Starting phenix.real_space_refine on Thu Dec 7 18:28:52 2023 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/12_2023/7ymn_33934.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/12_2023/7ymn_33934.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.46 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/12_2023/7ymn_33934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/12_2023/7ymn_33934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/12_2023/7ymn_33934.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/12_2023/7ymn_33934.pdb" } resolution = 3.46 write_initial_geo_file = False refinement { macro_cycles = 10 } qi { qm_restraints { package { program = *test } } } Starting job =============================================================================== ------------------------------------------------------------------------------- Citation: ********* Afonine PV, Poon BK, Read RJ, Sobolev OV, Terwilliger TC, Urzhumtsev A, Adams PD. (2018) Real-space refinement in PHENIX for cryo-EM and crystallography. Acta Cryst. D74:531-544. Validating inputs Origin is already at (0, 0, 0), no shifts will be applied ------------------------------------------------------------------------------- Processing inputs ***************** Set random seed Set to: 0 Set model cs if undefined Decide on map wrapping Map wrapping is set to: False Normalize map: mean=0, sd=1 Input map: mean= 0.000 sd= 0.003 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 6 5.16 5 C 2172 2.51 5 N 642 2.21 5 O 648 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "F TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "F GLU 342": "OE1" <-> "OE2" Residue "C TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "C GLU 342": "OE1" <-> "OE2" Residue "D TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "D GLU 342": "OE1" <-> "OE2" Residue "E TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "E GLU 342": "OE1" <-> "OE2" Residue "A TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "A GLU 342": "OE1" <-> "OE2" Residue "B TYR 310": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 342": "OE1" <-> "OE2" Time to flip residues: 0.01s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-1.21rc1-5172/modules/chem_data/mon_lib" Total number of atoms: 3468 Number of models: 1 Model: "" Number of chains: 6 Chain: "F" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "C" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "D" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "E" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "A" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Chain: "B" Number of atoms: 578 Number of conformers: 1 Conformer: "" Number of residues, atoms: 76, 578 Classifications: {'peptide': 76} Link IDs: {'PTRANS': 3, 'TRANS': 72} Time building chain proxies: 2.35, per 1000 atoms: 0.68 Number of scatterers: 3468 At special positions: 0 Unit cell: (77.19, 150.23, 34.86, 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 6 16.00 O 648 8.00 N 642 7.00 C 2172 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: 1.22 Conformation dependent library (CDL) restraints added in 634.8 milliseconds 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 792 Finding SS restraints... Secondary structure from input PDB file: 0 helices and 8 sheets defined 0.0% alpha, 7.9% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 0.35 Creating SS restraints... Processing sheet with id=AA1, first strand: chain 'C' and resid 307 through 308 removed outlier: 6.744A pdb=" N GLN F 307 " --> pdb=" O ILE C 308 " (cutoff:3.500A) Processing sheet with id=AA2, first strand: chain 'C' and resid 325 through 328 removed outlier: 6.882A pdb=" N ILE F 328 " --> pdb=" O ASN C 327 " (cutoff:3.500A) removed outlier: 6.221A pdb=" N LEU F 325 " --> pdb=" O GLY D 326 " (cutoff:3.500A) removed outlier: 6.584A pdb=" N ILE D 328 " --> pdb=" O LEU F 325 " (cutoff:3.500A) removed outlier: 7.722A pdb=" N ASN F 327 " --> pdb=" O ILE D 328 " (cutoff:3.500A) Processing sheet with id=AA3, first strand: chain 'C' and resid 343 through 344 removed outlier: 6.384A pdb=" N LYS F 343 " --> pdb=" O LEU C 344 " (cutoff:3.500A) Processing sheet with id=AA4, first strand: chain 'C' and resid 358 through 359 removed outlier: 6.558A pdb=" N ASP F 358 " --> pdb=" O ASN C 359 " (cutoff:3.500A) Processing sheet with id=AA5, first strand: chain 'A' and resid 307 through 308 removed outlier: 6.754A pdb=" N GLN E 307 " --> pdb=" O ILE A 308 " (cutoff:3.500A) Processing sheet with id=AA6, first strand: chain 'A' and resid 325 through 328 removed outlier: 6.901A pdb=" N ILE E 328 " --> pdb=" O ASN A 327 " (cutoff:3.500A) removed outlier: 6.220A pdb=" N LEU E 325 " --> pdb=" O GLY B 326 " (cutoff:3.500A) removed outlier: 6.585A pdb=" N ILE B 328 " --> pdb=" O LEU E 325 " (cutoff:3.500A) removed outlier: 7.721A pdb=" N ASN E 327 " --> pdb=" O ILE B 328 " (cutoff:3.500A) Processing sheet with id=AA7, first strand: chain 'A' and resid 343 through 344 removed outlier: 6.391A pdb=" N LYS E 343 " --> pdb=" O LEU A 344 " (cutoff:3.500A) Processing sheet with id=AA8, first strand: chain 'A' and resid 358 through 359 removed outlier: 6.565A pdb=" N ASP E 358 " --> pdb=" O ASN A 359 " (cutoff:3.500A) 10 hydrogen bonds defined for protein. 30 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: 0.67 Time building geometry restraints manager: 1.36 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.23 - 1.34: 1146 1.34 - 1.45: 369 1.45 - 1.56: 2001 1.56 - 1.68: 0 1.68 - 1.79: 6 Bond restraints: 3522 Sorted by residual: bond pdb=" C GLY C 335 " pdb=" O GLY C 335 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.02e-02 9.61e+03 1.16e+00 bond pdb=" C GLY F 335 " pdb=" O GLY F 335 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.02e-02 9.61e+03 1.16e+00 bond pdb=" C GLY B 335 " pdb=" O GLY B 335 " ideal model delta sigma weight residual 1.236 1.225 0.011 1.02e-02 9.61e+03 1.11e+00 bond pdb=" C GLY D 335 " pdb=" O GLY D 335 " ideal model delta sigma weight residual 1.236 1.226 0.011 1.02e-02 9.61e+03 1.08e+00 bond pdb=" C GLY A 335 " pdb=" O GLY A 335 " ideal model delta sigma weight residual 1.236 1.226 0.010 1.02e-02 9.61e+03 1.05e+00 ... (remaining 3517 not shown) Histogram of bond angle deviations from ideal: 102.70 - 108.45: 286 108.45 - 114.21: 2011 114.21 - 119.96: 815 119.96 - 125.72: 1556 125.72 - 131.47: 42 Bond angle restraints: 4710 Sorted by residual: angle pdb=" C LEU F 357 " pdb=" N ASP F 358 " pdb=" CA ASP F 358 " ideal model delta sigma weight residual 122.10 118.12 3.98 1.66e+00 3.63e-01 5.74e+00 angle pdb=" C LEU B 357 " pdb=" N ASP B 358 " pdb=" CA ASP B 358 " ideal model delta sigma weight residual 122.10 118.14 3.96 1.66e+00 3.63e-01 5.68e+00 angle pdb=" C LEU E 357 " pdb=" N ASP E 358 " pdb=" CA ASP E 358 " ideal model delta sigma weight residual 122.10 118.14 3.96 1.66e+00 3.63e-01 5.68e+00 angle pdb=" C LEU D 357 " pdb=" N ASP D 358 " pdb=" CA ASP D 358 " ideal model delta sigma weight residual 122.10 118.15 3.95 1.66e+00 3.63e-01 5.67e+00 angle pdb=" C LEU A 357 " pdb=" N ASP A 358 " pdb=" CA ASP A 358 " ideal model delta sigma weight residual 122.10 118.15 3.95 1.66e+00 3.63e-01 5.67e+00 ... (remaining 4705 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 12.42: 1854 12.42 - 24.84: 216 24.84 - 37.27: 60 37.27 - 49.69: 6 49.69 - 62.11: 6 Dihedral angle restraints: 2142 sinusoidal: 894 harmonic: 1248 Sorted by residual: dihedral pdb=" CB GLU C 342 " pdb=" CG GLU C 342 " pdb=" CD GLU C 342 " pdb=" OE1 GLU C 342 " ideal model delta sinusoidal sigma weight residual 0.00 -62.11 62.11 1 3.00e+01 1.11e-03 5.68e+00 dihedral pdb=" CB GLU B 342 " pdb=" CG GLU B 342 " pdb=" CD GLU B 342 " pdb=" OE1 GLU B 342 " ideal model delta sinusoidal sigma weight residual 0.00 -62.11 62.11 1 3.00e+01 1.11e-03 5.68e+00 dihedral pdb=" CB GLU A 342 " pdb=" CG GLU A 342 " pdb=" CD GLU A 342 " pdb=" OE1 GLU A 342 " ideal model delta sinusoidal sigma weight residual 0.00 -62.10 62.10 1 3.00e+01 1.11e-03 5.68e+00 ... (remaining 2139 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.024: 239 0.024 - 0.048: 126 0.048 - 0.072: 67 0.072 - 0.096: 40 0.096 - 0.120: 56 Chirality restraints: 528 Sorted by residual: chirality pdb=" CA VAL B 318 " pdb=" N VAL B 318 " pdb=" C VAL B 318 " pdb=" CB VAL B 318 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.60e-01 chirality pdb=" CA VAL F 318 " pdb=" N VAL F 318 " pdb=" C VAL F 318 " pdb=" CB VAL F 318 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 chirality pdb=" CA VAL D 318 " pdb=" N VAL D 318 " pdb=" C VAL D 318 " pdb=" CB VAL D 318 " both_signs ideal model delta sigma weight residual False 2.44 2.56 -0.12 2.00e-01 2.50e+01 3.59e-01 ... (remaining 525 not shown) Planarity restraints: 600 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C LYS D 311 " 0.020 5.00e-02 4.00e+02 3.07e-02 1.51e+00 pdb=" N PRO D 312 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO D 312 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO D 312 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 311 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO B 312 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO B 312 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO B 312 " 0.017 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS A 311 " 0.020 5.00e-02 4.00e+02 3.06e-02 1.50e+00 pdb=" N PRO A 312 " -0.053 5.00e-02 4.00e+02 pdb=" CA PRO A 312 " 0.016 5.00e-02 4.00e+02 pdb=" CD PRO A 312 " 0.017 5.00e-02 4.00e+02 ... (remaining 597 not shown) Histogram of nonbonded interaction distances: 2.23 - 2.77: 633 2.77 - 3.30: 3111 3.30 - 3.83: 5134 3.83 - 4.37: 5614 4.37 - 4.90: 12118 Nonbonded interactions: 26610 Sorted by model distance: nonbonded pdb=" NZ LYS B 370 " pdb=" OE2 GLU B 372 " model vdw 2.234 2.520 nonbonded pdb=" NZ LYS C 370 " pdb=" OE2 GLU C 372 " model vdw 2.234 2.520 nonbonded pdb=" NZ LYS E 370 " pdb=" OE2 GLU E 372 " model vdw 2.235 2.520 nonbonded pdb=" NZ LYS D 370 " pdb=" OE2 GLU D 372 " model vdw 2.235 2.520 nonbonded pdb=" NZ LYS F 370 " pdb=" OE2 GLU F 372 " model vdw 2.235 2.520 ... (remaining 26605 not shown) NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Find NCS groups from input model Found NCS groups: ncs_group { reference = chain 'A' selection = chain 'B' selection = chain 'C' selection = chain 'D' selection = chain 'E' selection = chain 'F' } 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: 0.990 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.010 Construct map_model_manager: 0.000 Extract box with map and model: 4.780 Check model and map are aligned: 0.050 Set scattering table: 0.040 Process input model: 14.080 Find NCS groups from input model: 0.240 Set up NCS constraints: 0.020 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:2.810 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.020 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7745 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 : 0.007 0.035 3522 Z= 0.486 Angle : 0.728 4.224 4710 Z= 0.414 Chirality : 0.052 0.120 528 Planarity : 0.004 0.031 600 Dihedral : 12.251 62.111 1350 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 11.60 Ramachandran Plot: Outliers : 0.00 % Allowed : 17.57 % Favored : 82.43 % Rotamer: Outliers : 0.00 % Allowed : 4.55 % Favored : 95.45 % 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: -5.43 (0.25), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -4.13 (0.19), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS E 362 PHE 0.009 0.003 PHE E 378 TYR 0.004 0.002 TYR E 310 ARG 0.001 0.000 ARG A 349 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 52 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 52 time to evaluate : 0.436 Fit side-chains revert: symmetry clash outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3619 time to fit residues: 21.1182 Evaluate side-chains 44 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 44 time to evaluate : 0.460 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6251 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 10.0000 chunk 31 optimal weight: 5.9990 chunk 17 optimal weight: 7.9990 chunk 10 optimal weight: 6.9990 chunk 21 optimal weight: 9.9990 chunk 32 optimal weight: 4.9990 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 6.9990 chunk 11 optimal weight: 4.9990 overall best weight: 4.3990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: F 359 ASN ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** F 368 ASN C 359 ASN ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 359 ASN ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 359 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** A 359 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 359 ASN ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 7 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7730 moved from start: 0.1073 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.025 3522 Z= 0.318 Angle : 0.623 4.522 4710 Z= 0.334 Chirality : 0.050 0.122 528 Planarity : 0.005 0.040 600 Dihedral : 5.212 11.977 468 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.47 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.59 % Favored : 89.41 % Rotamer: Outliers : 0.51 % Allowed : 10.10 % Favored : 89.39 % 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: -5.03 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.83 (0.20), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.004 0.001 HIS C 362 PHE 0.015 0.002 PHE F 378 TYR 0.006 0.002 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.423 Fit side-chains outliers start: 2 outliers final: 0 residues processed: 43 average time/residue: 0.3494 time to fit residues: 16.9024 Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 35 time to evaluate : 0.424 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.6010 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 31 optimal weight: 10.0000 chunk 25 optimal weight: 10.0000 chunk 10 optimal weight: 0.9990 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 0.0570 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 10.0000 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 10.0000 chunk 19 optimal weight: 10.0000 overall best weight: 4.8106 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 moved from start: 0.1260 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.027 3522 Z= 0.345 Angle : 0.638 4.721 4710 Z= 0.343 Chirality : 0.051 0.123 528 Planarity : 0.005 0.044 600 Dihedral : 5.294 12.559 468 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 12.45 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 1.01 % Allowed : 11.11 % Favored : 87.88 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.92 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.74 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.008 0.002 PHE A 378 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG B 349 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 4 poor density : 36 time to evaluate : 0.425 Fit side-chains outliers start: 4 outliers final: 3 residues processed: 38 average time/residue: 0.3117 time to fit residues: 13.5720 Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 34 time to evaluate : 0.423 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0366 time to fit residues: 0.7847 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 9.9990 chunk 18 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 6.9990 chunk 40 optimal weight: 5.9990 chunk 20 optimal weight: 0.0870 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 5.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 5.6166 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** E 368 ASN ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7747 moved from start: 0.1511 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.032 3522 Z= 0.399 Angle : 0.670 5.070 4710 Z= 0.361 Chirality : 0.051 0.124 528 Planarity : 0.005 0.048 600 Dihedral : 5.490 12.602 468 Min Nonbonded Distance : 2.194 Molprobity Statistics. All-atom Clashscore : 13.16 Ramachandran Plot: Outliers : 0.00 % Allowed : 13.51 % Favored : 86.49 % Rotamer: Outliers : 0.25 % Allowed : 15.40 % Favored : 84.34 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.88 (0.28), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.71 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.016 0.002 PHE F 378 TYR 0.011 0.002 TYR D 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 37 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 36 time to evaluate : 0.432 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 36 average time/residue: 0.3037 time to fit residues: 12.6849 Evaluate side-chains 35 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 34 time to evaluate : 0.441 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0388 time to fit residues: 0.6735 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 30 optimal weight: 3.9990 chunk 16 optimal weight: 9.9990 chunk 34 optimal weight: 2.9990 chunk 28 optimal weight: 8.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 8.9990 chunk 36 optimal weight: 8.9990 chunk 10 optimal weight: 6.9990 chunk 13 optimal weight: 5.9990 chunk 8 optimal weight: 9.9990 chunk 23 optimal weight: 0.7980 overall best weight: 4.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7719 moved from start: 0.1625 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3522 Z= 0.300 Angle : 0.617 5.024 4710 Z= 0.331 Chirality : 0.050 0.123 528 Planarity : 0.005 0.048 600 Dihedral : 5.191 12.368 468 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.68 % Favored : 90.32 % Rotamer: Outliers : 0.25 % Allowed : 16.67 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.78 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS B 362 PHE 0.017 0.002 PHE E 378 TYR 0.009 0.002 TYR D 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.394 Fit side-chains outliers start: 1 outliers final: 1 residues processed: 37 average time/residue: 0.3053 time to fit residues: 13.0735 Evaluate side-chains 38 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 37 time to evaluate : 0.435 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0517 time to fit residues: 0.7225 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 7.9990 chunk 40 optimal weight: 0.0000 chunk 33 optimal weight: 10.0000 chunk 18 optimal weight: 6.9990 chunk 3 optimal weight: 4.9990 chunk 13 optimal weight: 10.0000 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 6.9990 chunk 4 optimal weight: 10.0000 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 6.9990 overall best weight: 5.1992 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** C 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** D 368 ASN ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** B 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7739 moved from start: 0.1724 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.030 3522 Z= 0.372 Angle : 0.661 5.176 4710 Z= 0.356 Chirality : 0.051 0.122 528 Planarity : 0.006 0.049 600 Dihedral : 5.378 12.308 468 Min Nonbonded Distance : 2.190 Molprobity Statistics. All-atom Clashscore : 13.02 Ramachandran Plot: Outliers : 0.00 % Allowed : 15.09 % Favored : 84.91 % Rotamer: Outliers : 0.76 % Allowed : 16.67 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.77 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.63 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.018 0.002 PHE F 378 TYR 0.010 0.002 TYR B 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.430 Fit side-chains outliers start: 3 outliers final: 3 residues processed: 39 average time/residue: 0.2560 time to fit residues: 11.6525 Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 37 time to evaluate : 0.400 Switching outliers to nearest non-outliers outliers start: 3 outliers final: 0 residues processed: 3 average time/residue: 0.0370 time to fit residues: 0.7597 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 20.0000 chunk 34 optimal weight: 6.9990 chunk 40 optimal weight: 4.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 9.9990 chunk 18 optimal weight: 5.9990 chunk 16 optimal weight: 10.0000 chunk 12 optimal weight: 0.0170 chunk 7 optimal weight: 0.8980 chunk 27 optimal weight: 3.9990 chunk 20 optimal weight: 3.9990 overall best weight: 2.7824 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** B 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7691 moved from start: 0.1851 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.018 3522 Z= 0.217 Angle : 0.585 4.581 4710 Z= 0.312 Chirality : 0.049 0.125 528 Planarity : 0.005 0.050 600 Dihedral : 4.924 12.238 468 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 9.90 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.11 % Favored : 91.89 % Rotamer: Outliers : 0.51 % Allowed : 17.17 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.67 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.55 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 362 PHE 0.017 0.001 PHE E 378 TYR 0.007 0.001 TYR D 310 ARG 0.000 0.000 ARG F 349 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.434 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 0 residues processed: 42 average time/residue: 0.2813 time to fit residues: 13.6642 Evaluate side-chains 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.408 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.5877 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 10.0000 chunk 31 optimal weight: 8.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 4.9990 chunk 35 optimal weight: 2.9990 chunk 37 optimal weight: 2.9990 chunk 22 optimal weight: 9.9990 chunk 16 optimal weight: 10.0000 chunk 29 optimal weight: 3.9990 chunk 11 optimal weight: 5.9990 chunk 34 optimal weight: 10.0000 overall best weight: 4.1990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7718 moved from start: 0.1910 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.024 3522 Z= 0.307 Angle : 0.638 5.134 4710 Z= 0.341 Chirality : 0.050 0.122 528 Planarity : 0.006 0.053 600 Dihedral : 5.050 12.209 468 Min Nonbonded Distance : 2.196 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.81 % Favored : 89.19 % Rotamer: Outliers : 0.51 % Allowed : 17.42 % Favored : 82.07 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.69 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.57 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.018 0.002 PHE F 378 TYR 0.009 0.002 TYR B 310 ARG 0.002 0.000 ARG C 379 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 47 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 45 time to evaluate : 0.450 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 2 outliers final: 2 residues processed: 45 average time/residue: 0.3121 time to fit residues: 15.8916 Evaluate side-chains 42 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.386 Switching outliers to nearest non-outliers outliers start: 2 outliers final: 0 residues processed: 2 average time/residue: 0.0357 time to fit residues: 0.6758 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 6.9990 chunk 37 optimal weight: 2.9990 chunk 24 optimal weight: 5.9990 chunk 39 optimal weight: 20.0000 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 0.7980 chunk 38 optimal weight: 2.9990 chunk 33 optimal weight: 8.9990 chunk 3 optimal weight: 6.9990 chunk 25 optimal weight: 2.9990 overall best weight: 3.1588 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7693 moved from start: 0.2101 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3522 Z= 0.242 Angle : 0.617 6.420 4710 Z= 0.328 Chirality : 0.049 0.125 528 Planarity : 0.006 0.058 600 Dihedral : 4.867 12.091 468 Min Nonbonded Distance : 2.204 Molprobity Statistics. All-atom Clashscore : 9.62 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.23 % Favored : 90.77 % Rotamer: Outliers : 0.25 % Allowed : 16.67 % Favored : 83.08 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.64 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.53 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.001 HIS C 362 PHE 0.018 0.002 PHE F 378 TYR 0.008 0.002 TYR B 310 ARG 0.001 0.000 ARG F 379 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 42 time to evaluate : 0.487 Fit side-chains revert: symmetry clash revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 0 residues processed: 42 average time/residue: 0.3091 time to fit residues: 15.0482 Evaluate side-chains 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 39 time to evaluate : 0.691 Switching outliers to nearest non-outliers outliers start: 0 outliers final: 0 residues processed: 0 time to fit residues: 0.9927 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 4.9990 chunk 26 optimal weight: 3.9990 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 7.9990 chunk 30 optimal weight: 0.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 0.7980 chunk 33 optimal weight: 6.9990 chunk 13 optimal weight: 2.9990 chunk 34 optimal weight: 0.8980 chunk 6 optimal weight: 5.9990 overall best weight: 1.9386 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** F 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** D 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7660 moved from start: 0.2277 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.029 3522 Z= 0.178 Angle : 0.601 6.857 4710 Z= 0.317 Chirality : 0.048 0.124 528 Planarity : 0.006 0.063 600 Dihedral : 4.517 11.951 468 Min Nonbonded Distance : 2.224 Molprobity Statistics. All-atom Clashscore : 9.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.21 % Favored : 92.79 % Rotamer: Outliers : 0.25 % Allowed : 17.42 % Favored : 82.32 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.56 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.47 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS F 362 PHE 0.018 0.002 PHE F 378 TYR 0.007 0.001 TYR B 310 ARG 0.000 0.000 ARG F 379 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 888 Ramachandran restraints generated. 444 Oldfield, 0 Emsley, 444 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 40 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 39 time to evaluate : 0.438 Fit side-chains revert: symmetry clash revert: symmetry clash outliers start: 1 outliers final: 1 residues processed: 39 average time/residue: 0.3041 time to fit residues: 13.6211 Evaluate side-chains 39 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 38 time to evaluate : 0.402 Switching outliers to nearest non-outliers outliers start: 1 outliers final: 0 residues processed: 1 average time/residue: 0.0369 time to fit residues: 0.6374 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 7.9990 chunk 1 optimal weight: 9.9990 chunk 24 optimal weight: 5.9990 chunk 38 optimal weight: 2.9990 chunk 22 optimal weight: 7.9990 chunk 28 optimal weight: 0.6980 chunk 26 optimal weight: 6.9990 chunk 25 optimal weight: 0.9990 chunk 16 optimal weight: 10.0000 chunk 15 optimal weight: 8.9990 chunk 41 optimal weight: 3.9990 overall best weight: 2.9388 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** E 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** ** A 362 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 0 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4722 r_free = 0.4722 target = 0.258170 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 78)----------------| | r_work = 0.4943 r_free = 0.4943 target = 0.199448 restraints weight = 3827.510| |-----------------------------------------------------------------------------| r_work (start): 0.4622 rms_B_bonded: 0.98 r_work: 0.4978 rms_B_bonded: 0.50 restraints_weight: 0.5000 r_work: 0.4943 rms_B_bonded: 0.82 restraints_weight: 0.2500 r_work: 0.4751 rms_B_bonded: 2.88 restraints_weight: 0.1250 r_work (final): 0.4751 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7953 moved from start: 0.2250 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.025 3522 Z= 0.229 Angle : 0.606 6.613 4710 Z= 0.321 Chirality : 0.049 0.123 528 Planarity : 0.006 0.063 600 Dihedral : 4.654 11.858 468 Min Nonbonded Distance : 2.200 Molprobity Statistics. All-atom Clashscore : 9.48 Ramachandran Plot: Outliers : 0.00 % Allowed : 7.66 % Favored : 92.34 % Rotamer: Outliers : 0.25 % Allowed : 17.17 % Favored : 82.58 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: -4.57 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.48 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.001 HIS C 362 PHE 0.019 0.002 PHE F 378 TYR 0.007 0.001 TYR D 310 ARG 0.001 0.000 ARG F 379 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1239.90 seconds wall clock time: 23 minutes 33.11 seconds (1413.11 seconds total)