Starting phenix.real_space_refine on Fri Aug 2 16:48:55 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/08_2024/8qxa_18716.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/08_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_18716/08_2024/8qxa_18716.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/08_2024/8qxa_18716.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/08_2024/8qxa_18716.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8qxa_18716/08_2024/8qxa_18716.cif" } 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: 0.00s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/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: 2.26, per 1000 atoms: 0.61 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: 1.21 Conformation dependent library (CDL) restraints added in 683.6 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: 0.45 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: 0.74 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 Time spend for trying shortcut: 0.00 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: 0.480 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.010 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.130 Check model and map are aligned: 0.030 Set scattering table: 0.030 Process input model: 13.740 Find NCS groups from input model: 0.150 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:2.450 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.050 ------------------------------------------------------------------------------- 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 : 0.358 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: 0.1031 time to fit residues: 32.0902 Evaluate side-chains 157 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 157 time to evaluate : 0.396 ------------------------------------------------------------------------------- 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: 1.9990 chunk 36 optimal weight: 6.9990 chunk 20 optimal weight: 2.9990 chunk 12 optimal weight: 1.9990 chunk 24 optimal weight: 0.9990 chunk 19 optimal weight: 0.8980 chunk 37 optimal weight: 0.7980 chunk 14 optimal weight: 0.7980 chunk 22 optimal weight: 0.9980 chunk 28 optimal weight: 4.9990 chunk 43 optimal weight: 0.8980 overall best weight: 0.8780 ------------------------------------------------------------------------------- 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 345 ASN ** I 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 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: 0.7417 moved from start: 0.4501 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3744 Z= 0.238 Angle : 0.724 5.011 4980 Z= 0.396 Chirality : 0.039 0.133 480 Planarity : 0.004 0.043 684 Dihedral : 6.611 32.202 528 Min Nonbonded Distance : 2.633 Molprobity Statistics. All-atom Clashscore : 17.76 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Rotamer: Outliers : 0.00 % Allowed : 2.87 % Favored : 97.13 % 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: -4.41 (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 0.020 0.003 PHE G 316 *********************** 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 189 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 189 time to evaluate : 0.388 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: A 316 PHE cc_start: 0.7604 (m-80) cc_final: 0.5563 (p90) REVERT: B 311 MET cc_start: 0.7623 (ptp) cc_final: 0.6825 (mmt) REVERT: B 334 TRP cc_start: 0.7882 (p90) cc_final: 0.4465 (m100) REVERT: D 313 PHE cc_start: 0.8750 (m-10) cc_final: 0.7859 (m-10) REVERT: D 337 MET cc_start: 0.8755 (mtp) cc_final: 0.8057 (mtp) REVERT: E 336 MET cc_start: 0.6104 (tmm) cc_final: 0.5679 (tmm) REVERT: G 317 SER cc_start: 0.8470 (t) cc_final: 0.8059 (m) REVERT: I 313 PHE cc_start: 0.8200 (m-10) cc_final: 0.7701 (m-80) REVERT: I 337 MET cc_start: 0.7079 (tpp) cc_final: 0.6864 (tpp) REVERT: K 323 MET cc_start: 0.7098 (mtt) cc_final: 0.6882 (mtt) outliers start: 0 outliers final: 0 residues processed: 189 average time/residue: 0.1069 time to fit residues: 26.0615 Evaluate side-chains 148 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.346 ------------------------------------------------------------------------------- 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: 8.9990 chunk 13 optimal weight: 4.9990 chunk 36 optimal weight: 9.9990 chunk 29 optimal weight: 3.9990 chunk 12 optimal weight: 7.9990 chunk 43 optimal weight: 5.9990 chunk 47 optimal weight: 3.9990 chunk 38 optimal weight: 3.9990 chunk 14 optimal weight: 4.9990 chunk 35 optimal weight: 0.9980 chunk 32 optimal weight: 3.9990 overall best weight: 3.3988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** B 345 ASN C 331 GLN ** D 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 331 GLN ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** I 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** K 331 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7702 moved from start: 0.5812 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.044 3744 Z= 0.511 Angle : 0.860 6.091 4980 Z= 0.461 Chirality : 0.040 0.133 480 Planarity : 0.004 0.035 684 Dihedral : 7.222 31.441 528 Min Nonbonded Distance : 2.578 Molprobity Statistics. All-atom Clashscore : 24.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.75 % Favored : 92.25 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % 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: -4.50 (0.18), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.42 (0.14), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.021 0.004 TRP L 334 PHE 0.020 0.004 PHE D 313 *********************** 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 149 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 149 time to evaluate : 0.379 Fit side-chains revert: symmetry clash REVERT: A 317 SER cc_start: 0.8575 (t) cc_final: 0.8250 (m) REVERT: B 311 MET cc_start: 0.7595 (ptp) cc_final: 0.6700 (mmt) REVERT: D 313 PHE cc_start: 0.8725 (m-10) cc_final: 0.8212 (m-80) REVERT: D 322 MET cc_start: 0.8446 (mtt) cc_final: 0.8237 (mtt) REVERT: D 337 MET cc_start: 0.8645 (mtp) cc_final: 0.8333 (mtt) REVERT: H 337 MET cc_start: 0.8651 (mtt) cc_final: 0.8416 (mtp) REVERT: I 307 MET cc_start: 0.7334 (tpp) cc_final: 0.6689 (tpp) REVERT: J 307 MET cc_start: 0.8531 (ttt) cc_final: 0.8007 (ttt) REVERT: J 331 GLN cc_start: 0.8693 (mt0) cc_final: 0.8420 (mt0) REVERT: J 337 MET cc_start: 0.8727 (mtp) cc_final: 0.8018 (mtp) REVERT: L 313 PHE cc_start: 0.8293 (m-10) cc_final: 0.6070 (p90) REVERT: L 331 GLN cc_start: 0.8407 (mt0) cc_final: 0.8032 (mt0) REVERT: L 337 MET cc_start: 0.8367 (mtp) cc_final: 0.7937 (mtt) outliers start: 0 outliers final: 0 residues processed: 149 average time/residue: 0.1082 time to fit residues: 21.0236 Evaluate side-chains 121 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.365 ------------------------------------------------------------------------------- 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: 4.9990 chunk 29 optimal weight: 1.9990 chunk 43 optimal weight: 1.9990 chunk 46 optimal weight: 0.9990 chunk 41 optimal weight: 1.9990 chunk 12 optimal weight: 0.9980 chunk 38 optimal weight: 0.8980 chunk 26 optimal weight: 0.9990 chunk 0 optimal weight: 10.0000 overall best weight: 0.9784 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: B 344 GLN C 344 GLN F 344 GLN F 345 ASN H 327 GLN ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 345 ASN ** H 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 344 GLN Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7574 moved from start: 0.6120 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.023 3744 Z= 0.207 Angle : 0.652 6.030 4980 Z= 0.346 Chirality : 0.037 0.122 480 Planarity : 0.003 0.029 684 Dihedral : 6.370 30.353 528 Min Nonbonded Distance : 2.617 Molprobity Statistics. All-atom Clashscore : 17.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.00 % Allowed : 3.16 % Favored : 96.84 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.39 % 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: -4.41 (0.19), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.012 0.002 TRP E 334 PHE 0.012 0.002 PHE C 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 148 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 148 time to evaluate : 0.392 Fit side-chains revert: symmetry clash REVERT: A 317 SER cc_start: 0.8391 (t) cc_final: 0.8156 (m) REVERT: B 311 MET cc_start: 0.7253 (ptp) cc_final: 0.6584 (mmt) REVERT: I 307 MET cc_start: 0.7181 (tpp) cc_final: 0.6477 (tpp) REVERT: I 336 MET cc_start: 0.6918 (tmm) cc_final: 0.6458 (tmm) REVERT: I 337 MET cc_start: 0.7121 (tpp) cc_final: 0.6732 (tpp) outliers start: 0 outliers final: 0 residues processed: 148 average time/residue: 0.1130 time to fit residues: 21.6258 Evaluate side-chains 120 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 120 time to evaluate : 0.397 ------------------------------------------------------------------------------- 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: 10.0000 chunk 19 optimal weight: 0.9980 chunk 39 optimal weight: 5.9990 chunk 32 optimal weight: 6.9990 chunk 0 optimal weight: 10.0000 chunk 23 optimal weight: 3.9990 chunk 41 optimal weight: 8.9990 chunk 11 optimal weight: 1.9990 chunk 15 optimal weight: 0.9980 chunk 9 optimal weight: 4.9990 chunk 27 optimal weight: 0.9990 overall best weight: 1.7986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 346 GLN C 344 GLN ** D 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** G 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** H 327 GLN ** H 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 345 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** J 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7629 moved from start: 0.6513 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.032 3744 Z= 0.312 Angle : 0.689 5.576 4980 Z= 0.364 Chirality : 0.037 0.120 480 Planarity : 0.003 0.025 684 Dihedral : 6.456 29.726 528 Min Nonbonded Distance : 2.607 Molprobity Statistics. All-atom Clashscore : 20.13 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.11 % Favored : 90.89 % Rotamer: Outliers : 0.00 % Allowed : 2.59 % Favored : 97.41 % 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: -4.42 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP B 334 PHE 0.023 0.002 PHE A 313 *********************** 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 133 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 133 time to evaluate : 0.400 Fit side-chains revert: symmetry clash REVERT: B 311 MET cc_start: 0.7237 (ptp) cc_final: 0.6684 (mmt) REVERT: H 331 GLN cc_start: 0.8638 (mt0) cc_final: 0.8366 (mt0) REVERT: I 307 MET cc_start: 0.7446 (tpp) cc_final: 0.6839 (tpp) REVERT: I 336 MET cc_start: 0.6805 (tmm) cc_final: 0.6593 (tmm) REVERT: J 307 MET cc_start: 0.8489 (ttt) cc_final: 0.7975 (ttt) outliers start: 0 outliers final: 0 residues processed: 133 average time/residue: 0.1169 time to fit residues: 20.1303 Evaluate side-chains 116 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.395 ------------------------------------------------------------------------------- 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: 0.9990 chunk 3 optimal weight: 0.9980 chunk 15 optimal weight: 0.9980 chunk 24 optimal weight: 7.9990 chunk 44 optimal weight: 9.9990 chunk 5 optimal weight: 1.9990 chunk 26 optimal weight: 7.9990 chunk 33 optimal weight: 0.7980 overall best weight: 1.1584 ------------------------------------------------------------------------------- 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** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 331 GLN H 345 ASN ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN ** K 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** L 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7576 moved from start: 0.6803 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.028 3744 Z= 0.244 Angle : 0.662 6.238 4980 Z= 0.345 Chirality : 0.036 0.114 480 Planarity : 0.003 0.023 684 Dihedral : 6.393 29.323 528 Min Nonbonded Distance : 2.614 Molprobity Statistics. All-atom Clashscore : 17.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.78 % Favored : 93.22 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -4.37 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP C 334 PHE 0.014 0.002 PHE F 313 *********************** 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 130 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 130 time to evaluate : 0.389 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: B 311 MET cc_start: 0.7190 (ptp) cc_final: 0.6635 (mmt) REVERT: E 307 MET cc_start: 0.7764 (tpt) cc_final: 0.7360 (tpt) REVERT: G 317 SER cc_start: 0.8779 (t) cc_final: 0.8537 (m) REVERT: I 307 MET cc_start: 0.7538 (tpp) cc_final: 0.6647 (tpp) REVERT: I 336 MET cc_start: 0.6960 (tmm) cc_final: 0.6533 (tmm) REVERT: I 339 MET cc_start: 0.8161 (mtp) cc_final: 0.7868 (mtp) REVERT: K 307 MET cc_start: 0.6633 (tpp) cc_final: 0.5985 (tpp) REVERT: K 333 SER cc_start: 0.8893 (p) cc_final: 0.8687 (p) REVERT: K 339 MET cc_start: 0.8151 (mtp) cc_final: 0.7773 (mtp) REVERT: L 313 PHE cc_start: 0.7720 (m-10) cc_final: 0.6091 (p90) outliers start: 0 outliers final: 0 residues processed: 130 average time/residue: 0.1154 time to fit residues: 19.5547 Evaluate side-chains 118 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 118 time to evaluate : 0.414 ------------------------------------------------------------------------------- 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: 7.9990 chunk 39 optimal weight: 0.9980 chunk 25 optimal weight: 0.9990 chunk 46 optimal weight: 0.9990 chunk 28 optimal weight: 4.9990 chunk 21 optimal weight: 4.9990 chunk 18 optimal weight: 1.9990 chunk 27 optimal weight: 1.9990 chunk 13 optimal weight: 0.9980 chunk 9 optimal weight: 0.9990 chunk 8 optimal weight: 9.9990 overall best weight: 0.9986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: D 344 GLN ** F 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** H 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 331 GLN J 345 ASN L 344 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7539 moved from start: 0.6981 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.046 3744 Z= 0.232 Angle : 0.658 10.120 4980 Z= 0.338 Chirality : 0.036 0.113 480 Planarity : 0.002 0.021 684 Dihedral : 6.205 28.661 528 Min Nonbonded Distance : 2.622 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.17 % Favored : 92.83 % 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: -4.38 (0.20), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.33 (0.15), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP D 334 PHE 0.016 0.002 PHE D 313 *********************** 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 131 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 131 time to evaluate : 0.437 Fit side-chains REVERT: B 311 MET cc_start: 0.7411 (ptp) cc_final: 0.6739 (mmt) REVERT: G 317 SER cc_start: 0.8732 (t) cc_final: 0.8493 (m) REVERT: H 337 MET cc_start: 0.8376 (mtt) cc_final: 0.7900 (mtt) REVERT: I 307 MET cc_start: 0.7456 (tpp) cc_final: 0.6560 (tpp) REVERT: I 337 MET cc_start: 0.6958 (mmt) cc_final: 0.6691 (tpp) REVERT: I 339 MET cc_start: 0.8281 (mtp) cc_final: 0.8070 (mtp) REVERT: K 307 MET cc_start: 0.6489 (tpp) cc_final: 0.5932 (tpp) REVERT: K 333 SER cc_start: 0.8819 (p) cc_final: 0.8598 (p) REVERT: K 339 MET cc_start: 0.8003 (mtp) cc_final: 0.7745 (mtp) REVERT: L 313 PHE cc_start: 0.7717 (m-10) cc_final: 0.6141 (p90) outliers start: 0 outliers final: 0 residues processed: 131 average time/residue: 0.1218 time to fit residues: 20.5542 Evaluate side-chains 121 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 121 time to evaluate : 0.417 ------------------------------------------------------------------------------- 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: 4.9990 chunk 22 optimal weight: 0.8980 chunk 4 optimal weight: 9.9990 chunk 36 optimal weight: 10.0000 chunk 42 optimal weight: 6.9990 chunk 44 optimal weight: 0.9990 chunk 40 optimal weight: 7.9990 chunk 43 optimal weight: 3.9990 chunk 25 optimal weight: 5.9990 chunk 18 optimal weight: 1.9990 overall best weight: 2.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN ** J 331 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7624 moved from start: 0.7088 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.031 3744 Z= 0.355 Angle : 0.710 5.358 4980 Z= 0.377 Chirality : 0.038 0.115 480 Planarity : 0.003 0.023 684 Dihedral : 6.600 29.470 528 Min Nonbonded Distance : 2.603 Molprobity Statistics. All-atom Clashscore : 19.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.91 % Favored : 91.09 % Rotamer: Outliers : 0.00 % Allowed : 1.72 % Favored : 98.28 % 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: -4.39 (0.21), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.34 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.002 TRP L 334 PHE 0.014 0.002 PHE J 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 129 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 129 time to evaluate : 0.483 Fit side-chains REVERT: B 311 MET cc_start: 0.7566 (ptp) cc_final: 0.6651 (mmt) REVERT: D 313 PHE cc_start: 0.8855 (m-10) cc_final: 0.8631 (m-10) REVERT: E 333 SER cc_start: 0.8899 (p) cc_final: 0.8642 (p) REVERT: F 336 MET cc_start: 0.7871 (tpt) cc_final: 0.7574 (tpt) REVERT: G 317 SER cc_start: 0.8851 (t) cc_final: 0.8634 (m) REVERT: H 337 MET cc_start: 0.8497 (mtt) cc_final: 0.8065 (mtt) REVERT: K 333 SER cc_start: 0.8878 (p) cc_final: 0.8673 (p) REVERT: L 331 GLN cc_start: 0.8387 (mt0) cc_final: 0.7959 (mt0) outliers start: 0 outliers final: 0 residues processed: 129 average time/residue: 0.1086 time to fit residues: 18.1941 Evaluate side-chains 114 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 114 time to evaluate : 0.358 ------------------------------------------------------------------------------- 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: 4.9990 chunk 13 optimal weight: 2.9990 chunk 38 optimal weight: 2.9990 chunk 40 optimal weight: 10.0000 chunk 42 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 45 optimal weight: 3.9990 chunk 27 optimal weight: 5.9990 chunk 21 optimal weight: 0.8980 chunk 31 optimal weight: 1.9990 chunk 47 optimal weight: 3.9990 overall best weight: 2.5788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 344 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 344 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** J 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7639 moved from start: 0.7185 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3744 Z= 0.399 Angle : 0.776 7.762 4980 Z= 0.404 Chirality : 0.038 0.115 480 Planarity : 0.003 0.023 684 Dihedral : 6.685 27.936 528 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 20.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.47 % Favored : 89.53 % 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 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.026 0.003 TRP L 334 PHE 0.020 0.003 PHE F 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 127 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 127 time to evaluate : 0.366 Fit side-chains revert: symmetry clash REVERT: B 311 MET cc_start: 0.7526 (ptp) cc_final: 0.6447 (tpt) REVERT: B 313 PHE cc_start: 0.8557 (m-10) cc_final: 0.8256 (m-10) REVERT: C 344 GLN cc_start: 0.8751 (mt0) cc_final: 0.8453 (mp10) REVERT: D 313 PHE cc_start: 0.8886 (m-10) cc_final: 0.8533 (m-10) REVERT: G 317 SER cc_start: 0.8859 (t) cc_final: 0.8649 (m) REVERT: H 337 MET cc_start: 0.8165 (mtt) cc_final: 0.7773 (mtt) REVERT: I 307 MET cc_start: 0.7385 (tpp) cc_final: 0.6613 (tpp) REVERT: I 337 MET cc_start: 0.7219 (mmt) cc_final: 0.6993 (mmt) REVERT: K 307 MET cc_start: 0.7000 (tpt) cc_final: 0.6384 (tpp) REVERT: L 331 GLN cc_start: 0.8214 (mt0) cc_final: 0.7938 (mt0) outliers start: 0 outliers final: 0 residues processed: 127 average time/residue: 0.1170 time to fit residues: 19.1133 Evaluate side-chains 117 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 117 time to evaluate : 0.378 ------------------------------------------------------------------------------- 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: 0.0770 chunk 38 optimal weight: 6.9990 chunk 3 optimal weight: 0.0050 chunk 29 optimal weight: 2.9990 chunk 23 optimal weight: 0.0670 chunk 30 optimal weight: 0.9990 chunk 40 optimal weight: 8.9990 chunk 11 optimal weight: 0.9990 chunk 35 optimal weight: 2.9990 chunk 5 optimal weight: 0.0670 chunk 10 optimal weight: 9.9990 overall best weight: 0.2430 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 344 GLN B 327 GLN ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** F 327 GLN J 345 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7411 moved from start: 0.7519 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= 0.175 Angle : 0.648 5.890 4980 Z= 0.336 Chirality : 0.037 0.114 480 Planarity : 0.002 0.022 684 Dihedral : 6.198 27.483 528 Min Nonbonded Distance : 2.610 Molprobity Statistics. All-atom Clashscore : 15.38 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.04 % Favored : 94.96 % Rotamer: Outliers : 0.29 % Allowed : 0.86 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.37 (0.21), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.32 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.002 TRP G 334 PHE 0.012 0.002 PHE F 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 138 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 137 time to evaluate : 0.415 Fit side-chains REVERT: B 311 MET cc_start: 0.7382 (ptp) cc_final: 0.6428 (tpt) REVERT: B 313 PHE cc_start: 0.8108 (m-10) cc_final: 0.7869 (m-10) REVERT: C 344 GLN cc_start: 0.8826 (mt0) cc_final: 0.8325 (mp10) REVERT: D 307 MET cc_start: 0.7988 (ttm) cc_final: 0.7487 (ttm) REVERT: D 313 PHE cc_start: 0.8497 (m-10) cc_final: 0.7912 (m-10) REVERT: I 307 MET cc_start: 0.7732 (tpp) cc_final: 0.6697 (tpp) REVERT: I 337 MET cc_start: 0.7074 (mmt) cc_final: 0.6789 (mmt) REVERT: K 307 MET cc_start: 0.7015 (tpt) cc_final: 0.6624 (tpp) REVERT: L 313 PHE cc_start: 0.7450 (m-10) cc_final: 0.6099 (p90) outliers start: 1 outliers final: 0 residues processed: 137 average time/residue: 0.1124 time to fit residues: 19.9307 Evaluate side-chains 116 residues out of total 348 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 116 time to evaluate : 0.376 ------------------------------------------------------------------------------- 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: 4.9990 chunk 15 optimal weight: 4.9990 chunk 39 optimal weight: 0.9980 chunk 4 optimal weight: 2.9990 chunk 7 optimal weight: 1.9990 chunk 33 optimal weight: 5.9990 chunk 2 optimal weight: 0.0060 chunk 27 optimal weight: 6.9990 chunk 43 optimal weight: 1.9990 chunk 25 optimal weight: 0.0770 chunk 32 optimal weight: 2.9990 overall best weight: 1.0158 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** D 346 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** G 344 GLN J 345 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4609 r_free = 0.4609 target = 0.254442 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 58)----------------| | r_work = 0.4598 r_free = 0.4598 target = 0.181446 restraints weight = 6598.679| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 35)----------------| | r_work = 0.4601 r_free = 0.4601 target = 0.180577 restraints weight = 10348.757| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 42)----------------| | r_work = 0.4621 r_free = 0.4621 target = 0.180998 restraints weight = 9238.828| |-----------------------------------------------------------------------------| r_work (final): 0.4259 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6937 moved from start: 0.7543 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.032 3744 Z= 0.239 Angle : 0.717 8.083 4980 Z= 0.357 Chirality : 0.037 0.124 480 Planarity : 0.002 0.021 684 Dihedral : 6.255 27.360 528 Min Nonbonded Distance : 2.542 Molprobity Statistics. All-atom Clashscore : 15.94 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.72 % Favored : 91.28 % 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: -4.42 (0.21), residues: 516 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.36 (0.16), residues: 516 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.002 TRP D 334 PHE 0.019 0.002 PHE E 316 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1240.91 seconds wall clock time: 22 minutes 23.37 seconds (1343.37 seconds total)