Starting phenix.real_space_refine on Sun Mar 10 19:52:23 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/03_2024/7cz6_30507.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/03_2024/7cz6_30507.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=4.1 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/03_2024/7cz6_30507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/03_2024/7cz6_30507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/03_2024/7cz6_30507.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/03_2024/7cz6_30507.pdb" } resolution = 4.1 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 ------------------------------------------------------------------------------- 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= 1.000 Set stop_for_unknowns flag Set to: True Assert model is a single copy model Assert all atoms have isotropic ADPs Construct map_model_manager Extract box with map and model Check model and map are aligned Set scattering table Set to: electron Number of scattering types: 4 Type Number sf(0) Gaussians S 20 5.16 5 C 2900 2.51 5 N 700 2.21 5 O 915 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: 4535 Number of models: 1 Model: "" Number of chains: 5 Chain: "C" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 116} Chain: "A" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 116} Chain: "B" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 116} Chain: "D" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 116} Chain: "E" Number of atoms: 907 Number of conformers: 1 Conformer: "" Number of residues, atoms: 126, 907 Classifications: {'peptide': 126} Link IDs: {'PCIS': 1, 'PTRANS': 8, 'TRANS': 116} Time building chain proxies: 3.08, per 1000 atoms: 0.68 Number of scatterers: 4535 At special positions: 0 Unit cell: (71.94, 71.94, 90.47, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 4 Type Number sf(0) S 20 16.00 O 915 8.00 N 700 7.00 C 2900 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: 1.94 Conformation dependent library (CDL) restraints added in 827.7 milliseconds 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1140 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 10 sheets defined 0.0% alpha, 31.7% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.46 Creating SS restraints... Processing sheet with id= 1, first strand: chain 'C' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR C 275 " --> pdb=" O THR C 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR C 318 " --> pdb=" O TYR C 275 " (cutoff:3.500A) Processing sheet with id= 2, first strand: chain 'C' and resid 262 through 264 Processing sheet with id= 3, first strand: chain 'A' and resid 248 through 254 removed outlier: 5.248A pdb=" N TYR A 275 " --> pdb=" O THR A 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR A 318 " --> pdb=" O TYR A 275 " (cutoff:3.500A) Processing sheet with id= 4, first strand: chain 'A' and resid 262 through 264 Processing sheet with id= 5, first strand: chain 'B' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR B 275 " --> pdb=" O THR B 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR B 318 " --> pdb=" O TYR B 275 " (cutoff:3.500A) Processing sheet with id= 6, first strand: chain 'B' and resid 262 through 264 Processing sheet with id= 7, first strand: chain 'D' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR D 275 " --> pdb=" O THR D 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR D 318 " --> pdb=" O TYR D 275 " (cutoff:3.500A) Processing sheet with id= 8, first strand: chain 'D' and resid 262 through 264 Processing sheet with id= 9, first strand: chain 'E' and resid 248 through 254 removed outlier: 5.247A pdb=" N TYR E 275 " --> pdb=" O THR E 318 " (cutoff:3.500A) removed outlier: 3.713A pdb=" N THR E 318 " --> pdb=" O TYR E 275 " (cutoff:3.500A) Processing sheet with id= 10, first strand: chain 'E' and resid 262 through 264 150 hydrogen bonds defined for protein. 405 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.10 Time building geometry restraints manager: 2.08 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1362 1.34 - 1.46: 961 1.46 - 1.58: 2287 1.58 - 1.69: 0 1.69 - 1.81: 30 Bond restraints: 4640 Sorted by residual: bond pdb=" CA PRO E 269 " pdb=" C PRO E 269 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.45e+00 bond pdb=" CA PRO B 269 " pdb=" C PRO B 269 " ideal model delta sigma weight residual 1.520 1.556 -0.036 1.42e-02 4.96e+03 6.43e+00 bond pdb=" CA PRO C 269 " pdb=" C PRO C 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.38e+00 bond pdb=" CA PRO D 269 " pdb=" C PRO D 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.37e+00 bond pdb=" CA PRO A 269 " pdb=" C PRO A 269 " ideal model delta sigma weight residual 1.520 1.555 -0.036 1.42e-02 4.96e+03 6.37e+00 ... (remaining 4635 not shown) Histogram of bond angle deviations from ideal: 100.19 - 106.96: 245 106.96 - 113.73: 2647 113.73 - 120.50: 1602 120.50 - 127.27: 1866 127.27 - 134.03: 40 Bond angle restraints: 6400 Sorted by residual: angle pdb=" N TYR D 304 " pdb=" CA TYR D 304 " pdb=" C TYR D 304 " ideal model delta sigma weight residual 107.60 121.35 -13.75 1.83e+00 2.99e-01 5.65e+01 angle pdb=" N TYR B 304 " pdb=" CA TYR B 304 " pdb=" C TYR B 304 " ideal model delta sigma weight residual 107.60 121.34 -13.74 1.83e+00 2.99e-01 5.64e+01 angle pdb=" N TYR C 304 " pdb=" CA TYR C 304 " pdb=" C TYR C 304 " ideal model delta sigma weight residual 107.60 121.32 -13.72 1.83e+00 2.99e-01 5.62e+01 angle pdb=" N TYR A 304 " pdb=" CA TYR A 304 " pdb=" C TYR A 304 " ideal model delta sigma weight residual 107.60 121.31 -13.71 1.83e+00 2.99e-01 5.62e+01 angle pdb=" N TYR E 304 " pdb=" CA TYR E 304 " pdb=" C TYR E 304 " ideal model delta sigma weight residual 107.60 121.31 -13.71 1.83e+00 2.99e-01 5.61e+01 ... (remaining 6395 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 11.99: 2527 11.99 - 23.97: 123 23.97 - 35.95: 10 35.95 - 47.94: 15 47.94 - 59.92: 5 Dihedral angle restraints: 2680 sinusoidal: 900 harmonic: 1780 Sorted by residual: dihedral pdb=" CA GLY D 317 " pdb=" C GLY D 317 " pdb=" N THR D 318 " pdb=" CA THR D 318 " ideal model delta harmonic sigma weight residual 180.00 156.91 23.09 0 5.00e+00 4.00e-02 2.13e+01 dihedral pdb=" CA GLY B 317 " pdb=" C GLY B 317 " pdb=" N THR B 318 " pdb=" CA THR B 318 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 dihedral pdb=" CA GLY E 317 " pdb=" C GLY E 317 " pdb=" N THR E 318 " pdb=" CA THR E 318 " ideal model delta harmonic sigma weight residual 180.00 156.97 23.03 0 5.00e+00 4.00e-02 2.12e+01 ... (remaining 2677 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.061: 701 0.061 - 0.122: 108 0.122 - 0.182: 11 0.182 - 0.243: 0 0.243 - 0.304: 5 Chirality restraints: 825 Sorted by residual: chirality pdb=" CA TYR E 304 " pdb=" N TYR E 304 " pdb=" C TYR E 304 " pdb=" CB TYR E 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.31e+00 chirality pdb=" CA TYR D 304 " pdb=" N TYR D 304 " pdb=" C TYR D 304 " pdb=" CB TYR D 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 chirality pdb=" CA TYR C 304 " pdb=" N TYR C 304 " pdb=" C TYR C 304 " pdb=" CB TYR C 304 " both_signs ideal model delta sigma weight residual False 2.51 2.21 0.30 2.00e-01 2.50e+01 2.29e+00 ... (remaining 822 not shown) Planarity restraints: 795 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C SER B 260 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO B 261 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO B 261 " 0.030 5.00e-02 4.00e+02 pdb=" CD PRO B 261 " 0.037 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY D 268 " 0.041 5.00e-02 4.00e+02 6.24e-02 6.23e+00 pdb=" N PRO D 269 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO D 269 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO D 269 " 0.033 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C GLY C 268 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.22e+00 pdb=" N PRO C 269 " -0.108 5.00e-02 4.00e+02 pdb=" CA PRO C 269 " 0.034 5.00e-02 4.00e+02 pdb=" CD PRO C 269 " 0.033 5.00e-02 4.00e+02 ... (remaining 792 not shown) Histogram of nonbonded interaction distances: 1.05 - 1.82: 15 1.82 - 2.59: 135 2.59 - 3.36: 6419 3.36 - 4.13: 10246 4.13 - 4.90: 17972 Nonbonded interactions: 34787 Sorted by model distance: nonbonded pdb=" O ASP A 309 " pdb=" OD2 ASP B 309 " model vdw 1.047 3.040 nonbonded pdb=" O ASP B 309 " pdb=" OD2 ASP D 309 " model vdw 1.047 3.040 nonbonded pdb=" O ASP C 309 " pdb=" OD2 ASP A 309 " model vdw 1.048 3.040 nonbonded pdb=" OD2 ASP C 309 " pdb=" O ASP E 309 " model vdw 1.048 3.040 nonbonded pdb=" O ASP D 309 " pdb=" OD2 ASP E 309 " model vdw 1.048 3.040 ... (remaining 34782 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' } 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: 0.040 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.000 Extract box with map and model: 0.520 Check model and map are aligned: 0.080 Set scattering table: 0.050 Process input model: 17.440 Find NCS groups from input model: 0.300 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 21.480 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6568 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 : 0.009 0.041 4640 Z= 0.576 Angle : 1.616 13.750 6400 Z= 1.065 Chirality : 0.052 0.304 825 Planarity : 0.008 0.062 795 Dihedral : 8.570 59.920 1540 Min Nonbonded Distance : 1.047 Molprobity Statistics. All-atom Clashscore : 61.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.06 % Favored : 91.94 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.66 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.79 (0.37), residues: 180 loop : -1.29 (0.30), residues: 440 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.020 0.002 TRP E 331 PHE 0.010 0.002 PHE E 307 TYR 0.008 0.001 TYR B 275 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 243 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 243 time to evaluate : 0.499 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 277 THR cc_start: 0.7462 (p) cc_final: 0.6955 (p) REVERT: A 277 THR cc_start: 0.7645 (p) cc_final: 0.7384 (p) REVERT: A 341 MET cc_start: 0.7260 (tpp) cc_final: 0.6909 (tpp) REVERT: B 277 THR cc_start: 0.7265 (p) cc_final: 0.6680 (p) REVERT: D 277 THR cc_start: 0.7581 (p) cc_final: 0.7104 (p) REVERT: D 348 LYS cc_start: 0.7769 (mttt) cc_final: 0.7324 (mttt) REVERT: E 348 LYS cc_start: 0.7677 (mttt) cc_final: 0.7329 (mttt) outliers start: 0 outliers final: 0 residues processed: 243 average time/residue: 0.1234 time to fit residues: 39.5145 Evaluate side-chains 170 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.497 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 50 optimal weight: 9.9990 chunk 45 optimal weight: 4.9990 chunk 25 optimal weight: 6.9990 chunk 15 optimal weight: 5.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 8.9990 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 0.6980 chunk 28 optimal weight: 6.9990 chunk 35 optimal weight: 20.0000 chunk 54 optimal weight: 3.9990 overall best weight: 4.1388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN C 360 GLN A 282 GLN A 305 GLN A 360 GLN B 276 GLN B 282 GLN B 305 GLN B 360 GLN D 305 GLN D 360 GLN ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 344 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** E 360 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6685 moved from start: 0.3470 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4640 Z= 0.354 Angle : 0.807 8.570 6400 Z= 0.444 Chirality : 0.051 0.150 825 Planarity : 0.006 0.055 795 Dihedral : 7.837 24.451 640 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 21.55 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.19 % Allowed : 5.96 % Favored : 93.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.20 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -1.08 (0.34), residues: 245 loop : -1.76 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP E 331 PHE 0.024 0.003 PHE D 307 TYR 0.015 0.002 TYR D 275 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 227 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 226 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 276 GLN cc_start: 0.6855 (tt0) cc_final: 0.5534 (tt0) REVERT: B 300 LYS cc_start: 0.5896 (mttm) cc_final: 0.5659 (mttm) REVERT: D 247 ASP cc_start: 0.7888 (p0) cc_final: 0.7515 (p0) REVERT: D 348 LYS cc_start: 0.7706 (mttt) cc_final: 0.7478 (mtmt) outliers start: 1 outliers final: 1 residues processed: 226 average time/residue: 0.1308 time to fit residues: 38.8809 Evaluate side-chains 194 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.444 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 30 optimal weight: 4.9990 chunk 16 optimal weight: 8.9990 chunk 45 optimal weight: 20.0000 chunk 37 optimal weight: 6.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 20.0000 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 7.9990 chunk 53 optimal weight: 0.6980 overall best weight: 4.3388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN C 305 GLN A 282 GLN B 282 GLN D 282 GLN E 305 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6728 moved from start: 0.4379 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.048 4640 Z= 0.343 Angle : 0.725 6.739 6400 Z= 0.398 Chirality : 0.049 0.177 825 Planarity : 0.006 0.067 795 Dihedral : 7.060 21.285 640 Min Nonbonded Distance : 2.183 Molprobity Statistics. All-atom Clashscore : 17.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.26 % Favored : 92.74 % Rotamer: Outliers : 0.00 % Allowed : 3.65 % Favored : 96.35 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.25 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.95 (0.35), residues: 245 loop : -1.94 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP C 331 PHE 0.016 0.002 PHE D 311 TYR 0.020 0.002 TYR B 275 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 219 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.473 Fit side-chains REVERT: A 348 LYS cc_start: 0.8229 (mtmm) cc_final: 0.7991 (mtmm) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1178 time to fit residues: 34.3268 Evaluate side-chains 191 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 191 time to evaluate : 0.441 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 41 optimal weight: 5.9990 chunk 28 optimal weight: 10.0000 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 9.9990 chunk 54 optimal weight: 6.9990 chunk 57 optimal weight: 20.0000 chunk 51 optimal weight: 3.9990 chunk 15 optimal weight: 9.9990 chunk 48 optimal weight: 30.0000 chunk 32 optimal weight: 0.0010 overall best weight: 4.5994 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN A 282 GLN A 305 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** B 305 GLN ** D 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6743 moved from start: 0.4910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.045 4640 Z= 0.346 Angle : 0.696 6.371 6400 Z= 0.382 Chirality : 0.048 0.152 825 Planarity : 0.006 0.068 795 Dihedral : 6.966 21.413 640 Min Nonbonded Distance : 2.101 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.00 % Allowed : 2.69 % Favored : 97.31 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.27 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -1.01 (0.35), residues: 245 loop : -1.90 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.005 0.001 TRP A 331 PHE 0.020 0.002 PHE B 297 TYR 0.017 0.001 TYR E 275 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 220 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 220 time to evaluate : 0.512 Fit side-chains REVERT: E 348 LYS cc_start: 0.8147 (mtmm) cc_final: 0.7671 (mtmm) outliers start: 0 outliers final: 0 residues processed: 220 average time/residue: 0.1165 time to fit residues: 34.0941 Evaluate side-chains 195 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.486 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 0 optimal weight: 20.0000 chunk 43 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 49 optimal weight: 0.0040 chunk 40 optimal weight: 8.9990 chunk 29 optimal weight: 7.9990 chunk 52 optimal weight: 4.9990 chunk 14 optimal weight: 0.0770 chunk 19 optimal weight: 10.0000 chunk 11 optimal weight: 0.0470 chunk 34 optimal weight: 1.9990 overall best weight: 1.0252 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6633 moved from start: 0.5415 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 4640 Z= 0.191 Angle : 0.677 7.940 6400 Z= 0.359 Chirality : 0.050 0.165 825 Planarity : 0.006 0.066 795 Dihedral : 6.444 20.424 640 Min Nonbonded Distance : 2.089 Molprobity Statistics. All-atom Clashscore : 13.15 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.32 % Favored : 94.68 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.96 (0.33), residues: 245 loop : -1.83 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP B 331 PHE 0.021 0.002 PHE B 297 TYR 0.013 0.001 TYR A 275 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 234 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 234 time to evaluate : 0.500 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 234 average time/residue: 0.1178 time to fit residues: 36.9850 Evaluate side-chains 202 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 202 time to evaluate : 0.524 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 14 optimal weight: 0.0050 chunk 58 optimal weight: 9.9990 chunk 48 optimal weight: 3.9990 chunk 26 optimal weight: 3.9990 chunk 4 optimal weight: 10.0000 chunk 19 optimal weight: 8.9990 chunk 30 optimal weight: 9.9990 chunk 55 optimal weight: 3.9990 chunk 6 optimal weight: 2.9990 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 2.9990 overall best weight: 2.8002 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN A 256 ASN B 253 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6653 moved from start: 0.5670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4640 Z= 0.267 Angle : 0.679 6.866 6400 Z= 0.368 Chirality : 0.050 0.178 825 Planarity : 0.006 0.069 795 Dihedral : 6.374 19.502 640 Min Nonbonded Distance : 2.117 Molprobity Statistics. All-atom Clashscore : 15.14 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.13 % Favored : 93.87 % Rotamer: Outliers : 0.19 % Allowed : 2.12 % Favored : 97.69 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.18 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.89 (0.32), residues: 245 loop : -1.89 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 331 PHE 0.021 0.002 PHE D 297 TYR 0.011 0.001 TYR B 275 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 226 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 0.496 Fit side-chains REVERT: C 348 LYS cc_start: 0.8325 (ptpp) cc_final: 0.8107 (ptmt) outliers start: 1 outliers final: 1 residues processed: 226 average time/residue: 0.1159 time to fit residues: 35.0054 Evaluate side-chains 207 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 206 time to evaluate : 0.520 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 32 optimal weight: 8.9990 chunk 48 optimal weight: 0.0980 chunk 57 optimal weight: 7.9990 chunk 36 optimal weight: 0.0050 chunk 35 optimal weight: 20.0000 chunk 26 optimal weight: 10.0000 chunk 23 optimal weight: 7.9990 chunk 34 optimal weight: 3.9990 chunk 17 optimal weight: 6.9990 chunk 11 optimal weight: 0.8980 chunk 39 optimal weight: 6.9990 overall best weight: 2.3998 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN A 282 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6639 moved from start: 0.5897 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.042 4640 Z= 0.254 Angle : 0.680 7.177 6400 Z= 0.361 Chirality : 0.051 0.173 825 Planarity : 0.006 0.068 795 Dihedral : 6.297 19.927 640 Min Nonbonded Distance : 2.082 Molprobity Statistics. All-atom Clashscore : 15.25 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.15 % Favored : 98.85 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.15 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.86 (0.32), residues: 245 loop : -1.88 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 331 PHE 0.040 0.003 PHE B 314 TYR 0.009 0.001 TYR B 275 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 229 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 229 time to evaluate : 0.496 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 229 average time/residue: 0.1182 time to fit residues: 35.9475 Evaluate side-chains 203 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 203 time to evaluate : 0.484 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 28 optimal weight: 0.7980 chunk 5 optimal weight: 4.9990 chunk 45 optimal weight: 20.0000 chunk 52 optimal weight: 6.9990 chunk 55 optimal weight: 6.9990 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 2.9990 chunk 32 optimal weight: 2.9990 chunk 23 optimal weight: 20.0000 chunk 42 optimal weight: 10.0000 chunk 16 optimal weight: 20.0000 overall best weight: 2.9588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: C 282 GLN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 282 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 253 ASN E 305 GLN Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6649 moved from start: 0.6061 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.057 4640 Z= 0.279 Angle : 0.690 7.635 6400 Z= 0.365 Chirality : 0.051 0.196 825 Planarity : 0.006 0.066 795 Dihedral : 6.321 20.498 640 Min Nonbonded Distance : 2.087 Molprobity Statistics. All-atom Clashscore : 15.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.29 % Favored : 93.71 % Rotamer: Outliers : 0.19 % Allowed : 1.35 % Favored : 98.46 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.17 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.89 (0.32), residues: 245 loop : -1.89 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 331 PHE 0.039 0.002 PHE B 314 TYR 0.007 0.001 TYR C 275 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 224 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 223 time to evaluate : 0.479 Fit side-chains revert: symmetry clash REVERT: B 313 SER cc_start: 0.7988 (p) cc_final: 0.7658 (p) outliers start: 1 outliers final: 0 residues processed: 224 average time/residue: 0.1188 time to fit residues: 35.3693 Evaluate side-chains 195 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.491 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 0.0050 chunk 50 optimal weight: 4.9990 chunk 53 optimal weight: 2.9990 chunk 35 optimal weight: 20.0000 chunk 56 optimal weight: 2.9990 chunk 34 optimal weight: 0.9980 chunk 27 optimal weight: 1.9990 chunk 39 optimal weight: 0.9990 chunk 59 optimal weight: 5.9990 chunk 55 optimal weight: 2.9990 chunk 47 optimal weight: 9.9990 overall best weight: 1.4000 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN C 305 GLN A 256 ASN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 282 GLN Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6609 moved from start: 0.6338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.062 4640 Z= 0.236 Angle : 0.718 8.007 6400 Z= 0.372 Chirality : 0.053 0.185 825 Planarity : 0.006 0.060 795 Dihedral : 6.206 20.781 640 Min Nonbonded Distance : 2.097 Molprobity Statistics. All-atom Clashscore : 15.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.00 % Allowed : 1.92 % Favored : 98.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -1.99 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.63 (0.34), residues: 235 loop : -1.84 (0.29), residues: 385 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 331 PHE 0.027 0.002 PHE D 314 TYR 0.016 0.001 TYR D 275 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 216 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 216 time to evaluate : 0.518 Fit side-chains revert: symmetry clash REVERT: D 314 PHE cc_start: 0.6998 (m-10) cc_final: 0.6762 (m-10) REVERT: E 253 ASN cc_start: 0.6518 (t0) cc_final: 0.6115 (t0) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1176 time to fit residues: 33.8042 Evaluate side-chains 183 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 183 time to evaluate : 0.537 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 4 optimal weight: 20.0000 chunk 36 optimal weight: 30.0000 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 6.9990 chunk 50 optimal weight: 0.0020 chunk 14 optimal weight: 4.9990 chunk 43 optimal weight: 8.9990 chunk 7 optimal weight: 10.0000 chunk 13 optimal weight: 3.9990 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 10.0000 overall best weight: 4.5996 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6689 moved from start: 0.6330 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.052 4640 Z= 0.368 Angle : 0.732 6.760 6400 Z= 0.392 Chirality : 0.053 0.204 825 Planarity : 0.006 0.068 795 Dihedral : 6.597 21.420 640 Min Nonbonded Distance : 2.078 Molprobity Statistics. All-atom Clashscore : 16.46 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.94 % Favored : 93.06 % Rotamer: Outliers : 0.00 % Allowed : 0.38 % Favored : 99.62 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.13 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.92 (0.32), residues: 245 loop : -1.81 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 331 PHE 0.021 0.002 PHE D 314 TYR 0.013 0.001 TYR C 275 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1240 Ramachandran restraints generated. 620 Oldfield, 0 Emsley, 620 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 190 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 190 time to evaluate : 0.494 Fit side-chains revert: symmetry clash REVERT: C 282 GLN cc_start: 0.5439 (mt0) cc_final: 0.4962 (mt0) REVERT: B 348 LYS cc_start: 0.8011 (pttm) cc_final: 0.7781 (mtmm) outliers start: 0 outliers final: 0 residues processed: 190 average time/residue: 0.1248 time to fit residues: 31.2927 Evaluate side-chains 170 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.465 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 60 random chunks: chunk 48 optimal weight: 7.9990 chunk 6 optimal weight: 5.9990 chunk 8 optimal weight: 1.9990 chunk 41 optimal weight: 6.9990 chunk 2 optimal weight: 7.9990 chunk 34 optimal weight: 0.8980 chunk 54 optimal weight: 9.9990 chunk 32 optimal weight: 5.9990 chunk 40 optimal weight: 0.9990 chunk 1 optimal weight: 8.9990 chunk 38 optimal weight: 8.9990 overall best weight: 3.1788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN ** A 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 305 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4108 r_free = 0.4108 target = 0.175011 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 45)----------------| | r_work = 0.3509 r_free = 0.3509 target = 0.120074 restraints weight = 9096.688| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 30)----------------| | r_work = 0.3572 r_free = 0.3572 target = 0.123996 restraints weight = 5979.787| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 50)----------------| | r_work = 0.3606 r_free = 0.3606 target = 0.126765 restraints weight = 4537.025| |-----------------------------------------------------------------------------| r_work (final): 0.3570 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7447 moved from start: 0.6533 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.043 4640 Z= 0.295 Angle : 0.717 7.316 6400 Z= 0.380 Chirality : 0.052 0.190 825 Planarity : 0.006 0.065 795 Dihedral : 6.501 21.597 640 Min Nonbonded Distance : 2.091 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 0.77 % Favored : 99.23 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 11.11 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -2.16 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.96 (0.32), residues: 245 loop : -1.81 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP E 331 PHE 0.027 0.002 PHE D 314 TYR 0.014 0.001 TYR C 275 =============================================================================== Job complete usr+sys time: 1364.40 seconds wall clock time: 25 minutes 26.65 seconds (1526.65 seconds total)