Starting phenix.real_space_refine on Sun Mar 10 17:21:51 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/03_2024/7ymn_33934.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/03_2024/7ymn_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_33934/03_2024/7ymn_33934.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/03_2024/7ymn_33934.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/03_2024/7ymn_33934.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7ymn_33934/03_2024/7ymn_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-dev-5265/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 646.8 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: 0.32 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: 0.69 Time building geometry restraints manager: 1.33 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: 1.350 Set stop_for_unknowns flag: 0.000 Assert model is a single copy model: 0.000 Assert all atoms have isotropic ADPs: 0.000 Construct map_model_manager: 0.010 Extract box with map and model: 4.840 Check model and map are aligned: 0.060 Set scattering table: 0.040 Process input model: 14.240 Find NCS groups from input model: 0.250 Set up NCS constraints: 0.030 Set refine NCS operators: 0.000 Adjust number of macro_cycles: 0.000 Reset NCS operators: 0.000 Extract rigid body selections: 0.000 Check and reset occupancies: 0.000 Load rotamer database and sin/cos tables:3.030 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 23.850 ------------------------------------------------------------------------------- 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 : 0.383 Fit side-chains revert: symmetry clash REVERT: F 345 ASP cc_start: 0.8094 (t0) cc_final: 0.7412 (t0) REVERT: F 349 ARG cc_start: 0.7611 (mtt-85) cc_final: 0.7385 (mmm-85) REVERT: D 345 ASP cc_start: 0.7883 (t0) cc_final: 0.7235 (t0) REVERT: E 311 LYS cc_start: 0.7417 (ttpt) cc_final: 0.6840 (tmtt) REVERT: E 345 ASP cc_start: 0.8121 (t0) cc_final: 0.7619 (t0) REVERT: E 349 ARG cc_start: 0.7646 (mtt-85) cc_final: 0.7280 (mtt90) REVERT: E 358 ASP cc_start: 0.8097 (p0) cc_final: 0.7853 (p0) REVERT: A 311 LYS cc_start: 0.7976 (ttpt) cc_final: 0.7433 (tmtt) REVERT: A 345 ASP cc_start: 0.8414 (t0) cc_final: 0.7832 (t0) REVERT: A 349 ARG cc_start: 0.7793 (mtt-85) cc_final: 0.7460 (mmm-85) REVERT: B 345 ASP cc_start: 0.8063 (t0) cc_final: 0.7521 (t0) REVERT: B 347 LYS cc_start: 0.8210 (mmtp) cc_final: 0.7959 (mmmm) REVERT: B 349 ARG cc_start: 0.7835 (mtt-85) cc_final: 0.7520 (mmm-85) outliers start: 0 outliers final: 0 residues processed: 52 average time/residue: 0.3291 time to fit residues: 19.1092 Evaluate side-chains 47 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 47 time to evaluate : 0.377 ------------------------------------------------------------------------------- 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: 10.0000 chunk 32 optimal weight: 10.0000 chunk 12 optimal weight: 4.9990 chunk 20 optimal weight: 2.9990 chunk 24 optimal weight: 3.9990 chunk 38 optimal weight: 4.9990 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: 0.7725 moved from start: 0.0860 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= 0.310 Angle : 0.614 4.280 4710 Z= 0.329 Chirality : 0.050 0.122 528 Planarity : 0.004 0.040 600 Dihedral : 5.232 12.420 468 Min Nonbonded Distance : 2.201 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 10.36 % Favored : 89.64 % Rotamer: Outliers : 0.51 % Allowed : 10.35 % Favored : 89.14 % 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 0.005 0.001 HIS C 362 PHE 0.016 0.002 PHE F 378 TYR 0.006 0.002 TYR E 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 46 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 44 time to evaluate : 0.437 Fit side-chains REVERT: F 345 ASP cc_start: 0.8030 (t0) cc_final: 0.7686 (t0) REVERT: F 349 ARG cc_start: 0.7479 (mtt-85) cc_final: 0.7253 (mtt90) REVERT: C 349 ARG cc_start: 0.7731 (mtt90) cc_final: 0.7102 (mmm-85) REVERT: D 311 LYS cc_start: 0.7422 (ttpt) cc_final: 0.6851 (tmtt) REVERT: D 345 ASP cc_start: 0.7941 (t0) cc_final: 0.7377 (t0) REVERT: E 311 LYS cc_start: 0.7383 (ttpt) cc_final: 0.6758 (tmtt) REVERT: E 345 ASP cc_start: 0.8089 (t0) cc_final: 0.7299 (t0) REVERT: E 349 ARG cc_start: 0.7605 (mtt-85) cc_final: 0.7224 (mtt90) REVERT: A 311 LYS cc_start: 0.8069 (ttpt) cc_final: 0.7461 (tmtt) REVERT: A 349 ARG cc_start: 0.7776 (mtt-85) cc_final: 0.7465 (mmm-85) REVERT: B 345 ASP cc_start: 0.7981 (t0) cc_final: 0.7372 (t0) REVERT: B 347 LYS cc_start: 0.8118 (mmtp) cc_final: 0.7916 (mmmm) REVERT: B 349 ARG cc_start: 0.7863 (mtt-85) cc_final: 0.7520 (mmm-85) outliers start: 2 outliers final: 0 residues processed: 46 average time/residue: 0.3681 time to fit residues: 18.9002 Evaluate side-chains 42 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 42 time to evaluate : 0.441 ------------------------------------------------------------------------------- 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: 9.9990 chunk 10 optimal weight: 0.8980 chunk 38 optimal weight: 6.9990 chunk 41 optimal weight: 9.9990 chunk 34 optimal weight: 4.9990 chunk 37 optimal weight: 7.9990 chunk 13 optimal weight: 8.9990 chunk 30 optimal weight: 7.9990 chunk 28 optimal weight: 0.0060 chunk 19 optimal weight: 9.9990 overall best weight: 4.1802 ------------------------------------------------------------------------------- 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** ** 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: 0.7720 moved from start: 0.1011 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.023 3522 Z= 0.296 Angle : 0.598 4.329 4710 Z= 0.319 Chirality : 0.050 0.122 528 Planarity : 0.005 0.043 600 Dihedral : 5.141 12.263 468 Min Nonbonded Distance : 2.209 Molprobity Statistics. All-atom Clashscore : 10.05 Ramachandran Plot: Outliers : 0.00 % Allowed : 9.01 % Favored : 90.99 % Rotamer: Outliers : 0.51 % Allowed : 11.36 % Favored : 88.13 % 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: -4.91 (0.27), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.73 (0.21), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.007 0.002 PHE A 378 TYR 0.007 0.002 TYR B 310 ARG 0.001 0.000 ARG D 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 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.416 Fit side-chains REVERT: F 345 ASP cc_start: 0.8012 (t0) cc_final: 0.7597 (t0) REVERT: F 349 ARG cc_start: 0.7451 (mtt-85) cc_final: 0.7226 (mtt90) REVERT: C 349 ARG cc_start: 0.7734 (mtt90) cc_final: 0.7082 (mmm-85) REVERT: D 311 LYS cc_start: 0.7394 (ttpt) cc_final: 0.6827 (tmtt) REVERT: D 345 ASP cc_start: 0.7936 (t0) cc_final: 0.7304 (t0) REVERT: E 311 LYS cc_start: 0.7386 (ttpt) cc_final: 0.6747 (tmtt) REVERT: E 345 ASP cc_start: 0.8093 (t0) cc_final: 0.7275 (t0) REVERT: E 349 ARG cc_start: 0.7630 (mtt-85) cc_final: 0.7239 (mtt90) REVERT: A 311 LYS cc_start: 0.8048 (ttpt) cc_final: 0.7430 (tmtt) REVERT: A 349 ARG cc_start: 0.7781 (mtt-85) cc_final: 0.7462 (mmm-85) REVERT: B 345 ASP cc_start: 0.7964 (t0) cc_final: 0.7355 (t0) REVERT: B 349 ARG cc_start: 0.7920 (mtt-85) cc_final: 0.7567 (mmm-85) outliers start: 2 outliers final: 1 residues processed: 43 average time/residue: 0.3623 time to fit residues: 17.4063 Evaluate side-chains 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 1 poor density : 40 time to evaluate : 0.392 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 4 optimal weight: 10.0000 chunk 18 optimal weight: 8.9990 chunk 25 optimal weight: 10.0000 chunk 38 optimal weight: 7.9990 chunk 40 optimal weight: 3.9990 chunk 20 optimal weight: 9.9990 chunk 36 optimal weight: 9.9990 chunk 10 optimal weight: 10.0000 chunk 33 optimal weight: 8.9990 chunk 23 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 overall best weight: 7.9990 ------------------------------------------------------------------------------- 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: 0.7799 moved from start: 0.1294 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.008 0.046 3522 Z= 0.556 Angle : 0.758 4.798 4710 Z= 0.413 Chirality : 0.054 0.127 528 Planarity : 0.006 0.048 600 Dihedral : 6.036 13.902 468 Min Nonbonded Distance : 2.177 Molprobity Statistics. All-atom Clashscore : 13.72 Ramachandran Plot: Outliers : 0.00 % Allowed : 20.95 % Favored : 79.05 % Rotamer: Outliers : 0.76 % Allowed : 14.90 % 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: -4.92 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.75 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.017 0.003 PHE F 378 TYR 0.012 0.003 TYR B 310 ARG 0.002 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 46 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 43 time to evaluate : 0.431 Fit side-chains REVERT: F 311 LYS cc_start: 0.7505 (ttpt) cc_final: 0.6875 (tmtt) REVERT: D 311 LYS cc_start: 0.7448 (ttpt) cc_final: 0.6831 (tmtt) REVERT: D 345 ASP cc_start: 0.8088 (t0) cc_final: 0.7306 (t0) REVERT: E 311 LYS cc_start: 0.7513 (ttpt) cc_final: 0.6857 (tmtt) REVERT: E 345 ASP cc_start: 0.8116 (t0) cc_final: 0.7245 (t0) REVERT: E 349 ARG cc_start: 0.7694 (mtt-85) cc_final: 0.7393 (mtt90) REVERT: A 311 LYS cc_start: 0.8102 (ttpt) cc_final: 0.7506 (tmtt) REVERT: A 345 ASP cc_start: 0.8285 (t0) cc_final: 0.7822 (t0) REVERT: B 345 ASP cc_start: 0.8040 (t0) cc_final: 0.7589 (t0) REVERT: B 349 ARG cc_start: 0.7992 (mtt-85) cc_final: 0.7617 (mtt90) outliers start: 3 outliers final: 2 residues processed: 45 average time/residue: 0.3202 time to fit residues: 16.3201 Evaluate side-chains 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP 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: 10.0000 chunk 34 optimal weight: 7.9990 chunk 28 optimal weight: 9.9990 chunk 0 optimal weight: 20.0000 chunk 20 optimal weight: 4.9990 chunk 36 optimal weight: 10.0000 chunk 10 optimal weight: 9.9990 chunk 13 optimal weight: 0.2980 chunk 8 optimal weight: 6.9990 chunk 23 optimal weight: 0.9980 overall best weight: 3.4586 ------------------------------------------------------------------------------- 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: 0.7722 moved from start: 0.1448 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.021 3522 Z= 0.255 Angle : 0.598 4.456 4710 Z= 0.318 Chirality : 0.050 0.123 528 Planarity : 0.005 0.046 600 Dihedral : 5.261 12.919 468 Min Nonbonded Distance : 2.203 Molprobity Statistics. All-atom Clashscore : 11.04 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.76 % Allowed : 15.66 % Favored : 83.59 % 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: -4.83 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.68 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS B 362 PHE 0.016 0.002 PHE F 378 TYR 0.006 0.002 TYR B 310 ARG 0.001 0.000 ARG D 349 *********************** 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 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 40 time to evaluate : 0.375 Fit side-chains REVERT: F 345 ASP cc_start: 0.8074 (t70) cc_final: 0.7421 (t0) REVERT: D 345 ASP cc_start: 0.7952 (t0) cc_final: 0.7268 (t0) REVERT: E 311 LYS cc_start: 0.7492 (ttpt) cc_final: 0.6906 (tmtt) REVERT: E 345 ASP cc_start: 0.8027 (t0) cc_final: 0.7171 (t0) REVERT: E 349 ARG cc_start: 0.7593 (mtt-85) cc_final: 0.7267 (mtt90) REVERT: A 311 LYS cc_start: 0.8071 (ttpt) cc_final: 0.7459 (tmtt) REVERT: A 345 ASP cc_start: 0.8290 (t0) cc_final: 0.7709 (t0) REVERT: B 345 ASP cc_start: 0.7856 (t0) cc_final: 0.7340 (t0) REVERT: B 349 ARG cc_start: 0.7917 (mtt-85) cc_final: 0.7533 (mmm-85) outliers start: 3 outliers final: 2 residues processed: 42 average time/residue: 0.3178 time to fit residues: 15.1664 Evaluate side-chains 41 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 39 time to evaluate : 0.416 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 10 optimal weight: 6.9990 chunk 40 optimal weight: 9.9990 chunk 33 optimal weight: 0.9980 chunk 18 optimal weight: 8.9990 chunk 3 optimal weight: 7.9990 chunk 13 optimal weight: 0.7980 chunk 21 optimal weight: 20.0000 chunk 39 optimal weight: 0.0870 chunk 4 optimal weight: 6.9990 chunk 23 optimal weight: 9.9990 chunk 29 optimal weight: 0.0370 overall best weight: 1.7838 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.1644 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.014 3522 Z= 0.149 Angle : 0.528 4.312 4710 Z= 0.276 Chirality : 0.048 0.128 528 Planarity : 0.004 0.043 600 Dihedral : 4.624 12.169 468 Min Nonbonded Distance : 2.234 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 5.41 % Favored : 94.59 % Rotamer: Outliers : 0.51 % Allowed : 15.66 % Favored : 83.84 % 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: -4.72 (0.29), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.59 (0.22), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS F 362 PHE 0.015 0.001 PHE E 378 TYR 0.005 0.001 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 45 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 43 time to evaluate : 0.415 Fit side-chains REVERT: F 311 LYS cc_start: 0.7514 (ttpt) cc_final: 0.7011 (tmtt) REVERT: F 345 ASP cc_start: 0.8040 (t70) cc_final: 0.7757 (t0) REVERT: C 349 ARG cc_start: 0.7699 (mtt90) cc_final: 0.7027 (mmm-85) REVERT: D 311 LYS cc_start: 0.7720 (ttpt) cc_final: 0.6689 (tppt) REVERT: D 345 ASP cc_start: 0.7838 (t0) cc_final: 0.7320 (t0) REVERT: E 311 LYS cc_start: 0.7521 (ttpt) cc_final: 0.6990 (tmtt) REVERT: E 345 ASP cc_start: 0.8085 (t0) cc_final: 0.7376 (t0) REVERT: E 349 ARG cc_start: 0.7534 (mtt-85) cc_final: 0.7195 (mtt90) REVERT: A 311 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7417 (tmtt) REVERT: A 345 ASP cc_start: 0.8313 (t0) cc_final: 0.7846 (m-30) REVERT: B 311 LYS cc_start: 0.7684 (ttpt) cc_final: 0.6627 (tppt) REVERT: B 345 ASP cc_start: 0.7762 (t0) cc_final: 0.7541 (t0) REVERT: B 349 ARG cc_start: 0.7854 (mtt-85) cc_final: 0.7493 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 44 average time/residue: 0.3323 time to fit residues: 16.6691 Evaluate side-chains 42 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.362 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 22 optimal weight: 9.9990 chunk 34 optimal weight: 9.9990 chunk 40 optimal weight: 9.9990 chunk 25 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 18 optimal weight: 7.9990 chunk 16 optimal weight: 9.9990 chunk 12 optimal weight: 10.0000 chunk 7 optimal weight: 8.9990 chunk 27 optimal weight: 2.9990 chunk 20 optimal weight: 3.9990 overall best weight: 6.7990 ------------------------------------------------------------------------------- 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 368 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7773 moved from start: 0.1552 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.007 0.039 3522 Z= 0.469 Angle : 0.696 4.422 4710 Z= 0.377 Chirality : 0.053 0.126 528 Planarity : 0.006 0.046 600 Dihedral : 5.541 12.797 468 Min Nonbonded Distance : 2.180 Molprobity Statistics. All-atom Clashscore : 12.03 Ramachandran Plot: Outliers : 0.00 % Allowed : 18.24 % Favored : 81.76 % 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: -4.80 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.65 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.016 0.003 PHE E 378 TYR 0.011 0.002 TYR B 310 ARG 0.001 0.000 ARG F 379 *********************** 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: 3 poor density : 40 time to evaluate : 0.424 Fit side-chains REVERT: C 311 LYS cc_start: 0.7882 (ttpt) cc_final: 0.7310 (tmtt) REVERT: D 345 ASP cc_start: 0.7962 (t0) cc_final: 0.7523 (m-30) REVERT: E 311 LYS cc_start: 0.7484 (ttpt) cc_final: 0.6862 (tmtt) REVERT: E 345 ASP cc_start: 0.8092 (t0) cc_final: 0.7215 (t0) REVERT: E 349 ARG cc_start: 0.7672 (mtt-85) cc_final: 0.7393 (mtt90) REVERT: A 311 LYS cc_start: 0.8104 (ttpt) cc_final: 0.7524 (tmtt) REVERT: B 345 ASP cc_start: 0.7956 (t0) cc_final: 0.7495 (t0) REVERT: B 349 ARG cc_start: 0.7950 (mtt-85) cc_final: 0.7661 (mtt90) outliers start: 3 outliers final: 2 residues processed: 41 average time/residue: 0.3335 time to fit residues: 15.4758 Evaluate side-chains 42 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 40 time to evaluate : 0.513 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 3 optimal weight: 2.9990 chunk 31 optimal weight: 6.9990 chunk 36 optimal weight: 9.9990 chunk 38 optimal weight: 2.9990 chunk 35 optimal weight: 0.7980 chunk 37 optimal weight: 6.9990 chunk 22 optimal weight: 5.9990 chunk 16 optimal weight: 6.9990 chunk 29 optimal weight: 9.9990 chunk 11 optimal weight: 1.9990 chunk 34 optimal weight: 0.9990 overall best weight: 1.9588 ------------------------------------------------------------------------------- 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: 0.7682 moved from start: 0.1761 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.018 3522 Z= 0.163 Angle : 0.550 4.051 4710 Z= 0.291 Chirality : 0.049 0.128 528 Planarity : 0.005 0.044 600 Dihedral : 4.824 12.167 468 Min Nonbonded Distance : 2.220 Molprobity Statistics. All-atom Clashscore : 8.77 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.08 % Favored : 93.92 % 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: -4.69 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.56 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.007 0.002 HIS B 362 PHE 0.017 0.002 PHE F 378 TYR 0.005 0.001 TYR B 310 ARG 0.001 0.000 ARG C 349 *********************** 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 44 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 42 time to evaluate : 0.455 Fit side-chains REVERT: F 345 ASP cc_start: 0.8050 (t70) cc_final: 0.7409 (t0) REVERT: C 311 LYS cc_start: 0.7934 (ttpt) cc_final: 0.7309 (tmtt) REVERT: D 345 ASP cc_start: 0.7831 (t0) cc_final: 0.7153 (t0) REVERT: E 311 LYS cc_start: 0.7473 (ttpt) cc_final: 0.6928 (tmtt) REVERT: E 345 ASP cc_start: 0.7954 (t0) cc_final: 0.7423 (m-30) REVERT: E 349 ARG cc_start: 0.7529 (mtt-85) cc_final: 0.7197 (mtt90) REVERT: A 311 LYS cc_start: 0.8080 (ttpt) cc_final: 0.7426 (tmtt) REVERT: B 311 LYS cc_start: 0.7732 (ttpt) cc_final: 0.6648 (tppt) REVERT: B 345 ASP cc_start: 0.7779 (t0) cc_final: 0.7263 (t0) REVERT: B 349 ARG cc_start: 0.7858 (mtt-85) cc_final: 0.7510 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 43 average time/residue: 0.3475 time to fit residues: 16.8217 Evaluate side-chains 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.395 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 35 optimal weight: 0.9990 chunk 37 optimal weight: 0.9980 chunk 24 optimal weight: 9.9990 chunk 39 optimal weight: 6.9990 chunk 18 optimal weight: 5.9990 chunk 27 optimal weight: 9.9990 chunk 41 optimal weight: 1.9990 chunk 38 optimal weight: 8.9990 chunk 33 optimal weight: 9.9990 chunk 3 optimal weight: 0.9980 chunk 25 optimal weight: 5.9990 overall best weight: 2.1986 ------------------------------------------------------------------------------- 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: 0.7673 moved from start: 0.1796 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.017 3522 Z= 0.172 Angle : 0.539 4.230 4710 Z= 0.284 Chirality : 0.049 0.127 528 Planarity : 0.005 0.046 600 Dihedral : 4.606 11.891 468 Min Nonbonded Distance : 2.219 Molprobity Statistics. All-atom Clashscore : 9.20 Ramachandran Plot: Outliers : 0.00 % Allowed : 6.76 % Favored : 93.24 % 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: -4.63 (0.30), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.52 (0.23), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.006 0.002 HIS E 362 PHE 0.016 0.001 PHE E 378 TYR 0.007 0.001 TYR D 310 ARG 0.000 0.000 ARG C 349 *********************** 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: 2 poor density : 41 time to evaluate : 0.426 Fit side-chains REVERT: F 345 ASP cc_start: 0.8064 (t70) cc_final: 0.7821 (t0) REVERT: C 349 ARG cc_start: 0.7766 (mtt90) cc_final: 0.7088 (mmm-85) REVERT: D 311 LYS cc_start: 0.7511 (ttpt) cc_final: 0.6474 (tppt) REVERT: D 345 ASP cc_start: 0.7795 (t0) cc_final: 0.7337 (m-30) REVERT: E 311 LYS cc_start: 0.7568 (ttpt) cc_final: 0.7022 (tmtt) REVERT: E 345 ASP cc_start: 0.8012 (t0) cc_final: 0.7411 (m-30) REVERT: E 349 ARG cc_start: 0.7531 (mtt-85) cc_final: 0.7176 (mtt90) REVERT: A 311 LYS cc_start: 0.8065 (ttpt) cc_final: 0.7446 (tmtt) REVERT: A 345 ASP cc_start: 0.8144 (t0) cc_final: 0.7805 (t0) REVERT: B 311 LYS cc_start: 0.7748 (ttpt) cc_final: 0.6661 (tppt) REVERT: B 345 ASP cc_start: 0.7755 (t0) cc_final: 0.7215 (t0) REVERT: B 349 ARG cc_start: 0.7865 (mtt-85) cc_final: 0.7465 (mmm-85) outliers start: 2 outliers final: 2 residues processed: 42 average time/residue: 0.3454 time to fit residues: 16.3498 Evaluate side-chains 43 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 2 poor density : 41 time to evaluate : 0.399 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 20 optimal weight: 5.9990 chunk 26 optimal weight: 10.0000 chunk 35 optimal weight: 10.0000 chunk 10 optimal weight: 6.9990 chunk 30 optimal weight: 7.9990 chunk 4 optimal weight: 10.0000 chunk 9 optimal weight: 3.9990 chunk 33 optimal weight: 2.9990 chunk 13 optimal weight: 0.8980 chunk 34 optimal weight: 9.9990 chunk 6 optimal weight: 4.9990 overall best weight: 3.7788 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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: 0.7699 moved from start: 0.1762 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.020 3522 Z= 0.269 Angle : 0.587 4.077 4710 Z= 0.313 Chirality : 0.050 0.123 528 Planarity : 0.005 0.055 600 Dihedral : 4.886 12.133 468 Min Nonbonded Distance : 2.189 Molprobity Statistics. All-atom Clashscore : 10.19 Ramachandran Plot: Outliers : 0.00 % Allowed : 8.78 % Favored : 91.22 % Rotamer: Outliers : 0.76 % Allowed : 16.92 % 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: -4.65 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.54 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS B 362 PHE 0.017 0.002 PHE F 378 TYR 0.008 0.002 TYR D 310 ARG 0.001 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 49 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 46 time to evaluate : 0.441 Fit side-chains REVERT: F 321 LYS cc_start: 0.6966 (mttt) cc_final: 0.6206 (ttpt) REVERT: F 345 ASP cc_start: 0.8097 (t70) cc_final: 0.7485 (t0) REVERT: D 345 ASP cc_start: 0.7894 (t0) cc_final: 0.7403 (m-30) REVERT: E 345 ASP cc_start: 0.7994 (t0) cc_final: 0.7579 (m-30) REVERT: E 347 LYS cc_start: 0.7868 (tppt) cc_final: 0.7563 (tppt) REVERT: E 349 ARG cc_start: 0.7571 (mtt-85) cc_final: 0.7234 (mtt90) REVERT: A 311 LYS cc_start: 0.8072 (ttpt) cc_final: 0.7464 (tmtt) REVERT: A 345 ASP cc_start: 0.8143 (t0) cc_final: 0.7819 (m-30) REVERT: B 345 ASP cc_start: 0.7819 (t0) cc_final: 0.7321 (t0) REVERT: B 349 ARG cc_start: 0.7900 (mtt-85) cc_final: 0.7567 (mmm-85) outliers start: 3 outliers final: 3 residues processed: 47 average time/residue: 0.3229 time to fit residues: 17.1495 Evaluate side-chains 47 residues out of total 396 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 44 time to evaluate : 0.401 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain F residue 358 ASP Chi-restraints excluded: chain C residue 358 ASP Chi-restraints excluded: chain E residue 358 ASP Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 42 random chunks: chunk 29 optimal weight: 9.9990 chunk 1 optimal weight: 10.0000 chunk 24 optimal weight: 10.0000 chunk 38 optimal weight: 5.9990 chunk 22 optimal weight: 8.9990 chunk 28 optimal weight: 9.9990 chunk 26 optimal weight: 2.9990 chunk 25 optimal weight: 5.9990 chunk 16 optimal weight: 5.9990 chunk 15 optimal weight: 7.9990 chunk 41 optimal weight: 6.9990 overall best weight: 5.5990 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: ** 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 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.4663 r_free = 0.4663 target = 0.250131 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 71)----------------| | r_work = 0.4865 r_free = 0.4865 target = 0.192236 restraints weight = 3948.869| |-----------------------------------------------------------------------------| r_work (start): 0.3897 rms_B_bonded: 0.96 r_work: 0.3812 rms_B_bonded: 1.07 restraints_weight: 0.5000 r_work: 0.3735 rms_B_bonded: 1.73 restraints_weight: 0.2500 r_work: 0.3491 rms_B_bonded: 4.66 restraints_weight: 0.1250 r_work (final): 0.3491 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8122 moved from start: 0.1743 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.006 0.030 3522 Z= 0.390 Angle : 0.658 4.349 4710 Z= 0.355 Chirality : 0.052 0.125 528 Planarity : 0.006 0.055 600 Dihedral : 5.352 12.464 468 Min Nonbonded Distance : 2.167 Molprobity Statistics. All-atom Clashscore : 10.89 Ramachandran Plot: Outliers : 0.00 % Allowed : 14.86 % Favored : 85.14 % Rotamer: Outliers : 0.76 % Allowed : 17.17 % 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: -4.76 (0.31), residues: 444 helix: None (None), residues: 0 sheet: None (None), residues: 0 loop : -3.62 (0.24), residues: 444 Max deviation from planes: Type MaxDev MeanDev LineInFile HIS 0.005 0.001 HIS D 362 PHE 0.018 0.003 PHE F 378 TYR 0.011 0.002 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: 1251.55 seconds wall clock time: 23 minutes 31.16 seconds (1411.16 seconds total)