Starting phenix.real_space_refine on Mon Sep 23 18:25:44 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/09_2024/7cz6_30507.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/09_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_30507/09_2024/7cz6_30507.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/09_2024/7cz6_30507.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/09_2024/7cz6_30507.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7cz6_30507/09_2024/7cz6_30507.cif" } 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 Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5461/modules/chem_data/mon_lib" Total number of atoms: 4535 Number of models: 1 Model: "" Number of chains: 1 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} Restraints were copied for chains: C, B, E, D Time building chain proxies: 2.36, per 1000 atoms: 0.52 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 - 3.00 Amino acid : True - 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 615.7 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: 0.53 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: 1.02 Time building geometry restraints manager: 1.40 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: 960 1.46 - 1.58: 2288 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: 0.00 - 2.75: 5874 2.75 - 5.50: 426 5.50 - 8.25: 90 8.25 - 11.00: 5 11.00 - 13.75: 5 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 180.00 156.98 23.02 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: 702 0.061 - 0.122: 107 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 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 delta sigma weight rms_deltas residual plane pdb=" C SER B 260 " 0.041 5.00e-02 4.00e+02 6.23e-02 6.21e+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 ... (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 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' } 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: 0.230 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: 0.010 Extract box with map and model: 0.200 Check model and map are aligned: 0.030 Set scattering table: 0.050 Process input model: 14.260 Find NCS groups from input model: 0.150 Set up NCS constraints: 0.010 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:2.760 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.700 ------------------------------------------------------------------------------- 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 : 0.451 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: 0.6956 (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: 0.1239 time to fit residues: 39.7839 Evaluate side-chains 170 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 170 time to evaluate : 0.452 ------------------------------------------------------------------------------- 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: 10.0000 chunk 45 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 15 optimal weight: 2.9990 chunk 30 optimal weight: 4.9990 chunk 24 optimal weight: 6.9990 chunk 47 optimal weight: 20.0000 chunk 18 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 35 optimal weight: 5.9990 chunk 54 optimal weight: 3.9990 overall best weight: 4.1990 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** C 360 GLN A 282 GLN A 305 GLN A 360 GLN B 276 GLN B 305 GLN B 360 GLN D 305 GLN D 360 GLN E 305 GLN E 360 GLN Total number of N/Q/H flips: 12 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6684 moved from start: 0.3475 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.043 4640 Z= 0.366 Angle : 0.816 8.334 6400 Z= 0.448 Chirality : 0.053 0.155 825 Planarity : 0.007 0.055 795 Dihedral : 7.890 26.092 640 Min Nonbonded Distance : 2.552 Molprobity Statistics. All-atom Clashscore : 20.00 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.68 % Favored : 95.32 % Rotamer: Outliers : 0.19 % Allowed : 5.00 % Favored : 94.81 % 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: -2.05 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.99 (0.34), residues: 245 loop : -1.65 (0.28), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.002 TRP A 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 230 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 229 time to evaluate : 0.726 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 276 GLN cc_start: 0.6921 (tt0) cc_final: 0.5578 (tt0) REVERT: C 292 VAL cc_start: 0.8085 (p) cc_final: 0.7881 (p) REVERT: C 300 LYS cc_start: 0.5947 (mttm) cc_final: 0.5678 (mttm) REVERT: D 247 ASP cc_start: 0.7853 (p0) cc_final: 0.7564 (p0) outliers start: 1 outliers final: 1 residues processed: 229 average time/residue: 0.1255 time to fit residues: 37.5597 Evaluate side-chains 194 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 193 time to evaluate : 0.518 ------------------------------------------------------------------------------- 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: 5.9990 chunk 16 optimal weight: 5.9990 chunk 45 optimal weight: 5.9990 chunk 37 optimal weight: 4.9990 chunk 15 optimal weight: 10.0000 chunk 54 optimal weight: 3.9990 chunk 58 optimal weight: 3.9990 chunk 48 optimal weight: 7.9990 chunk 18 optimal weight: 4.9990 chunk 43 optimal weight: 6.9990 chunk 53 optimal weight: 3.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- 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 276 GLN B 282 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6723 moved from start: 0.4457 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.053 4640 Z= 0.347 Angle : 0.727 6.767 6400 Z= 0.399 Chirality : 0.048 0.157 825 Planarity : 0.006 0.062 795 Dihedral : 7.078 23.004 640 Min Nonbonded Distance : 2.577 Molprobity Statistics. All-atom Clashscore : 15.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.61 % Favored : 93.39 % Rotamer: Outliers : 0.00 % Allowed : 3.08 % Favored : 96.92 % 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: -2.06 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.78 (0.36), residues: 245 loop : -1.84 (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 0.019 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 225 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 225 time to evaluate : 0.510 Fit side-chains revert: symmetry clash revert: symmetry clash REVERT: C 247 ASP cc_start: 0.7230 (p0) cc_final: 0.6870 (p0) REVERT: A 348 LYS cc_start: 0.8164 (mtmm) cc_final: 0.7936 (mtmm) REVERT: D 276 GLN cc_start: 0.7261 (tt0) cc_final: 0.6455 (tt0) outliers start: 0 outliers final: 0 residues processed: 225 average time/residue: 0.1209 time to fit residues: 36.0470 Evaluate side-chains 195 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 195 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 3.9990 chunk 28 optimal weight: 20.0000 chunk 6 optimal weight: 6.9990 chunk 26 optimal weight: 5.9990 chunk 36 optimal weight: 6.9990 chunk 54 optimal weight: 0.9990 chunk 57 optimal weight: 20.0000 chunk 51 optimal weight: 4.9990 chunk 15 optimal weight: 5.9990 chunk 48 optimal weight: 8.9990 chunk 32 optimal weight: 5.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** C 253 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** C 282 GLN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6742 moved from start: 0.5083 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= 0.329 Angle : 0.695 6.234 6400 Z= 0.381 Chirality : 0.048 0.160 825 Planarity : 0.007 0.071 795 Dihedral : 6.882 23.839 640 Min Nonbonded Distance : 2.594 Molprobity Statistics. All-atom Clashscore : 14.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 4.84 % Favored : 95.16 % Rotamer: Outliers : 0.19 % Allowed : 2.69 % Favored : 97.12 % 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: -2.04 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.80 (0.35), residues: 245 loop : -1.79 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP E 331 PHE 0.019 0.002 PHE B 297 TYR 0.014 0.002 TYR B 304 *********************** 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 226 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 225 time to evaluate : 0.678 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash REVERT: C 300 LYS cc_start: 0.5925 (mmtm) cc_final: 0.5619 (mmtm) REVERT: B 339 LEU cc_start: 0.6933 (mt) cc_final: 0.6727 (mt) outliers start: 1 outliers final: 1 residues processed: 226 average time/residue: 0.1161 time to fit residues: 35.0283 Evaluate side-chains 195 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 194 time to evaluate : 0.526 ------------------------------------------------------------------------------- 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: 10.0000 chunk 43 optimal weight: 5.9990 chunk 23 optimal weight: 20.0000 chunk 49 optimal weight: 0.6980 chunk 40 optimal weight: 20.0000 chunk 29 optimal weight: 0.9990 chunk 52 optimal weight: 10.0000 chunk 14 optimal weight: 0.3980 chunk 19 optimal weight: 7.9990 chunk 11 optimal weight: 0.0770 chunk 34 optimal weight: 6.9990 overall best weight: 1.6342 ------------------------------------------------------------------------------- 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 A 282 GLN D 253 ASN D 282 GLN E 256 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 6 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6648 moved from start: 0.5583 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.039 4640 Z= 0.218 Angle : 0.668 7.252 6400 Z= 0.357 Chirality : 0.049 0.182 825 Planarity : 0.006 0.063 795 Dihedral : 6.470 22.283 640 Min Nonbonded Distance : 2.598 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.65 % Favored : 94.35 % Rotamer: Outliers : 0.19 % Allowed : 1.92 % Favored : 97.88 % 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: -1.91 (0.33), residues: 620 helix: None (None), residues: 0 sheet: -0.71 (0.34), residues: 245 loop : -1.71 (0.31), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.004 0.001 TRP C 331 PHE 0.019 0.002 PHE B 297 TYR 0.014 0.001 TYR E 304 *********************** 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 229 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 228 time to evaluate : 0.521 Fit side-chains revert: symmetry clash REVERT: B 300 LYS cc_start: 0.6579 (mttm) cc_final: 0.6326 (mttm) outliers start: 1 outliers final: 0 residues processed: 229 average time/residue: 0.1197 time to fit residues: 36.3619 Evaluate side-chains 208 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 208 time to evaluate : 0.461 ------------------------------------------------------------------------------- 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: 2.9990 chunk 58 optimal weight: 7.9990 chunk 48 optimal weight: 5.9990 chunk 26 optimal weight: 6.9990 chunk 4 optimal weight: 0.4980 chunk 19 optimal weight: 1.9990 chunk 30 optimal weight: 6.9990 chunk 55 optimal weight: 5.9990 chunk 6 optimal weight: 1.9990 chunk 33 optimal weight: 20.0000 chunk 42 optimal weight: 5.9990 overall best weight: 2.6988 ------------------------------------------------------------------------------- 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** D 282 GLN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6654 moved from start: 0.5848 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.046 4640 Z= 0.281 Angle : 0.689 6.965 6400 Z= 0.368 Chirality : 0.051 0.183 825 Planarity : 0.007 0.066 795 Dihedral : 6.561 22.445 640 Min Nonbonded Distance : 2.537 Molprobity Statistics. All-atom Clashscore : 13.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.16 % Favored : 94.84 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -1.93 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.64 (0.33), residues: 245 loop : -1.78 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP E 331 PHE 0.028 0.002 PHE B 314 TYR 0.011 0.001 TYR E 304 *********************** 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 223 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 223 time to evaluate : 0.530 Fit side-chains REVERT: C 314 PHE cc_start: 0.7743 (m-80) cc_final: 0.7503 (m-10) REVERT: A 278 THR cc_start: 0.7909 (p) cc_final: 0.7639 (p) REVERT: B 348 LYS cc_start: 0.7677 (pttm) cc_final: 0.7288 (mtmm) REVERT: E 247 ASP cc_start: 0.7194 (p0) cc_final: 0.6935 (p0) outliers start: 0 outliers final: 0 residues processed: 223 average time/residue: 0.1184 time to fit residues: 35.1482 Evaluate side-chains 206 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 206 time to evaluate : 0.503 ------------------------------------------------------------------------------- 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: 9.9990 chunk 48 optimal weight: 2.9990 chunk 57 optimal weight: 9.9990 chunk 36 optimal weight: 3.9990 chunk 35 optimal weight: 20.0000 chunk 26 optimal weight: 50.0000 chunk 23 optimal weight: 8.9990 chunk 34 optimal weight: 0.9980 chunk 17 optimal weight: 5.9990 chunk 11 optimal weight: 20.0000 chunk 39 optimal weight: 3.9990 overall best weight: 3.5988 ------------------------------------------------------------------------------- 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 ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN B 253 ASN ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 256 ASN ** E 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 5 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6692 moved from start: 0.6033 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.049 4640 Z= 0.311 Angle : 0.699 6.773 6400 Z= 0.374 Chirality : 0.051 0.201 825 Planarity : 0.007 0.071 795 Dihedral : 6.555 21.958 640 Min Nonbonded Distance : 2.525 Molprobity Statistics. All-atom Clashscore : 13.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.45 % Favored : 93.55 % Rotamer: Outliers : 0.00 % Allowed : 1.35 % Favored : 98.65 % 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: -1.93 (0.32), residues: 620 helix: None (None), residues: 0 sheet: -0.61 (0.33), residues: 245 loop : -1.81 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 331 PHE 0.034 0.003 PHE B 314 TYR 0.009 0.001 TYR E 304 *********************** 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 219 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 219 time to evaluate : 0.512 Fit side-chains REVERT: A 264 LEU cc_start: 0.7173 (mm) cc_final: 0.6876 (mm) REVERT: B 348 LYS cc_start: 0.7886 (pttm) cc_final: 0.7582 (mtmm) REVERT: E 262 GLN cc_start: 0.7006 (tp40) cc_final: 0.6776 (tp40) outliers start: 0 outliers final: 0 residues processed: 219 average time/residue: 0.1194 time to fit residues: 34.7110 Evaluate side-chains 181 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 181 time to evaluate : 0.501 ------------------------------------------------------------------------------- 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: 20.0000 chunk 5 optimal weight: 10.0000 chunk 45 optimal weight: 6.9990 chunk 52 optimal weight: 20.0000 chunk 55 optimal weight: 6.9990 chunk 50 optimal weight: 20.0000 chunk 53 optimal weight: 6.9990 chunk 32 optimal weight: 8.9990 chunk 23 optimal weight: 4.9990 chunk 42 optimal weight: 9.9990 chunk 16 optimal weight: 9.9990 overall best weight: 6.9990 ------------------------------------------------------------------------------- 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** A 276 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 282 GLN E 305 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6806 moved from start: 0.6073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.066 4640 Z= 0.472 Angle : 0.766 6.395 6400 Z= 0.419 Chirality : 0.053 0.258 825 Planarity : 0.007 0.074 795 Dihedral : 6.945 23.448 640 Min Nonbonded Distance : 2.502 Molprobity Statistics. All-atom Clashscore : 14.92 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.77 % Favored : 93.23 % Rotamer: Outliers : 0.00 % Allowed : 2.12 % Favored : 97.88 % 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: -2.14 (0.31), residues: 620 helix: None (None), residues: 0 sheet: -0.67 (0.32), residues: 245 loop : -2.02 (0.29), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.017 0.002 TRP D 331 PHE 0.031 0.003 PHE B 314 TYR 0.007 0.001 TYR A 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 192 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 192 time to evaluate : 0.558 Fit side-chains revert: symmetry clash REVERT: A 264 LEU cc_start: 0.7132 (mm) cc_final: 0.6827 (mm) REVERT: E 262 GLN cc_start: 0.6956 (tp40) cc_final: 0.6706 (tp40) outliers start: 0 outliers final: 0 residues processed: 192 average time/residue: 0.1265 time to fit residues: 32.0497 Evaluate side-chains 173 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 173 time to evaluate : 0.540 ------------------------------------------------------------------------------- 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: 30.0000 chunk 50 optimal weight: 2.9990 chunk 53 optimal weight: 10.0000 chunk 35 optimal weight: 30.0000 chunk 56 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 chunk 27 optimal weight: 2.9990 chunk 39 optimal weight: 6.9990 chunk 59 optimal weight: 7.9990 chunk 55 optimal weight: 0.6980 chunk 47 optimal weight: 20.0000 overall best weight: 1.9388 ------------------------------------------------------------------------------- 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 ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 282 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** 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: 0.6687 moved from start: 0.6363 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.037 4640 Z= 0.242 Angle : 0.726 8.373 6400 Z= 0.386 Chirality : 0.053 0.190 825 Planarity : 0.007 0.065 795 Dihedral : 6.731 23.304 640 Min Nonbonded Distance : 2.518 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.48 % Favored : 94.52 % Rotamer: Outliers : 0.00 % Allowed : 1.73 % Favored : 98.27 % 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: -2.00 (0.31), residues: 620 helix: None (None), residues: 0 sheet: -0.60 (0.32), residues: 245 loop : -1.91 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 331 PHE 0.031 0.003 PHE E 297 TYR 0.020 0.001 TYR C 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 : 0.500 Fit side-chains revert: symmetry clash REVERT: B 259 THR cc_start: 0.6302 (t) cc_final: 0.6048 (t) outliers start: 0 outliers final: 0 residues processed: 216 average time/residue: 0.1169 time to fit residues: 33.5028 Evaluate side-chains 188 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 188 time to evaluate : 0.502 ------------------------------------------------------------------------------- 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: 0.5980 chunk 36 optimal weight: 20.0000 chunk 29 optimal weight: 6.9990 chunk 37 optimal weight: 1.9990 chunk 50 optimal weight: 2.9990 chunk 14 optimal weight: 30.0000 chunk 43 optimal weight: 10.0000 chunk 7 optimal weight: 0.0030 chunk 13 optimal weight: 6.9990 chunk 47 optimal weight: 9.9990 chunk 19 optimal weight: 2.9990 overall best weight: 1.7196 ------------------------------------------------------------------------------- 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** ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 276 GLN A 282 GLN ** B 256 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.6651 moved from start: 0.6499 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.055 4640 Z= 0.248 Angle : 0.706 8.666 6400 Z= 0.374 Chirality : 0.053 0.177 825 Planarity : 0.007 0.070 795 Dihedral : 6.647 21.836 640 Min Nonbonded Distance : 2.507 Molprobity Statistics. All-atom Clashscore : 12.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.97 % Favored : 94.03 % Rotamer: Outliers : 0.00 % Allowed : 0.58 % Favored : 99.42 % 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: -1.94 (0.31), residues: 620 helix: None (None), residues: 0 sheet: -0.61 (0.31), residues: 245 loop : -1.83 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.014 0.001 TRP A 331 PHE 0.027 0.002 PHE E 314 TYR 0.011 0.001 TYR E 304 ********************** 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 210 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 210 time to evaluate : 0.540 Fit side-chains revert: symmetry clash REVERT: C 300 LYS cc_start: 0.6127 (mmmt) cc_final: 0.5760 (mmtt) REVERT: B 259 THR cc_start: 0.6330 (t) cc_final: 0.6062 (t) REVERT: E 253 ASN cc_start: 0.6759 (t0) cc_final: 0.6517 (t0) outliers start: 0 outliers final: 0 residues processed: 210 average time/residue: 0.1357 time to fit residues: 37.3275 Evaluate side-chains 185 residues out of total 520 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 185 time to evaluate : 0.602 ------------------------------------------------------------------------------- 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: 30.0000 chunk 6 optimal weight: 8.9990 chunk 8 optimal weight: 0.0970 chunk 41 optimal weight: 1.9990 chunk 2 optimal weight: 2.9990 chunk 34 optimal weight: 6.9990 chunk 54 optimal weight: 0.8980 chunk 32 optimal weight: 10.0000 chunk 40 optimal weight: 20.0000 chunk 1 optimal weight: 7.9990 chunk 38 optimal weight: 50.0000 overall best weight: 2.5984 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 256 ASN ** A 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** A 282 GLN ** B 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 282 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** D 282 GLN E 256 ASN ** E 262 GLN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4129 r_free = 0.4129 target = 0.175762 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 40)----------------| | r_work = 0.3537 r_free = 0.3537 target = 0.121435 restraints weight = 8908.932| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 2; iterations = 32)----------------| | r_work = 0.3597 r_free = 0.3597 target = 0.125505 restraints weight = 5688.503| |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 3; iterations = 52)----------------| | r_work = 0.3630 r_free = 0.3630 target = 0.128489 restraints weight = 4289.771| |-----------------------------------------------------------------------------| r_work (final): 0.3557 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7460 moved from start: 0.6670 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.044 4640 Z= 0.260 Angle : 0.701 8.303 6400 Z= 0.371 Chirality : 0.052 0.177 825 Planarity : 0.006 0.068 795 Dihedral : 6.546 21.130 640 Min Nonbonded Distance : 2.353 Molprobity Statistics. All-atom Clashscore : 11.27 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.81 % Favored : 94.19 % Rotamer: Outliers : 0.19 % Allowed : 0.77 % Favored : 99.04 % 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: -1.88 (0.31), residues: 620 helix: None (None), residues: 0 sheet: -0.48 (0.31), residues: 245 loop : -1.85 (0.30), residues: 375 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.019 0.001 TRP A 331 PHE 0.023 0.002 PHE E 297 TYR 0.019 0.001 TYR B 275 =============================================================================== Job complete usr+sys time: 1372.15 seconds wall clock time: 25 minutes 20.30 seconds (1520.30 seconds total)