Starting phenix.real_space_refine on Fri Aug 2 14:13:27 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttg_41607/08_2024/8ttg_41607.cif Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttg_41607/08_2024/8ttg_41607.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.35 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttg_41607/08_2024/8ttg_41607.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttg_41607/08_2024/8ttg_41607.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttg_41607/08_2024/8ttg_41607.cif" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/8ttg_41607/08_2024/8ttg_41607.cif" } resolution = 3.35 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.002 sd= 0.066 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 18 5.16 5 C 2037 2.51 5 N 461 2.21 5 O 510 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A PHE 170": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A TYR 292": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 323": "OE1" <-> "OE2" Residue "C TYR 135": "CD1" <-> "CD2" "CE1" <-> "CE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5409/modules/chem_data/mon_lib" Total number of atoms: 3026 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 2877 Number of conformers: 1 Conformer: "" Number of residues, atoms: 374, 2877 Classifications: {'peptide': 374} Link IDs: {'PTRANS': 14, 'TRANS': 359} Chain breaks: 1 Chain: "C" Number of atoms: 149 Number of conformers: 1 Conformer: "" Number of residues, atoms: 15, 149 Classifications: {'peptide': 15} Modifications used: {'COO': 1} Link IDs: {'PTRANS': 1, 'TRANS': 13} Time building chain proxies: 2.58, per 1000 atoms: 0.85 Number of scatterers: 3026 At special positions: 0 Unit cell: (72.6, 70.95, 58.575, 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 18 16.00 O 510 8.00 N 461 7.00 C 2037 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: 1.12 Conformation dependent library (CDL) restraints added in 701.3 milliseconds 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 702 Finding SS restraints... Secondary structure from input PDB file: 16 helices and 1 sheets defined 87.7% alpha, 1.5% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.27 Creating SS restraints... Processing helix chain 'A' and resid 2 through 21 removed outlier: 3.688A pdb=" N ILE A 15 " --> pdb=" O ASN A 11 " (cutoff:3.500A) Processing helix chain 'A' and resid 22 through 24 No H-bonds generated for 'chain 'A' and resid 22 through 24' Processing helix chain 'A' and resid 25 through 34 Processing helix chain 'A' and resid 36 through 65 removed outlier: 3.783A pdb=" N LEU A 40 " --> pdb=" O THR A 36 " (cutoff:3.500A) removed outlier: 4.089A pdb=" N VAL A 44 " --> pdb=" O LEU A 40 " (cutoff:3.500A) Proline residue: A 56 - end of helix Processing helix chain 'A' and resid 66 through 87 removed outlier: 4.129A pdb=" N ILE A 70 " --> pdb=" O GLY A 66 " (cutoff:3.500A) Processing helix chain 'A' and resid 90 through 120 removed outlier: 3.555A pdb=" N LEU A 94 " --> pdb=" O ASN A 90 " (cutoff:3.500A) Proline residue: A 110 - end of helix Processing helix chain 'A' and resid 124 through 141 Processing helix chain 'A' and resid 141 through 151 removed outlier: 3.958A pdb=" N GLY A 145 " --> pdb=" O ILE A 141 " (cutoff:3.500A) Processing helix chain 'A' and resid 156 through 177 removed outlier: 3.521A pdb=" N TYR A 160 " --> pdb=" O ARG A 156 " (cutoff:3.500A) Processing helix chain 'A' and resid 204 through 232 removed outlier: 3.903A pdb=" N SER A 226 " --> pdb=" O GLN A 222 " (cutoff:3.500A) Processing helix chain 'A' and resid 236 through 264 removed outlier: 5.968A pdb=" N ASP A 260 " --> pdb=" O ILE A 256 " (cutoff:3.500A) removed outlier: 5.549A pdb=" N LYS A 261 " --> pdb=" O TYR A 257 " (cutoff:3.500A) Processing helix chain 'A' and resid 267 through 288 removed outlier: 3.859A pdb=" N PHE A 288 " --> pdb=" O ILE A 284 " (cutoff:3.500A) Processing helix chain 'A' and resid 291 through 300 Processing helix chain 'A' and resid 301 through 322 removed outlier: 4.385A pdb=" N GLY A 305 " --> pdb=" O VAL A 301 " (cutoff:3.500A) removed outlier: 4.207A pdb=" N PHE A 306 " --> pdb=" O VAL A 302 " (cutoff:3.500A) Proline residue: A 311 - end of helix removed outlier: 3.504A pdb=" N GLY A 322 " --> pdb=" O SER A 318 " (cutoff:3.500A) Processing helix chain 'A' and resid 324 through 354 Proline residue: A 344 - end of helix removed outlier: 3.588A pdb=" N ALA A 349 " --> pdb=" O LEU A 345 " (cutoff:3.500A) Processing helix chain 'A' and resid 356 through 386 Processing sheet with id=AA1, first strand: chain 'C' and resid 129 through 132 removed outlier: 3.612A pdb=" N TYR C 135 " --> pdb=" O TYR C 132 " (cutoff:3.500A) 254 hydrogen bonds defined for protein. 762 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 0.89 Time building geometry restraints manager: 1.23 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.20 - 1.32: 451 1.32 - 1.44: 885 1.44 - 1.57: 1737 1.57 - 1.69: 0 1.69 - 1.81: 35 Bond restraints: 3108 Sorted by residual: bond pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta sigma weight residual 1.460 1.548 -0.088 1.19e-02 7.06e+03 5.50e+01 bond pdb=" CA SER A 138 " pdb=" CB SER A 138 " ideal model delta sigma weight residual 1.530 1.452 0.078 1.69e-02 3.50e+03 2.12e+01 bond pdb=" CE1 HIS C 130 " pdb=" NE2 HIS C 130 " ideal model delta sigma weight residual 1.321 1.362 -0.041 1.00e-02 1.00e+04 1.67e+01 bond pdb=" C ILE A 135 " pdb=" O ILE A 135 " ideal model delta sigma weight residual 1.237 1.197 0.040 1.12e-02 7.97e+03 1.24e+01 bond pdb=" N ILE A 136 " pdb=" CA ILE A 136 " ideal model delta sigma weight residual 1.459 1.494 -0.035 1.25e-02 6.40e+03 8.00e+00 ... (remaining 3103 not shown) Histogram of bond angle deviations from ideal: 94.51 - 102.45: 23 102.45 - 110.40: 608 110.40 - 118.35: 1751 118.35 - 126.29: 1789 126.29 - 134.24: 42 Bond angle restraints: 4213 Sorted by residual: angle pdb=" O ALA A 134 " pdb=" C ALA A 134 " pdb=" N ILE A 135 " ideal model delta sigma weight residual 122.07 115.67 6.40 1.03e+00 9.43e-01 3.86e+01 angle pdb=" C ALA A 134 " pdb=" N ILE A 135 " pdb=" CA ILE A 135 " ideal model delta sigma weight residual 120.56 128.26 -7.70 1.28e+00 6.10e-01 3.62e+01 angle pdb=" CA ALA A 134 " pdb=" C ALA A 134 " pdb=" N ILE A 135 " ideal model delta sigma weight residual 117.07 123.62 -6.55 1.14e+00 7.69e-01 3.30e+01 angle pdb=" N TYR C 132 " pdb=" CA TYR C 132 " pdb=" C TYR C 132 " ideal model delta sigma weight residual 109.79 102.15 7.64 1.56e+00 4.11e-01 2.40e+01 angle pdb=" CB PRO A 27 " pdb=" CG PRO A 27 " pdb=" CD PRO A 27 " ideal model delta sigma weight residual 106.10 94.51 11.59 3.20e+00 9.77e-02 1.31e+01 ... (remaining 4208 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 16.20: 1489 16.20 - 32.40: 211 32.40 - 48.59: 59 48.59 - 64.79: 14 64.79 - 80.99: 2 Dihedral angle restraints: 1775 sinusoidal: 670 harmonic: 1105 Sorted by residual: dihedral pdb=" CA ASN A 137 " pdb=" CB ASN A 137 " pdb=" CG ASN A 137 " pdb=" OD1 ASN A 137 " ideal model delta sinusoidal sigma weight residual -90.00 -153.93 63.93 2 2.00e+01 2.50e-03 9.68e+00 dihedral pdb=" N PHE A 317 " pdb=" CA PHE A 317 " pdb=" CB PHE A 317 " pdb=" CG PHE A 317 " ideal model delta sinusoidal sigma weight residual -60.00 -116.59 56.59 3 1.50e+01 4.44e-03 9.41e+00 dihedral pdb=" CA GLU A 356 " pdb=" CB GLU A 356 " pdb=" CG GLU A 356 " pdb=" CD GLU A 356 " ideal model delta sinusoidal sigma weight residual 60.00 115.72 -55.72 3 1.50e+01 4.44e-03 9.36e+00 ... (remaining 1772 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.038: 327 0.038 - 0.076: 114 0.076 - 0.113: 34 0.113 - 0.151: 4 0.151 - 0.189: 5 Chirality restraints: 484 Sorted by residual: chirality pdb=" CA ILE A 136 " pdb=" N ILE A 136 " pdb=" C ILE A 136 " pdb=" CB ILE A 136 " both_signs ideal model delta sigma weight residual False 2.43 2.62 -0.19 2.00e-01 2.50e+01 8.94e-01 chirality pdb=" CB ILE A 375 " pdb=" CA ILE A 375 " pdb=" CG1 ILE A 375 " pdb=" CG2 ILE A 375 " both_signs ideal model delta sigma weight residual False 2.64 2.46 0.19 2.00e-01 2.50e+01 8.65e-01 chirality pdb=" CA PHE C 134 " pdb=" N PHE C 134 " pdb=" C PHE C 134 " pdb=" CB PHE C 134 " both_signs ideal model delta sigma weight residual False 2.51 2.34 0.17 2.00e-01 2.50e+01 7.55e-01 ... (remaining 481 not shown) Planarity restraints: 512 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" CA ILE A 135 " 0.011 2.00e-02 2.50e+03 2.30e-02 5.30e+00 pdb=" C ILE A 135 " -0.040 2.00e-02 2.50e+03 pdb=" O ILE A 135 " 0.015 2.00e-02 2.50e+03 pdb=" N ILE A 136 " 0.013 2.00e-02 2.50e+03 delta sigma weight rms_deltas residual plane pdb=" C MET A 157 " 0.034 5.00e-02 4.00e+02 5.20e-02 4.32e+00 pdb=" N PRO A 158 " -0.090 5.00e-02 4.00e+02 pdb=" CA PRO A 158 " 0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 158 " 0.029 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C SER A 236 " -0.033 5.00e-02 4.00e+02 5.06e-02 4.10e+00 pdb=" N PRO A 237 " 0.088 5.00e-02 4.00e+02 pdb=" CA PRO A 237 " -0.026 5.00e-02 4.00e+02 pdb=" CD PRO A 237 " -0.028 5.00e-02 4.00e+02 ... (remaining 509 not shown) Histogram of nonbonded interaction distances: 2.11 - 2.67: 26 2.67 - 3.23: 3056 3.23 - 3.79: 5009 3.79 - 4.34: 6292 4.34 - 4.90: 10376 Nonbonded interactions: 24759 Sorted by model distance: nonbonded pdb=" O GLY A 145 " pdb=" OG SER A 241 " model vdw 2.114 3.040 nonbonded pdb=" O GLY A 74 " pdb=" OG SER A 104 " model vdw 2.307 3.040 nonbonded pdb=" O GLN A 124 " pdb=" ND2 ASN A 128 " model vdw 2.349 3.120 nonbonded pdb=" O LEU A 77 " pdb=" OG SER A 81 " model vdw 2.407 3.040 nonbonded pdb=" NE2 HIS A 354 " pdb=" OE1 GLU A 356 " model vdw 2.433 3.120 ... (remaining 24754 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 ========== WARNING! ============ No NCS relation were found !!! ================================ Found NCS groups: found none. Set up NCS constraints No NCS constraints will be used in refinement. Set refine NCS operators Adjust number of macro_cycles Number of macro_cycles: 10 Reset NCS operators Extract rigid body selections Check and reset occupancies Occupancies: min=1.00 max=1.00 mean=1.00 Load rotamer database and sin/cos tables Set ADP refinement strategy ADPs will be refined as individual isotropic 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: 0.780 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: 0.020 Extract box with map and model: 0.130 Check model and map are aligned: 0.020 Set scattering table: 0.050 Process input model: 14.020 Find NCS groups from input model: 0.030 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: 0.010 Load rotamer database and sin/cos tables:2.850 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 17.920 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7524 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 : 0.004 0.088 3108 Z= 0.245 Angle : 0.743 11.592 4213 Z= 0.433 Chirality : 0.045 0.189 484 Planarity : 0.005 0.052 512 Dihedral : 16.511 80.988 1073 Min Nonbonded Distance : 2.114 Molprobity Statistics. All-atom Clashscore : 12.06 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.35 % Favored : 97.65 % Rotamer: Outliers : 0.62 % Allowed : 30.34 % Favored : 69.04 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.46), residues: 383 helix: 1.91 (0.30), residues: 326 sheet: -1.55 (1.67), residues: 10 loop : -1.83 (0.89), residues: 47 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP C 136 HIS 0.006 0.001 HIS A 379 PHE 0.015 0.001 PHE A 351 TYR 0.012 0.001 TYR C 135 ARG 0.002 0.000 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 73 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 71 time to evaluate : 0.342 Fit side-chains REVERT: A 377 LYS cc_start: 0.7389 (tptt) cc_final: 0.6598 (ttpt) outliers start: 2 outliers final: 1 residues processed: 72 average time/residue: 0.1222 time to fit residues: 11.1488 Evaluate side-chains 67 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 66 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 317 PHE Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 32 optimal weight: 2.9990 chunk 28 optimal weight: 2.9990 chunk 15 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 19 optimal weight: 0.0040 chunk 29 optimal weight: 1.9990 chunk 11 optimal weight: 0.8980 chunk 18 optimal weight: 0.0670 chunk 22 optimal weight: 0.9990 chunk 34 optimal weight: 1.9990 chunk 10 optimal weight: 2.9990 overall best weight: 0.5532 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 128 ASN ** A 137 ASN ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7659 moved from start: 0.1271 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3108 Z= 0.189 Angle : 0.614 6.811 4213 Z= 0.306 Chirality : 0.041 0.169 484 Planarity : 0.005 0.052 512 Dihedral : 4.730 51.424 411 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 8.80 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 4.95 % Allowed : 26.32 % Favored : 68.73 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.15 (0.45), residues: 383 helix: 1.98 (0.30), residues: 327 sheet: -1.35 (1.57), residues: 10 loop : -2.04 (0.84), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 136 HIS 0.002 0.001 HIS A 178 PHE 0.019 0.002 PHE C 134 TYR 0.009 0.001 TYR C 137 ARG 0.004 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 77 time to evaluate : 0.316 Fit side-chains REVERT: A 135 ILE cc_start: 0.7422 (OUTLIER) cc_final: 0.7197 (tt) REVERT: A 293 TRP cc_start: 0.8254 (m100) cc_final: 0.7710 (m-10) outliers start: 16 outliers final: 8 residues processed: 87 average time/residue: 0.1160 time to fit residues: 12.7451 Evaluate side-chains 79 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 9 poor density : 70 time to evaluate : 0.346 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 299 SER Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 28 optimal weight: 0.8980 chunk 23 optimal weight: 3.9990 chunk 9 optimal weight: 0.6980 chunk 34 optimal weight: 2.9990 chunk 37 optimal weight: 0.9990 chunk 30 optimal weight: 0.7980 chunk 11 optimal weight: 0.5980 chunk 27 optimal weight: 1.9990 chunk 25 optimal weight: 0.9990 chunk 17 optimal weight: 2.9990 chunk 3 optimal weight: 0.6980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... No N/Q/H corrections needed this macrocycle ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7741 moved from start: 0.1875 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.036 3108 Z= 0.212 Angle : 0.598 6.858 4213 Z= 0.304 Chirality : 0.042 0.171 484 Planarity : 0.005 0.055 512 Dihedral : 4.799 49.225 411 Min Nonbonded Distance : 2.579 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.19 % Allowed : 26.63 % Favored : 67.18 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.14 (0.45), residues: 383 helix: 1.99 (0.30), residues: 327 sheet: -1.23 (1.73), residues: 10 loop : -2.21 (0.83), residues: 46 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 136 HIS 0.003 0.001 HIS A 379 PHE 0.017 0.002 PHE A 16 TYR 0.007 0.001 TYR A 278 ARG 0.003 0.001 ARG A 380 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 72 time to evaluate : 0.328 Fit side-chains REVERT: A 135 ILE cc_start: 0.7473 (OUTLIER) cc_final: 0.7215 (tt) REVERT: A 263 MET cc_start: 0.6850 (mmm) cc_final: 0.5874 (mmm) REVERT: A 293 TRP cc_start: 0.8263 (m100) cc_final: 0.7687 (m-10) outliers start: 20 outliers final: 12 residues processed: 88 average time/residue: 0.1259 time to fit residues: 13.7681 Evaluate side-chains 82 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 13 poor density : 69 time to evaluate : 0.293 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 16 optimal weight: 3.9990 chunk 23 optimal weight: 0.9980 chunk 34 optimal weight: 1.9990 chunk 36 optimal weight: 1.9990 chunk 18 optimal weight: 0.0010 chunk 32 optimal weight: 1.9990 chunk 9 optimal weight: 0.7980 chunk 30 optimal weight: 0.9980 chunk 20 optimal weight: 1.9990 chunk 0 optimal weight: 2.9990 chunk 27 optimal weight: 0.6980 overall best weight: 0.6986 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2129 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.042 3108 Z= 0.213 Angle : 0.598 8.259 4213 Z= 0.303 Chirality : 0.041 0.173 484 Planarity : 0.005 0.056 512 Dihedral : 4.848 48.433 411 Min Nonbonded Distance : 2.576 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.57 % Favored : 98.43 % Rotamer: Outliers : 6.19 % Allowed : 26.93 % Favored : 66.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.03 (0.45), residues: 383 helix: 1.90 (0.29), residues: 328 sheet: -1.50 (1.70), residues: 10 loop : -2.18 (0.84), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 136 HIS 0.001 0.000 HIS A 178 PHE 0.017 0.001 PHE C 134 TYR 0.007 0.001 TYR A 278 ARG 0.002 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 84 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 64 time to evaluate : 0.328 Fit side-chains REVERT: A 17 LEU cc_start: 0.8442 (OUTLIER) cc_final: 0.8092 (tt) REVERT: A 135 ILE cc_start: 0.7458 (OUTLIER) cc_final: 0.7229 (tt) REVERT: A 258 PHE cc_start: 0.6837 (m-80) cc_final: 0.6452 (m-80) REVERT: A 263 MET cc_start: 0.6931 (mmm) cc_final: 0.6048 (mmm) REVERT: A 293 TRP cc_start: 0.8275 (m100) cc_final: 0.7691 (m-10) outliers start: 20 outliers final: 14 residues processed: 81 average time/residue: 0.1189 time to fit residues: 12.1722 Evaluate side-chains 77 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 61 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 17 LEU Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 15 optimal weight: 0.4980 chunk 31 optimal weight: 1.9990 chunk 25 optimal weight: 0.8980 chunk 0 optimal weight: 2.9990 chunk 18 optimal weight: 0.0970 chunk 32 optimal weight: 0.7980 chunk 9 optimal weight: 1.9990 chunk 12 optimal weight: 0.6980 chunk 33 optimal weight: 0.7980 chunk 7 optimal weight: 0.9980 chunk 21 optimal weight: 0.9980 overall best weight: 0.5778 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 moved from start: 0.2171 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3108 Z= 0.196 Angle : 0.585 7.299 4213 Z= 0.297 Chirality : 0.040 0.170 484 Planarity : 0.005 0.056 512 Dihedral : 4.829 47.782 411 Min Nonbonded Distance : 2.512 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 6.19 % Allowed : 27.24 % Favored : 66.56 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.07 (0.45), residues: 383 helix: 1.94 (0.29), residues: 328 sheet: -1.55 (1.66), residues: 10 loop : -2.22 (0.83), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 136 HIS 0.001 0.000 HIS A 178 PHE 0.016 0.001 PHE C 134 TYR 0.008 0.001 TYR C 137 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.331 Fit side-chains REVERT: A 44 VAL cc_start: 0.6515 (OUTLIER) cc_final: 0.6270 (m) REVERT: A 135 ILE cc_start: 0.7418 (OUTLIER) cc_final: 0.7184 (tt) REVERT: A 263 MET cc_start: 0.6909 (mmm) cc_final: 0.6138 (mmm) REVERT: A 293 TRP cc_start: 0.8269 (m100) cc_final: 0.7716 (m-10) outliers start: 20 outliers final: 13 residues processed: 80 average time/residue: 0.1200 time to fit residues: 12.1846 Evaluate side-chains 79 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 64 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 177 ILE Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 9 optimal weight: 1.9990 chunk 36 optimal weight: 0.7980 chunk 30 optimal weight: 0.5980 chunk 17 optimal weight: 0.7980 chunk 3 optimal weight: 2.9990 chunk 12 optimal weight: 0.9980 chunk 19 optimal weight: 2.9990 chunk 35 optimal weight: 0.9980 chunk 4 optimal weight: 0.5980 chunk 20 optimal weight: 1.9990 chunk 26 optimal weight: 0.9980 overall best weight: 0.7580 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 200 ASN A 319 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7780 moved from start: 0.2377 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.041 3108 Z= 0.223 Angle : 0.617 8.986 4213 Z= 0.310 Chirality : 0.041 0.171 484 Planarity : 0.005 0.056 512 Dihedral : 4.068 16.312 409 Min Nonbonded Distance : 2.540 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 7.12 % Allowed : 27.24 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.44), residues: 383 helix: 1.90 (0.29), residues: 328 sheet: -1.85 (1.51), residues: 10 loop : -2.22 (0.84), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.010 0.001 TRP C 136 HIS 0.001 0.000 HIS A 379 PHE 0.016 0.002 PHE C 134 TYR 0.007 0.001 TYR A 278 ARG 0.002 0.001 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 66 time to evaluate : 0.340 Fit side-chains REVERT: A 44 VAL cc_start: 0.6587 (OUTLIER) cc_final: 0.6334 (m) REVERT: A 135 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7202 (tt) REVERT: A 263 MET cc_start: 0.6927 (mmm) cc_final: 0.6173 (mmm) REVERT: A 293 TRP cc_start: 0.8258 (m100) cc_final: 0.7734 (m-10) outliers start: 23 outliers final: 18 residues processed: 82 average time/residue: 0.1290 time to fit residues: 13.1046 Evaluate side-chains 85 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.322 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 256 ILE Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 20 optimal weight: 2.9990 chunk 30 optimal weight: 0.8980 chunk 36 optimal weight: 1.9990 chunk 22 optimal weight: 3.9990 chunk 16 optimal weight: 0.9990 chunk 14 optimal weight: 0.6980 chunk 21 optimal weight: 0.5980 chunk 11 optimal weight: 0.0370 chunk 7 optimal weight: 0.5980 chunk 23 optimal weight: 2.9990 chunk 24 optimal weight: 0.5980 overall best weight: 0.5058 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7750 moved from start: 0.2338 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3108 Z= 0.187 Angle : 0.600 9.074 4213 Z= 0.302 Chirality : 0.040 0.169 484 Planarity : 0.005 0.055 512 Dihedral : 4.024 15.381 409 Min Nonbonded Distance : 2.526 Molprobity Statistics. All-atom Clashscore : 9.78 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 7.12 % Allowed : 28.17 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.09 (0.44), residues: 383 helix: 1.96 (0.29), residues: 328 sheet: -1.84 (1.50), residues: 10 loop : -2.24 (0.83), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 136 HIS 0.001 0.000 HIS A 379 PHE 0.016 0.001 PHE C 134 TYR 0.008 0.001 TYR C 137 ARG 0.001 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 69 time to evaluate : 0.334 Fit side-chains REVERT: A 44 VAL cc_start: 0.6540 (OUTLIER) cc_final: 0.6305 (m) REVERT: A 135 ILE cc_start: 0.7476 (OUTLIER) cc_final: 0.7237 (tt) REVERT: A 258 PHE cc_start: 0.6812 (m-80) cc_final: 0.6437 (m-80) REVERT: A 263 MET cc_start: 0.6926 (mmm) cc_final: 0.6147 (mmm) REVERT: A 293 TRP cc_start: 0.8262 (m100) cc_final: 0.7735 (m-10) REVERT: A 379 HIS cc_start: 0.6048 (OUTLIER) cc_final: 0.5095 (t-90) outliers start: 23 outliers final: 16 residues processed: 86 average time/residue: 0.1300 time to fit residues: 13.9181 Evaluate side-chains 85 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 66 time to evaluate : 0.324 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 18 optimal weight: 0.0070 chunk 3 optimal weight: 5.9990 chunk 28 optimal weight: 3.9990 chunk 33 optimal weight: 0.9990 chunk 35 optimal weight: 0.7980 chunk 32 optimal weight: 2.9990 chunk 34 optimal weight: 0.5980 chunk 20 optimal weight: 0.6980 chunk 14 optimal weight: 0.7980 chunk 26 optimal weight: 0.6980 chunk 10 optimal weight: 0.8980 overall best weight: 0.5598 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7753 moved from start: 0.2370 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.037 3108 Z= 0.194 Angle : 0.611 9.487 4213 Z= 0.304 Chirality : 0.040 0.168 484 Planarity : 0.005 0.055 512 Dihedral : 4.018 15.393 409 Min Nonbonded Distance : 2.561 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.81 % Allowed : 28.79 % Favored : 64.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.05 (0.44), residues: 383 helix: 1.94 (0.29), residues: 328 sheet: -1.84 (1.50), residues: 10 loop : -2.24 (0.84), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 136 HIS 0.001 0.000 HIS A 178 PHE 0.016 0.001 PHE C 134 TYR 0.008 0.001 TYR C 137 ARG 0.002 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 22 poor density : 66 time to evaluate : 0.339 Fit side-chains REVERT: A 135 ILE cc_start: 0.7460 (OUTLIER) cc_final: 0.7240 (tt) REVERT: A 258 PHE cc_start: 0.6814 (m-80) cc_final: 0.6431 (m-80) REVERT: A 263 MET cc_start: 0.6950 (mmm) cc_final: 0.6128 (mmm) REVERT: A 293 TRP cc_start: 0.8253 (m100) cc_final: 0.7764 (m-10) REVERT: A 296 MET cc_start: 0.6680 (tpp) cc_final: 0.6391 (ttt) REVERT: A 379 HIS cc_start: 0.6028 (OUTLIER) cc_final: 0.5087 (t-90) outliers start: 22 outliers final: 19 residues processed: 82 average time/residue: 0.1346 time to fit residues: 13.8226 Evaluate side-chains 86 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 21 poor density : 65 time to evaluate : 0.330 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 257 TYR Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 30 optimal weight: 0.6980 chunk 32 optimal weight: 0.9990 chunk 34 optimal weight: 0.9990 chunk 22 optimal weight: 2.9990 chunk 36 optimal weight: 0.7980 chunk 17 optimal weight: 0.6980 chunk 25 optimal weight: 0.4980 chunk 37 optimal weight: 3.9990 chunk 3 optimal weight: 5.9990 chunk 23 optimal weight: 0.6980 chunk 18 optimal weight: 0.9990 overall best weight: 0.6780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.2480 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.040 3108 Z= 0.210 Angle : 0.625 9.105 4213 Z= 0.313 Chirality : 0.041 0.169 484 Planarity : 0.005 0.055 512 Dihedral : 4.062 15.511 409 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.12 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.09 % Favored : 97.91 % Rotamer: Outliers : 7.12 % Allowed : 28.17 % Favored : 64.71 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.00 (0.44), residues: 383 helix: 1.90 (0.29), residues: 328 sheet: -1.77 (1.52), residues: 10 loop : -2.22 (0.84), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 136 HIS 0.000 0.000 HIS A 155 PHE 0.015 0.001 PHE C 134 TYR 0.007 0.001 TYR C 137 ARG 0.002 0.000 ARG A 324 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 88 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 23 poor density : 65 time to evaluate : 0.321 Fit side-chains REVERT: A 135 ILE cc_start: 0.7438 (OUTLIER) cc_final: 0.7225 (tt) REVERT: A 157 MET cc_start: 0.8047 (tmm) cc_final: 0.7802 (tmm) REVERT: A 258 PHE cc_start: 0.6863 (m-80) cc_final: 0.6449 (m-80) REVERT: A 263 MET cc_start: 0.6962 (mmm) cc_final: 0.6123 (mmm) REVERT: A 293 TRP cc_start: 0.8232 (m100) cc_final: 0.7743 (m-10) REVERT: A 296 MET cc_start: 0.6705 (tpp) cc_final: 0.6476 (ttt) REVERT: A 379 HIS cc_start: 0.5987 (OUTLIER) cc_final: 0.5066 (t-90) outliers start: 23 outliers final: 18 residues processed: 82 average time/residue: 0.1216 time to fit residues: 12.4514 Evaluate side-chains 85 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 65 time to evaluate : 0.319 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 23 optimal weight: 0.9980 chunk 32 optimal weight: 2.9990 chunk 9 optimal weight: 1.9990 chunk 27 optimal weight: 2.9990 chunk 4 optimal weight: 0.5980 chunk 8 optimal weight: 1.9990 chunk 30 optimal weight: 0.6980 chunk 12 optimal weight: 0.2980 chunk 31 optimal weight: 0.8980 chunk 3 optimal weight: 0.0170 chunk 5 optimal weight: 0.9980 overall best weight: 0.5018 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7749 moved from start: 0.2412 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 3108 Z= 0.191 Angle : 0.626 9.776 4213 Z= 0.310 Chirality : 0.041 0.168 484 Planarity : 0.005 0.055 512 Dihedral : 4.059 15.418 409 Min Nonbonded Distance : 2.570 Molprobity Statistics. All-atom Clashscore : 9.29 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.83 % Favored : 98.17 % Rotamer: Outliers : 6.19 % Allowed : 28.17 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 2.06 (0.44), residues: 383 helix: 1.91 (0.29), residues: 329 sheet: -1.68 (1.56), residues: 10 loop : -2.10 (0.84), residues: 44 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP C 136 HIS 0.001 0.000 HIS A 123 PHE 0.015 0.001 PHE C 134 TYR 0.008 0.001 TYR A 29 ARG 0.002 0.000 ARG A 324 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 766 Ramachandran restraints generated. 383 Oldfield, 0 Emsley, 383 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 89 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 69 time to evaluate : 0.316 Fit side-chains REVERT: A 135 ILE cc_start: 0.7432 (OUTLIER) cc_final: 0.7198 (tt) REVERT: A 149 PHE cc_start: 0.6769 (t80) cc_final: 0.6541 (t80) REVERT: A 258 PHE cc_start: 0.6849 (m-80) cc_final: 0.6460 (m-80) REVERT: A 263 MET cc_start: 0.6961 (mmm) cc_final: 0.6145 (mmm) REVERT: A 293 TRP cc_start: 0.8221 (m100) cc_final: 0.7750 (m-10) REVERT: A 296 MET cc_start: 0.6637 (tpp) cc_final: 0.6431 (ttt) REVERT: A 379 HIS cc_start: 0.6064 (OUTLIER) cc_final: 0.4979 (t-90) outliers start: 20 outliers final: 18 residues processed: 85 average time/residue: 0.1302 time to fit residues: 13.6964 Evaluate side-chains 86 residues out of total 323 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 20 poor density : 66 time to evaluate : 0.336 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 19 ILE Chi-restraints excluded: chain A residue 28 VAL Chi-restraints excluded: chain A residue 44 VAL Chi-restraints excluded: chain A residue 96 LEU Chi-restraints excluded: chain A residue 107 MET Chi-restraints excluded: chain A residue 115 LEU Chi-restraints excluded: chain A residue 135 ILE Chi-restraints excluded: chain A residue 138 SER Chi-restraints excluded: chain A residue 195 LEU Chi-restraints excluded: chain A residue 213 VAL Chi-restraints excluded: chain A residue 218 LEU Chi-restraints excluded: chain A residue 281 VAL Chi-restraints excluded: chain A residue 314 THR Chi-restraints excluded: chain A residue 317 PHE Chi-restraints excluded: chain A residue 341 PHE Chi-restraints excluded: chain A residue 370 VAL Chi-restraints excluded: chain A residue 374 LEU Chi-restraints excluded: chain A residue 379 HIS Chi-restraints excluded: chain C residue 126 SER Chi-restraints excluded: chain C residue 127 VAL Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 38 random chunks: chunk 26 optimal weight: 0.8980 chunk 1 optimal weight: 0.6980 chunk 21 optimal weight: 1.9990 chunk 34 optimal weight: 0.9980 chunk 20 optimal weight: 0.6980 chunk 25 optimal weight: 0.8980 chunk 24 optimal weight: 0.7980 chunk 23 optimal weight: 1.9990 chunk 14 optimal weight: 0.9980 chunk 37 optimal weight: 2.9990 chunk 0 optimal weight: 0.5980 overall best weight: 0.7380 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 319 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4112 r_free = 0.4112 target = 0.186898 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 39)----------------| | r_work = 0.3927 r_free = 0.3927 target = 0.167565 restraints weight = 3449.455| |-----------------------------------------------------------------------------| r_work (start): 0.3945 rms_B_bonded: 1.52 r_work: 0.3814 rms_B_bonded: 2.64 restraints_weight: 0.5000 r_work: 0.3681 rms_B_bonded: 4.54 restraints_weight: 0.2500 r_work (final): 0.3681 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7784 moved from start: 0.2588 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.041 3108 Z= 0.227 Angle : 0.647 9.506 4213 Z= 0.324 Chirality : 0.042 0.167 484 Planarity : 0.005 0.056 512 Dihedral : 4.077 15.492 409 Min Nonbonded Distance : 2.529 Molprobity Statistics. All-atom Clashscore : 9.61 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.61 % Favored : 97.39 % Rotamer: Outliers : 6.81 % Allowed : 27.55 % Favored : 65.63 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.98 (0.44), residues: 383 helix: 1.88 (0.29), residues: 328 sheet: -1.78 (1.53), residues: 10 loop : -2.24 (0.85), residues: 45 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.009 0.001 TRP C 136 HIS 0.000 0.000 HIS A 379 PHE 0.016 0.001 PHE A 16 TYR 0.007 0.001 TYR A 29 ARG 0.002 0.001 ARG A 324 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1107.64 seconds wall clock time: 20 minutes 18.30 seconds (1218.30 seconds total)