chunk 38 optimal weight: 5.9990 chunk 14 optimal weight: 9.9990 chunk 35 optimal weight: 0.8980 chunk 32 optimal weight: 1.9990 overall best weight: 1.0798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN B 344 GLN C 331 GLN D 319 ASN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 346 GLN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 346 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7498 moved from start: 0.5223 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.027 3744 Z= 0.243 Angle : 0.679 6.068 4980 Z= 0.360 Chirality : 0.036 0.122 480 Planarity : 0.004 0.036 684 Dihedral : 6.420 31.752 528 Min Nonbonded Distance : 2.374 Molprobity Statistics. All-atom Clashscore : 17.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 3.45 % Favored : 96.55 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.78 % 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: -4.40 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.002 TRP E 334 PHE 0.020 0.003 PHE E 316 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 166 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 166 time to evaluate : 0.405 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 MET cc_start: 0.7449 (ptp) cc_final: 0.6744 (mmt) REVERT: B 313 PHE cc_start: 0.8340 (m-80) cc_final: 0.7781 (m-10) REVERT: D 307 MET cc_start: 0.8837 (ttt) cc_final: 0.8631 (ttt) REVERT: D 313 PHE cc_start: 0.8690 (m-10) cc_final: 0.8056 (m-80) REVERT: F 337 MET cc_start: 0.8742 (mtt) cc_final: 0.8128 (mtt) REVERT: G 317 SER cc_start: 0.8579 (t) cc_final: 0.8148 (m) REVERT: I 307 MET cc_start: 0.6941 (tpp) cc_final: 0.6141 (tpp) REVERT: I 317 SER cc_start: 0.8628 (t) cc_final: 0.8377 (m) REVERT: I 337 MET cc_start: 0.7080 (mmt) cc_final: 0.6720 (tpp) REVERT: J 307 MET cc_start: 0.8404 (ttt) cc_final: 0.8075 (ttt) REVERT: J 337 MET cc_start: 0.8475 (mtt) cc_final: 0.8140 (mtp) REVERT: K 307 MET cc_start: 0.5697 (tpp) cc_final: 0.5446 (tpp) REVERT: L 337 MET cc_start: 0.8173 (mtp) cc_final: 0.7888 (mtt) outliers start: 0 outliers final: 0 residues processed: 166 average time/residue: 0.1156 time to fit residues: 24.5572 Evaluate side-chains 135 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 135 time to evaluate : 0.356 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 22 optimal weight: 0.9980 chunk 4 optimal weight: 10.0000 chunk 20 optimal weight: 10.0000 chunk 29 optimal weight: 0.9990 chunk 43 optimal weight: 5.9990 chunk 46 optimal weight: 0.6980 chunk 41 optimal weight: 9.9990 chunk 12 optimal weight: 2.9990 chunk 38 optimal weight: 4.9990 chunk 26 optimal weight: 4.9990 chunk 0 optimal weight: 10.0000 overall best weight: 2.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN I 331 GLN J 345 ASN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7636 moved from start: 0.5951 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.038 3744 Z= 0.343 Angle : 0.726 5.277 4980 Z= 0.383 Chirality : 0.037 0.127 480 Planarity : 0.003 0.027 684 Dihedral : 6.599 30.783 528 Min Nonbonded Distance : 2.366 Molprobity Statistics. All-atom Clashscore : 22.37 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.59 % Favored : 93.41 % Rotamer: Outliers : 0.29 % Allowed : 2.01 % Favored : 97.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.58 % 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: -4.44 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.37 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.002 TRP E 334 PHE 0.013 0.002 PHE L 316 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 154 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 153 time to evaluate : 0.413 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 MET cc_start: 0.7252 (ptp) cc_final: 0.6430 (mmt) REVERT: B 337 MET cc_start: 0.7875 (mtt) cc_final: 0.7673 (mtt) REVERT: D 313 PHE cc_start: 0.8947 (m-10) cc_final: 0.8545 (m-10) REVERT: F 313 PHE cc_start: 0.9075 (m-10) cc_final: 0.8765 (m-80) REVERT: F 337 MET cc_start: 0.8794 (mtt) cc_final: 0.8478 (mtt) REVERT: G 317 SER cc_start: 0.8645 (t) cc_final: 0.8362 (m) REVERT: H 337 MET cc_start: 0.8628 (mtt) cc_final: 0.8296 (mtp) outliers start: 1 outliers final: 0 residues processed: 154 average time/residue: 0.1183 time to fit residues: 23.4650 Evaluate side-chains 125 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 125 time to evaluate : 0.403 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 34 optimal weight: 7.9990 chunk 19 optimal weight: 5.9990 chunk 39 optimal weight: 0.0050 chunk 32 optimal weight: 10.0000 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 2.9990 chunk 41 optimal weight: 5.9990 chunk 11 optimal weight: 0.9980 chunk 15 optimal weight: 0.9990 chunk 9 optimal weight: 3.9990 chunk 27 optimal weight: 0.8980 overall best weight: 1.1798 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7581 moved from start: 0.6401 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3744 Z= 0.237 Angle : 0.668 7.478 4980 Z= 0.347 Chirality : 0.036 0.117 480 Planarity : 0.003 0.025 684 Dihedral : 6.334 29.882 528 Min Nonbonded Distance : 2.392 Molprobity Statistics. All-atom Clashscore : 21.11 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.20 % Favored : 93.80 % Rotamer: Outliers : 0.00 % Allowed : 2.01 % Favored : 97.99 % 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: -4.34 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.30 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 334 PHE 0.014 0.003 PHE E 316 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 147 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 147 time to evaluate : 0.418 Fit side-chains REVERT: B 311 MET cc_start: 0.7031 (ptp) cc_final: 0.6414 (mmt) REVERT: H 316 PHE cc_start: 0.8340 (m-80) cc_final: 0.7564 (m-80) REVERT: I 307 MET cc_start: 0.7209 (tpp) cc_final: 0.6536 (tpp) REVERT: I 337 MET cc_start: 0.7075 (mmt) cc_final: 0.6650 (mmt) outliers start: 0 outliers final: 0 residues processed: 147 average time/residue: 0.1187 time to fit residues: 22.3804 Evaluate side-chains 124 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 124 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 11 optimal weight: 7.9990 chunk 46 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 21 optimal weight: 2.9990 chunk 3 optimal weight: 0.8980 chunk 15 optimal weight: 3.9990 chunk 24 optimal weight: 8.9990 chunk 44 optimal weight: 10.0000 chunk 5 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 33 optimal weight: 1.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 345 ASN ** F 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** F 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 345 ASN ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN K 331 GLN ** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7671 moved from start: 0.6652 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.041 3744 Z= 0.404 Angle : 0.774 9.156 4980 Z= 0.398 Chirality : 0.037 0.120 480 Planarity : 0.003 0.025 684 Dihedral : 6.741 29.891 528 Min Nonbonded Distance : 2.297 Molprobity Statistics. All-atom Clashscore : 24.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.66 % Favored : 89.34 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -4.40 (0.21), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.003 TRP D 334 PHE 0.022 0.003 PHE E 316 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.339 Fit side-chains revert: symmetry clash REVERT: B 311 MET cc_start: 0.7231 (ptp) cc_final: 0.6540 (mmt) REVERT: C 344 GLN cc_start: 0.8778 (mt0) cc_final: 0.7954 (mp10) REVERT: E 333 SER cc_start: 0.8953 (p) cc_final: 0.8736 (p) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1176 time to fit residues: 21.3151 Evaluate side-chains 114 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.396 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 26 optimal weight: 6.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 2.9990 chunk 46 optimal weight: 0.8980 chunk 28 optimal weight: 6.9990 chunk 21 optimal weight: 2.9990 chunk 18 optimal weight: 0.8980 chunk 27 optimal weight: 0.9980 chunk 13 optimal weight: 0.8980 chunk 9 optimal weight: 3.9990 chunk 8 optimal weight: 1.9990 overall best weight: 0.9380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 GLN D 344 GLN F 344 GLN G 331 GLN H 344 GLN I 331 GLN J 344 GLN J 345 ASN L 344 GLN Total number of N/Q/H flips: 9 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7547 moved from start: 0.6931 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.030 3744 Z= 0.217 Angle : 0.681 7.512 4980 Z= 0.346 Chirality : 0.037 0.117 480 Planarity : 0.002 0.021 684 Dihedral : 6.451 29.628 528 Min Nonbonded Distance : 2.403 Molprobity Statistics. All-atom Clashscore : 18.88 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.43 % Favored : 94.57 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -4.40 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.35 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 334 PHE 0.016 0.002 PHE E 316 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 140 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 140 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 311 MET cc_start: 0.7018 (ptp) cc_final: 0.6417 (mmt) REVERT: C 344 GLN cc_start: 0.8609 (mt0) cc_final: 0.7899 (mp10) REVERT: L 313 PHE cc_start: 0.7472 (m-10) cc_final: 0.6186 (p90) outliers start: 0 outliers final: 0 residues processed: 140 average time/residue: 0.1177 time to fit residues: 21.0621 Evaluate side-chains 115 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 115 time to evaluate : 0.398 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 29 optimal weight: 2.9990 chunk 31 optimal weight: 2.9990 chunk 22 optimal weight: 5.9990 chunk 4 optimal weight: 8.9990 chunk 36 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 0.9980 chunk 40 optimal weight: 10.0000 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.7980 chunk 18 optimal weight: 0.9980 overall best weight: 1.5584 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7598 moved from start: 0.7068 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.032 3744 Z= 0.285 Angle : 0.705 8.797 4980 Z= 0.359 Chirality : 0.036 0.117 480 Planarity : 0.002 0.021 684 Dihedral : 6.457 29.115 528 Min Nonbonded Distance : 2.300 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.69 % Favored : 90.31 % Rotamer: Outliers : 0.00 % Allowed : 1.44 % Favored : 98.56 % 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: -4.49 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.41 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 334 PHE 0.010 0.002 PHE E 316 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 138 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 138 time to evaluate : 0.422 Fit side-chains revert: symmetry clash REVERT: B 311 MET cc_start: 0.7414 (ptp) cc_final: 0.6479 (mmt) REVERT: B 337 MET cc_start: 0.7994 (mtt) cc_final: 0.7772 (mtp) REVERT: B 346 GLN cc_start: 0.7316 (mp10) cc_final: 0.7032 (mp10) REVERT: C 344 GLN cc_start: 0.8744 (mt0) cc_final: 0.8382 (mp10) REVERT: I 307 MET cc_start: 0.7734 (tpp) cc_final: 0.6901 (tpp) REVERT: J 331 GLN cc_start: 0.8551 (mt0) cc_final: 0.8329 (mt0) REVERT: J 337 MET cc_start: 0.8641 (mmm) cc_final: 0.8356 (mmm) REVERT: K 317 SER cc_start: 0.8333 (t) cc_final: 0.8068 (m) outliers start: 0 outliers final: 0 residues processed: 138 average time/residue: 0.1156 time to fit residues: 20.5094 Evaluate side-chains 118 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 33 optimal weight: 0.9990 chunk 13 optimal weight: 4.9990 chunk 38 optimal weight: 4.9990 chunk 40 optimal weight: 4.9990 chunk 42 optimal weight: 0.5980 chunk 28 optimal weight: 1.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 3.9990 chunk 21 optimal weight: 1.9990 chunk 31 optimal weight: 2.9990 chunk 47 optimal weight: 3.9990 overall best weight: 1.7188 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 344 GLN ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 319 ASN J 345 ASN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7593 moved from start: 0.7231 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.035 3744 Z= 0.302 Angle : 0.737 9.061 4980 Z= 0.371 Chirality : 0.036 0.114 480 Planarity : 0.002 0.020 684 Dihedral : 6.610 28.994 528 Min Nonbonded Distance : 2.340 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 0.86 % Favored : 99.14 % 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: -4.55 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.46 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.002 TRP D 334 PHE 0.013 0.002 PHE E 316 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 134 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 134 time to evaluate : 0.361 Fit side-chains REVERT: B 311 MET cc_start: 0.7223 (ptp) cc_final: 0.6501 (mmt) REVERT: B 337 MET cc_start: 0.8061 (mtt) cc_final: 0.7771 (mtp) REVERT: C 344 GLN cc_start: 0.8717 (mt0) cc_final: 0.8406 (mp10) REVERT: H 307 MET cc_start: 0.7688 (ttt) cc_final: 0.7023 (ttt) REVERT: I 307 MET cc_start: 0.7747 (tpp) cc_final: 0.6907 (tpp) REVERT: J 337 MET cc_start: 0.8542 (mmm) cc_final: 0.8275 (mmt) REVERT: K 317 SER cc_start: 0.8339 (t) cc_final: 0.8067 (m) REVERT: K 333 SER cc_start: 0.8805 (p) cc_final: 0.8599 (p) outliers start: 0 outliers final: 0 residues processed: 134 average time/residue: 0.1103 time to fit residues: 18.9984 Evaluate side-chains 117 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.370 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 44 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 0.3980 chunk 29 optimal weight: 0.5980 chunk 23 optimal weight: 3.9990 chunk 30 optimal weight: 0.7980 chunk 40 optimal weight: 10.0000 chunk 11 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 5 optimal weight: 0.0170 chunk 10 optimal weight: 7.9990 overall best weight: 0.5618 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN ** L 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.7450 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.033 3744 Z= 0.191 Angle : 0.666 10.000 4980 Z= 0.333 Chirality : 0.036 0.118 480 Planarity : 0.002 0.020 684 Dihedral : 6.265 27.453 528 Min Nonbonded Distance : 2.354 Molprobity Statistics. All-atom Clashscore : 16.64 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.23 % Favored : 94.77 % Rotamer: Outliers : 0.00 % Allowed : 0.00 % Favored : 100.00 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.51 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.43 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP D 334 PHE 0.011 0.002 PHE G 316 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1032 Ramachandran restraints generated. 516 Oldfield, 0 Emsley, 516 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 142 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 142 time to evaluate : 0.397 Fit side-chains REVERT: B 311 MET cc_start: 0.7137 (ptp) cc_final: 0.6371 (mmt) REVERT: C 344 GLN cc_start: 0.8696 (mt0) cc_final: 0.8450 (mp10) REVERT: E 333 SER cc_start: 0.8953 (p) cc_final: 0.8736 (p) REVERT: G 323 MET cc_start: 0.7191 (mtt) cc_final: 0.6958 (mtt) REVERT: L 313 PHE cc_start: 0.7056 (m-10) cc_final: 0.6091 (p90) outliers start: 0 outliers final: 0 residues processed: 142 average time/residue: 0.1163 time to fit residues: 21.1422 Evaluate side-chains 116 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 48 random chunks: chunk 38 optimal weight: 0.9990 chunk 15 optimal weight: 3.9990 chunk 39 optimal weight: 3.9990 chunk 4 optimal weight: 7.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 0.7980 chunk 2 optimal weight: 7.9990 chunk 27 optimal weight: 0.9990 chunk 43 optimal weight: 0.8980 chunk 25 optimal weight: 7.9990 chunk 32 optimal weight: 3.9990 overall best weight: 1.1386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4375 r_free = 0.4375 target = 0.204041 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 48)----------------| | r_work = 0.4275 r_free = 0.4275 target = 0.123249 restraints weight = 5986.611| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 38)----------------| | r_work = 0.4339 r_free = 0.4339 target = 0.127662 restraints weight = 3339.648| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 34)----------------| | r_work = 0.4374 r_free = 0.4374 target = 0.130527 restraints weight = 2240.916| |-----------------------------------------------------------------------------| r_work (final): 0.4199 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7445 moved from start: 0.7518 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 3744 Z= 0.246 Angle : 0.730 11.695 4980 Z= 0.356 Chirality : 0.036 0.121 480 Planarity : 0.002 0.019 684 Dihedral : 6.297 27.434 528 Min Nonbonded Distance : 2.341 Molprobity Statistics. All-atom Clashscore : 19.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 0.29 % Favored : 99.71 % 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: -4.56 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP D 334 PHE 0.009 0.002 PHE H 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1249.25 seconds wall clock time: 23 minutes 2.05 seconds (1382.05 seconds total)