Starting phenix.real_space_refine on Tue Feb 13 12:16:57 2024 by dcliebschner =============================================================================== Processing files: ------------------------------------------------------------------------------- Found model, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4l_25679/02_2024/7t4l_25679_updated.pdb Found real_map, /net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4l_25679/02_2024/7t4l_25679.map Processing PHIL parameters: ------------------------------------------------------------------------------- Adding command-line PHIL: ------------------------- refinement.macro_cycles=10 scattering_table=electron resolution=3.28 write_initial_geo_file=False Final processed PHIL parameters: ------------------------------------------------------------------------------- data_manager { real_map_files = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4l_25679/02_2024/7t4l_25679.map" default_real_map = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4l_25679/02_2024/7t4l_25679.map" model { file = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4l_25679/02_2024/7t4l_25679_updated.pdb" } default_model = "/net/marbles/raid1/dorothee/rerefine/cryoem/data_no_H/7t4l_25679/02_2024/7t4l_25679_updated.pdb" } resolution = 3.28 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= 0.009 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: 5 Type Number sf(0) Gaussians P 2 5.49 5 S 40 5.16 5 C 3873 2.51 5 N 1022 2.21 5 O 1125 1.98 5 sf(0) = scattering factor at diffraction angle 0. Process input model Symmetric amino acids flipped Residue "A GLU 158": "OE1" <-> "OE2" Residue "A ASP 160": "OD1" <-> "OD2" Residue "A GLU 163": "OE1" <-> "OE2" Residue "A GLU 201": "OE1" <-> "OE2" Residue "A GLU 214": "OE1" <-> "OE2" Residue "A ASP 343": "OD1" <-> "OD2" Residue "A ASP 357": "OD1" <-> "OD2" Residue "A GLU 492": "OE1" <-> "OE2" Residue "A GLU 547": "OE1" <-> "OE2" Residue "B ASP 334": "OD1" <-> "OD2" Residue "B PHE 399": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 445": "OE1" <-> "OE2" Residue "B TYR 546": "CD1" <-> "CD2" "CE1" <-> "CE2" Residue "B GLU 570": "OE1" <-> "OE2" Time to flip residues: 0.02s Monomer Library directory: "/net/cci-filer2/raid1/xp/phenix/phenix-dev-5238/modules/chem_data/mon_lib" Total number of atoms: 6062 Number of models: 1 Model: "" Number of chains: 2 Chain: "A" Number of atoms: 3042 Number of conformers: 1 Conformer: "" Number of residues, atoms: 378, 3042 Classifications: {'peptide': 378} Incomplete info: {'truncation_to_alanine': 3} Link IDs: {'PTRANS': 17, 'TRANS': 360} Chain breaks: 5 Unresolved non-hydrogen bonds: 17 Unresolved non-hydrogen angles: 22 Unresolved non-hydrogen dihedrals: 15 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 1, 'ARG:plan': 1} Unresolved non-hydrogen planarities: 12 Chain: "B" Number of atoms: 3020 Number of conformers: 1 Conformer: "" Number of residues, atoms: 377, 3020 Classifications: {'peptide': 377} Incomplete info: {'truncation_to_alanine': 6} Link IDs: {'PTRANS': 18, 'TRANS': 358} Chain breaks: 5 Unresolved non-hydrogen bonds: 31 Unresolved non-hydrogen angles: 39 Unresolved non-hydrogen dihedrals: 29 Unresolved non-hydrogen chiralities: 1 Planarities with less than four sites: {'TYR:plan': 2, 'GLU:plan': 1} Unresolved non-hydrogen planarities: 18 Time building chain proxies: 3.72, per 1000 atoms: 0.61 Number of scatterers: 6062 At special positions: 0 Unit cell: (116.22, 77.22, 75.66, 90, 90, 90) Space group: P 1 (No. 1) Number of sites at special positions: 0 Number of scattering types: 5 Type Number sf(0) S 40 16.00 P 2 15.00 O 1125 8.00 N 1022 7.00 C 3873 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: 2.15 Conformation dependent library (CDL) restraints added in 1.2 seconds 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. Adding C-beta torsion restraints... Number of C-beta restraints generated: 1466 Finding SS restraints... running ksdssp... Secondary structure from input PDB file: 27 helices and 7 sheets defined 39.1% alpha, 10.3% beta 0 base pairs and 0 stacking pairs defined. Time for finding SS restraints: 1.48 Creating SS restraints... Processing helix chain 'A' and resid 120 through 135 Processing helix chain 'A' and resid 204 through 214 Processing helix chain 'A' and resid 297 through 303 Processing helix chain 'A' and resid 308 through 327 Processing helix chain 'A' and resid 389 through 392 No H-bonds generated for 'chain 'A' and resid 389 through 392' Processing helix chain 'A' and resid 407 through 419 removed outlier: 3.883A pdb=" N TYR A 417 " --> pdb=" O GLY A 413 " (cutoff:3.500A) removed outlier: 4.162A pdb=" N GLU A 418 " --> pdb=" O ALA A 414 " (cutoff:3.500A) Processing helix chain 'A' and resid 452 through 461 Processing helix chain 'A' and resid 472 through 484 Processing helix chain 'A' and resid 487 through 490 No H-bonds generated for 'chain 'A' and resid 487 through 490' Processing helix chain 'A' and resid 499 through 510 Processing helix chain 'A' and resid 543 through 555 Processing helix chain 'A' and resid 558 through 573 removed outlier: 3.610A pdb=" N HIS A 572 " --> pdb=" O ILE A 568 " (cutoff:3.500A) Processing helix chain 'B' and resid 121 through 136 removed outlier: 4.292A pdb=" N GLY B 126 " --> pdb=" O ASP B 122 " (cutoff:3.500A) removed outlier: 4.988A pdb=" N ILE B 127 " --> pdb=" O GLU B 123 " (cutoff:3.500A) Processing helix chain 'B' and resid 204 through 217 removed outlier: 4.257A pdb=" N VAL B 216 " --> pdb=" O TYR B 212 " (cutoff:3.500A) Proline residue: B 217 - end of helix Processing helix chain 'B' and resid 297 through 303 Processing helix chain 'B' and resid 308 through 327 Processing helix chain 'B' and resid 358 through 360 No H-bonds generated for 'chain 'B' and resid 358 through 360' Processing helix chain 'B' and resid 389 through 392 No H-bonds generated for 'chain 'B' and resid 389 through 392' Processing helix chain 'B' and resid 407 through 419 removed outlier: 3.692A pdb=" N TYR B 417 " --> pdb=" O GLY B 413 " (cutoff:3.500A) removed outlier: 4.170A pdb=" N GLU B 418 " --> pdb=" O ALA B 414 " (cutoff:3.500A) Processing helix chain 'B' and resid 425 through 427 No H-bonds generated for 'chain 'B' and resid 425 through 427' Processing helix chain 'B' and resid 440 through 442 No H-bonds generated for 'chain 'B' and resid 440 through 442' Processing helix chain 'B' and resid 452 through 461 Processing helix chain 'B' and resid 472 through 484 Processing helix chain 'B' and resid 487 through 490 No H-bonds generated for 'chain 'B' and resid 487 through 490' Processing helix chain 'B' and resid 499 through 515 Processing helix chain 'B' and resid 543 through 555 removed outlier: 3.790A pdb=" N ARG B 555 " --> pdb=" O SER B 551 " (cutoff:3.500A) Processing helix chain 'B' and resid 558 through 573 removed outlier: 3.524A pdb=" N HIS B 572 " --> pdb=" O ILE B 568 " (cutoff:3.500A) Processing sheet with id= A, first strand: chain 'A' and resid 171 through 177 removed outlier: 3.895A pdb=" N SER A 251 " --> pdb=" O VAL A 289 " (cutoff:3.500A) removed outlier: 7.256A pdb=" N LYS A 291 " --> pdb=" O MET A 249 " (cutoff:3.500A) removed outlier: 7.350A pdb=" N MET A 249 " --> pdb=" O LYS A 291 " (cutoff:3.500A) Processing sheet with id= B, first strand: chain 'A' and resid 340 through 343 Processing sheet with id= C, first strand: chain 'A' and resid 370 through 372 Processing sheet with id= D, first strand: chain 'B' and resid 159 through 161 removed outlier: 3.915A pdb=" N SER B 251 " --> pdb=" O VAL B 289 " (cutoff:3.500A) removed outlier: 7.375A pdb=" N LYS B 291 " --> pdb=" O MET B 249 " (cutoff:3.500A) removed outlier: 7.510A pdb=" N MET B 249 " --> pdb=" O LYS B 291 " (cutoff:3.500A) Processing sheet with id= E, first strand: chain 'B' and resid 164 through 166 Processing sheet with id= F, first strand: chain 'B' and resid 340 through 343 Processing sheet with id= G, first strand: chain 'B' and resid 370 through 372 229 hydrogen bonds defined for protein. 678 hydrogen bond angles defined for protein. Restraints generated for nucleic acids: 0 hydrogen bonds 0 hydrogen bond angles 0 basepair planarities 0 basepair parallelities 0 stacking parallelities Total time for adding SS restraints: 1.60 Time building geometry restraints manager: 2.32 seconds NOTE: a complete listing of the restraints can be obtained by requesting output of .geo file. Histogram of bond lengths: 1.22 - 1.34: 1845 1.34 - 1.46: 1246 1.46 - 1.58: 3020 1.58 - 1.70: 8 1.70 - 1.83: 63 Bond restraints: 6182 Sorted by residual: bond pdb=" C VAL B 216 " pdb=" N PRO B 217 " ideal model delta sigma weight residual 1.334 1.385 -0.051 2.34e-02 1.83e+03 4.76e+00 bond pdb=" C LEU A 543 " pdb=" N PRO A 544 " ideal model delta sigma weight residual 1.334 1.362 -0.028 1.51e-02 4.39e+03 3.50e+00 bond pdb=" CB VAL A 354 " pdb=" CG1 VAL A 354 " ideal model delta sigma weight residual 1.521 1.468 0.053 3.30e-02 9.18e+02 2.56e+00 bond pdb=" C LEU B 543 " pdb=" N PRO B 544 " ideal model delta sigma weight residual 1.334 1.358 -0.024 1.51e-02 4.39e+03 2.55e+00 bond pdb=" CB PRO A 217 " pdb=" CG PRO A 217 " ideal model delta sigma weight residual 1.492 1.415 0.077 5.00e-02 4.00e+02 2.35e+00 ... (remaining 6177 not shown) Histogram of bond angle deviations from ideal: 98.67 - 105.86: 154 105.86 - 113.06: 3356 113.06 - 120.26: 2217 120.26 - 127.46: 2572 127.46 - 134.66: 71 Bond angle restraints: 8370 Sorted by residual: angle pdb=" C GLU A 163 " pdb=" N PRO A 164 " pdb=" CD PRO A 164 " ideal model delta sigma weight residual 125.00 106.50 18.50 4.10e+00 5.95e-02 2.04e+01 angle pdb=" CA LEU A 344 " pdb=" CB LEU A 344 " pdb=" CG LEU A 344 " ideal model delta sigma weight residual 116.30 130.79 -14.49 3.50e+00 8.16e-02 1.71e+01 angle pdb=" CA PRO A 164 " pdb=" N PRO A 164 " pdb=" CD PRO A 164 " ideal model delta sigma weight residual 112.00 106.83 5.17 1.40e+00 5.10e-01 1.37e+01 angle pdb=" N MET B 211 " pdb=" CA MET B 211 " pdb=" CB MET B 211 " ideal model delta sigma weight residual 110.07 115.32 -5.25 1.45e+00 4.76e-01 1.31e+01 angle pdb=" CB GLU B 570 " pdb=" CG GLU B 570 " pdb=" CD GLU B 570 " ideal model delta sigma weight residual 112.60 118.61 -6.01 1.70e+00 3.46e-01 1.25e+01 ... (remaining 8365 not shown) Histogram of dihedral angle deviations from ideal: 0.00 - 15.87: 3371 15.87 - 31.74: 312 31.74 - 47.61: 74 47.61 - 63.48: 17 63.48 - 79.35: 6 Dihedral angle restraints: 3780 sinusoidal: 1540 harmonic: 2240 Sorted by residual: dihedral pdb=" C VAL B 216 " pdb=" N VAL B 216 " pdb=" CA VAL B 216 " pdb=" CB VAL B 216 " ideal model delta harmonic sigma weight residual -122.00 -130.37 8.37 0 2.50e+00 1.60e-01 1.12e+01 dihedral pdb=" N SEP A 202 " pdb=" CA SEP A 202 " pdb=" CB SEP A 202 " pdb=" OG SEP A 202 " ideal model delta sinusoidal sigma weight residual -60.00 -5.69 -54.31 3 1.50e+01 4.44e-03 9.27e+00 dihedral pdb=" CG ARG B 469 " pdb=" CD ARG B 469 " pdb=" NE ARG B 469 " pdb=" CZ ARG B 469 " ideal model delta sinusoidal sigma weight residual 180.00 139.20 40.80 2 1.50e+01 4.44e-03 9.11e+00 ... (remaining 3777 not shown) Histogram of chiral volume deviations from ideal: 0.000 - 0.044: 630 0.044 - 0.088: 214 0.088 - 0.132: 80 0.132 - 0.176: 18 0.176 - 0.220: 5 Chirality restraints: 947 Sorted by residual: chirality pdb=" CG LEU A 558 " pdb=" CB LEU A 558 " pdb=" CD1 LEU A 558 " pdb=" CD2 LEU A 558 " both_signs ideal model delta sigma weight residual False -2.59 -2.37 -0.22 2.00e-01 2.50e+01 1.21e+00 chirality pdb=" CA VAL B 216 " pdb=" N VAL B 216 " pdb=" C VAL B 216 " pdb=" CB VAL B 216 " both_signs ideal model delta sigma weight residual False 2.44 2.23 0.21 2.00e-01 2.50e+01 1.11e+00 chirality pdb=" CA ILE A 450 " pdb=" N ILE A 450 " pdb=" C ILE A 450 " pdb=" CB ILE A 450 " both_signs ideal model delta sigma weight residual False 2.43 2.63 -0.20 2.00e-01 2.50e+01 9.96e-01 ... (remaining 944 not shown) Planarity restraints: 1056 Sorted by residual: delta sigma weight rms_deltas residual plane pdb=" C GLU A 163 " -0.122 5.00e-02 4.00e+02 1.85e-01 5.50e+01 pdb=" N PRO A 164 " 0.321 5.00e-02 4.00e+02 pdb=" CA PRO A 164 " -0.109 5.00e-02 4.00e+02 pdb=" CD PRO A 164 " -0.089 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" C LYS B 395 " 0.055 5.00e-02 4.00e+02 8.40e-02 1.13e+01 pdb=" N PRO B 396 " -0.145 5.00e-02 4.00e+02 pdb=" CA PRO B 396 " 0.044 5.00e-02 4.00e+02 pdb=" CD PRO B 396 " 0.046 5.00e-02 4.00e+02 delta sigma weight rms_deltas residual plane pdb=" CB TYR A 373 " 0.020 2.00e-02 2.50e+03 1.74e-02 6.07e+00 pdb=" CG TYR A 373 " -0.043 2.00e-02 2.50e+03 pdb=" CD1 TYR A 373 " 0.009 2.00e-02 2.50e+03 pdb=" CD2 TYR A 373 " 0.001 2.00e-02 2.50e+03 pdb=" CE1 TYR A 373 " 0.002 2.00e-02 2.50e+03 pdb=" CE2 TYR A 373 " 0.010 2.00e-02 2.50e+03 pdb=" CZ TYR A 373 " 0.004 2.00e-02 2.50e+03 pdb=" OH TYR A 373 " -0.003 2.00e-02 2.50e+03 ... (remaining 1053 not shown) Histogram of nonbonded interaction distances: 2.27 - 2.80: 1292 2.80 - 3.32: 5716 3.32 - 3.85: 9839 3.85 - 4.37: 11579 4.37 - 4.90: 19840 Nonbonded interactions: 48266 Sorted by model distance: nonbonded pdb=" O THR A 215 " pdb=" OH TYR A 221 " model vdw 2.269 2.440 nonbonded pdb=" OD2 ASP B 428 " pdb=" OG1 THR B 430 " model vdw 2.310 2.440 nonbonded pdb=" OH TYR A 438 " pdb=" O LEU A 462 " model vdw 2.315 2.440 nonbonded pdb=" O TYR A 198 " pdb=" OG SER A 204 " model vdw 2.334 2.440 nonbonded pdb=" OH TYR B 438 " pdb=" O LEU B 462 " model vdw 2.345 2.440 ... (remaining 48261 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' and ((resid 120 and (name N or name CA or name C or name O or name CB \ )) or resid 121 through 178 or (resid 179 and (name N or name CA or name C or n \ ame O or name CB )) or resid 188 through 223 or resid 236 through 256 or resid 2 \ 85 through 493 or (resid 494 and (name N or name CA or name C or name O or name \ CB )) or resid 495 through 574)) selection = (chain 'B' and (resid 120 through 136 or resid 148 through 256 or resid 285 thro \ ugh 511 or resid 541 through 574)) } 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: 6.210 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: 16.570 Check model and map are aligned: 0.090 Set scattering table: 0.050 Process input model: 20.510 Find NCS groups from input model: 0.380 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: 0.010 Load rotamer database and sin/cos tables:2.770 Set ADP refinement strategy: 0.000 Make a string to write initial .geo file:0.000 Internal consistency checks: 0.000 Total: 46.630 ------------------------------------------------------------------------------- Set refinement monitor ********************** ------------------------------------------------------------------------------- Setup refinement engine *********************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7737 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 : 0.005 0.077 6182 Z= 0.322 Angle : 0.948 18.498 8370 Z= 0.506 Chirality : 0.053 0.220 947 Planarity : 0.009 0.185 1056 Dihedral : 13.459 79.353 2314 Min Nonbonded Distance : 2.269 Molprobity Statistics. All-atom Clashscore : 5.36 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 0.00 % Allowed : 1.94 % Favored : 98.06 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.35 (0.30), residues: 725 helix: 2.77 (0.30), residues: 303 sheet: -0.42 (0.46), residues: 111 loop : -0.49 (0.31), residues: 311 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.022 0.002 TRP A 505 HIS 0.007 0.002 HIS A 243 PHE 0.023 0.003 PHE B 399 TYR 0.043 0.003 TYR A 373 ARG 0.007 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 1 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 105 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 105 time to evaluate : 0.755 Fit side-chains REVERT: A 377 ASP cc_start: 0.8323 (m-30) cc_final: 0.8042 (t0) REVERT: A 504 GLN cc_start: 0.8248 (tm-30) cc_final: 0.8018 (tm-30) REVERT: B 350 TYR cc_start: 0.7914 (m-80) cc_final: 0.7621 (m-10) REVERT: B 547 GLU cc_start: 0.7717 (tp30) cc_final: 0.7476 (mt-10) outliers start: 0 outliers final: 0 residues processed: 105 average time/residue: 0.1475 time to fit residues: 21.6519 Evaluate side-chains 75 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 0 poor density : 75 time to evaluate : 0.660 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Rotamers are restrained with sigma=5.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 0.0070 chunk 56 optimal weight: 0.9980 chunk 31 optimal weight: 0.5980 chunk 19 optimal weight: 0.7980 chunk 37 optimal weight: 0.0470 chunk 29 optimal weight: 0.5980 chunk 58 optimal weight: 0.3980 chunk 22 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 43 optimal weight: 0.0050 chunk 67 optimal weight: 0.5980 overall best weight: 0.2110 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 326 ASN Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7759 moved from start: 0.1050 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.028 6182 Z= 0.146 Angle : 0.504 6.923 8370 Z= 0.253 Chirality : 0.039 0.173 947 Planarity : 0.005 0.102 1056 Dihedral : 5.116 82.101 818 Min Nonbonded Distance : 2.210 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 1.24 % Favored : 98.76 % Rotamer: Outliers : 0.90 % Allowed : 7.31 % Favored : 91.79 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.88 (0.31), residues: 725 helix: 2.95 (0.29), residues: 306 sheet: -0.28 (0.46), residues: 110 loop : 0.13 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.011 0.001 TRP A 505 HIS 0.003 0.001 HIS A 243 PHE 0.017 0.001 PHE A 253 TYR 0.013 0.001 TYR A 373 ARG 0.001 0.000 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 2 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 92 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 6 poor density : 86 time to evaluate : 0.738 Fit side-chains REVERT: A 377 ASP cc_start: 0.8319 (m-30) cc_final: 0.8028 (t0) REVERT: B 376 GLU cc_start: 0.7150 (mp0) cc_final: 0.6716 (mp0) REVERT: B 547 GLU cc_start: 0.7677 (tp30) cc_final: 0.7453 (mt-10) outliers start: 6 outliers final: 3 residues processed: 88 average time/residue: 0.1545 time to fit residues: 18.9769 Evaluate side-chains 78 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 3 poor density : 75 time to evaluate : 0.713 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 305 THR Rotamers are restrained with sigma=4.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 37 optimal weight: 0.9980 chunk 20 optimal weight: 0.9980 chunk 55 optimal weight: 0.9980 chunk 45 optimal weight: 0.9990 chunk 18 optimal weight: 0.5980 chunk 67 optimal weight: 0.9990 chunk 72 optimal weight: 0.9980 chunk 59 optimal weight: 0.7980 chunk 66 optimal weight: 1.9990 chunk 22 optimal weight: 0.6980 chunk 54 optimal weight: 2.9990 overall best weight: 0.8180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 326 ASN B 189 GLN Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7917 moved from start: 0.1825 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.005 0.042 6182 Z= 0.340 Angle : 0.568 7.086 8370 Z= 0.286 Chirality : 0.042 0.161 947 Planarity : 0.005 0.069 1056 Dihedral : 5.112 83.343 818 Min Nonbonded Distance : 2.159 Molprobity Statistics. All-atom Clashscore : 7.01 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.64 % Allowed : 8.96 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.31), residues: 725 helix: 2.49 (0.29), residues: 304 sheet: -0.33 (0.46), residues: 112 loop : 0.34 (0.34), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.013 0.001 TRP A 505 HIS 0.005 0.001 HIS A 559 PHE 0.016 0.002 PHE B 452 TYR 0.026 0.002 TYR A 373 ARG 0.004 0.001 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 3 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 82 time to evaluate : 0.724 Fit side-chains REVERT: A 189 GLN cc_start: 0.7537 (pt0) cc_final: 0.7331 (pp30) REVERT: A 383 ASN cc_start: 0.8161 (m110) cc_final: 0.7641 (p0) REVERT: B 213 ARG cc_start: 0.7095 (OUTLIER) cc_final: 0.6488 (ttp80) REVERT: B 547 GLU cc_start: 0.7720 (tp30) cc_final: 0.7498 (mt-10) outliers start: 11 outliers final: 7 residues processed: 88 average time/residue: 0.1687 time to fit residues: 20.1973 Evaluate side-chains 83 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 8 poor density : 75 time to evaluate : 0.784 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=4.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 66 optimal weight: 0.8980 chunk 50 optimal weight: 0.7980 chunk 34 optimal weight: 2.9990 chunk 7 optimal weight: 2.9990 chunk 32 optimal weight: 1.9990 chunk 45 optimal weight: 0.8980 chunk 67 optimal weight: 0.0980 chunk 71 optimal weight: 0.9990 chunk 35 optimal weight: 0.5980 chunk 64 optimal weight: 0.6980 chunk 19 optimal weight: 0.6980 overall best weight: 0.5780 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 326 ASN ** A 572 HIS ** both conformations clash, **PLEASE CHECK MANUALLY** Total number of N/Q/H flips: 2 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7909 moved from start: 0.2079 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.038 6182 Z= 0.241 Angle : 0.491 6.939 8370 Z= 0.248 Chirality : 0.040 0.163 947 Planarity : 0.004 0.055 1056 Dihedral : 4.992 82.632 818 Min Nonbonded Distance : 2.192 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.21 % Favored : 97.79 % Rotamer: Outliers : 1.79 % Allowed : 8.51 % Favored : 89.70 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.31), residues: 725 helix: 2.55 (0.29), residues: 304 sheet: -0.36 (0.46), residues: 112 loop : 0.37 (0.35), residues: 309 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 505 HIS 0.003 0.001 HIS A 559 PHE 0.011 0.001 PHE A 253 TYR 0.016 0.001 TYR A 373 ARG 0.002 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 4 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 79 time to evaluate : 0.689 Fit side-chains REVERT: A 377 ASP cc_start: 0.8347 (m-30) cc_final: 0.8011 (m-30) REVERT: A 383 ASN cc_start: 0.8160 (m110) cc_final: 0.7674 (p0) REVERT: B 213 ARG cc_start: 0.7008 (OUTLIER) cc_final: 0.6361 (ttp80) REVERT: B 547 GLU cc_start: 0.7700 (tp30) cc_final: 0.7472 (mt-10) outliers start: 12 outliers final: 10 residues processed: 86 average time/residue: 0.1521 time to fit residues: 18.1655 Evaluate side-chains 84 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 73 time to evaluate : 0.720 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=3.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 59 optimal weight: 0.4980 chunk 40 optimal weight: 0.4980 chunk 1 optimal weight: 0.0870 chunk 53 optimal weight: 1.9990 chunk 29 optimal weight: 0.0970 chunk 61 optimal weight: 0.7980 chunk 49 optimal weight: 0.6980 chunk 0 optimal weight: 2.9990 chunk 36 optimal weight: 0.0980 chunk 64 optimal weight: 0.3980 chunk 18 optimal weight: 0.9990 overall best weight: 0.2356 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 328 HIS A 572 HIS B 189 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7875 moved from start: 0.2147 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.029 6182 Z= 0.145 Angle : 0.465 7.691 8370 Z= 0.232 Chirality : 0.038 0.157 947 Planarity : 0.004 0.047 1056 Dihedral : 4.861 81.839 818 Min Nonbonded Distance : 2.211 Molprobity Statistics. All-atom Clashscore : 6.52 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 1.64 % Allowed : 8.96 % Favored : 89.40 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.84 (0.31), residues: 725 helix: 2.71 (0.28), residues: 305 sheet: -0.25 (0.48), residues: 105 loop : 0.33 (0.34), residues: 315 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.003 0.001 HIS B 332 PHE 0.013 0.001 PHE A 253 TYR 0.010 0.001 TYR B 482 ARG 0.002 0.000 ARG B 239 *********************** REFINEMENT MACRO_CYCLE 5 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 86 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 11 poor density : 75 time to evaluate : 0.721 Fit side-chains REVERT: A 377 ASP cc_start: 0.8351 (m-30) cc_final: 0.8038 (m-30) REVERT: A 383 ASN cc_start: 0.8089 (m110) cc_final: 0.7646 (p0) REVERT: A 504 GLN cc_start: 0.8295 (tm-30) cc_final: 0.7804 (tm-30) REVERT: B 213 ARG cc_start: 0.6933 (OUTLIER) cc_final: 0.6334 (ttp80) REVERT: B 293 TYR cc_start: 0.8434 (m-80) cc_final: 0.8110 (m-80) REVERT: B 547 GLU cc_start: 0.7642 (tp30) cc_final: 0.7422 (mt-10) outliers start: 11 outliers final: 9 residues processed: 80 average time/residue: 0.1608 time to fit residues: 17.8956 Evaluate side-chains 83 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 10 poor density : 73 time to evaluate : 0.731 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 189 GLN Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=3.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 24 optimal weight: 0.9990 chunk 64 optimal weight: 0.9990 chunk 14 optimal weight: 0.9980 chunk 41 optimal weight: 4.9990 chunk 17 optimal weight: 0.8980 chunk 71 optimal weight: 1.9990 chunk 59 optimal weight: 0.9980 chunk 33 optimal weight: 0.6980 chunk 5 optimal weight: 0.9980 chunk 23 optimal weight: 0.0470 chunk 37 optimal weight: 0.7980 overall best weight: 0.6878 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7941 moved from start: 0.2462 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.048 6182 Z= 0.282 Angle : 0.511 6.979 8370 Z= 0.256 Chirality : 0.040 0.157 947 Planarity : 0.004 0.043 1056 Dihedral : 4.922 81.044 818 Min Nonbonded Distance : 2.195 Molprobity Statistics. All-atom Clashscore : 7.34 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.24 % Allowed : 9.40 % Favored : 88.36 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.31), residues: 725 helix: 2.46 (0.29), residues: 306 sheet: -0.38 (0.47), residues: 112 loop : 0.39 (0.35), residues: 307 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.004 0.001 HIS A 559 PHE 0.013 0.001 PHE B 452 TYR 0.014 0.001 TYR A 373 ARG 0.003 0.000 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 6 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 90 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 75 time to evaluate : 0.734 Fit side-chains REVERT: A 377 ASP cc_start: 0.8383 (m-30) cc_final: 0.8120 (m-30) REVERT: A 383 ASN cc_start: 0.8188 (m110) cc_final: 0.7729 (p0) REVERT: A 504 GLN cc_start: 0.8313 (tm-30) cc_final: 0.7805 (tm-30) REVERT: B 213 ARG cc_start: 0.6945 (OUTLIER) cc_final: 0.6384 (ttp80) REVERT: B 547 GLU cc_start: 0.7702 (tp30) cc_final: 0.7451 (mt-10) outliers start: 15 outliers final: 11 residues processed: 85 average time/residue: 0.1525 time to fit residues: 18.1557 Evaluate side-chains 85 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 73 time to evaluate : 0.696 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=2.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 69 optimal weight: 0.7980 chunk 8 optimal weight: 1.9990 chunk 40 optimal weight: 0.0570 chunk 52 optimal weight: 0.6980 chunk 60 optimal weight: 0.9990 chunk 39 optimal weight: 2.9990 chunk 71 optimal weight: 1.9990 chunk 44 optimal weight: 0.7980 chunk 43 optimal weight: 8.9990 chunk 32 optimal weight: 1.9990 chunk 28 optimal weight: 0.9980 overall best weight: 0.6698 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN A 378 GLN A 572 HIS Total number of N/Q/H flips: 3 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7946 moved from start: 0.2622 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.004 0.040 6182 Z= 0.273 Angle : 0.509 6.881 8370 Z= 0.254 Chirality : 0.040 0.174 947 Planarity : 0.004 0.039 1056 Dihedral : 4.919 80.241 818 Min Nonbonded Distance : 2.197 Molprobity Statistics. All-atom Clashscore : 7.10 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.84 % Allowed : 10.30 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.60 (0.31), residues: 725 helix: 2.41 (0.29), residues: 304 sheet: -0.42 (0.48), residues: 105 loop : 0.35 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.008 0.001 TRP A 401 HIS 0.004 0.001 HIS A 559 PHE 0.011 0.001 PHE B 452 TYR 0.018 0.001 TYR A 494 ARG 0.004 0.000 ARG B 455 *********************** REFINEMENT MACRO_CYCLE 7 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 19 poor density : 72 time to evaluate : 0.766 Fit side-chains REVERT: A 377 ASP cc_start: 0.8351 (m-30) cc_final: 0.8116 (m-30) REVERT: A 383 ASN cc_start: 0.8232 (m110) cc_final: 0.7836 (p0) REVERT: A 390 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8052 (pm20) REVERT: B 213 ARG cc_start: 0.6997 (OUTLIER) cc_final: 0.6399 (ttp80) REVERT: B 547 GLU cc_start: 0.7708 (tp30) cc_final: 0.7466 (mt-10) outliers start: 19 outliers final: 14 residues processed: 85 average time/residue: 0.1652 time to fit residues: 19.5099 Evaluate side-chains 88 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 72 time to evaluate : 0.722 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 135 VAL Chi-restraints excluded: chain B residue 213 ARG Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=2.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 42 optimal weight: 0.5980 chunk 21 optimal weight: 0.8980 chunk 14 optimal weight: 0.7980 chunk 13 optimal weight: 0.1980 chunk 45 optimal weight: 0.6980 chunk 48 optimal weight: 0.7980 chunk 35 optimal weight: 0.5980 chunk 6 optimal weight: 2.9990 chunk 56 optimal weight: 0.0040 chunk 64 optimal weight: 0.9980 chunk 68 optimal weight: 0.6980 overall best weight: 0.4192 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 189 GLN A 326 ASN A 378 GLN B 378 GLN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7924 moved from start: 0.2694 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.034 6182 Z= 0.196 Angle : 0.482 6.844 8370 Z= 0.239 Chirality : 0.039 0.163 947 Planarity : 0.004 0.039 1056 Dihedral : 4.790 79.264 818 Min Nonbonded Distance : 2.217 Molprobity Statistics. All-atom Clashscore : 6.68 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.62 % Favored : 97.38 % Rotamer: Outliers : 2.39 % Allowed : 10.90 % Favored : 86.72 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.71 (0.31), residues: 725 helix: 2.58 (0.29), residues: 303 sheet: -0.41 (0.48), residues: 105 loop : 0.36 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.003 0.001 HIS A 559 PHE 0.010 0.001 PHE B 452 TYR 0.019 0.001 TYR A 494 ARG 0.001 0.000 ARG B 248 *********************** REFINEMENT MACRO_CYCLE 8 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 91 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.707 Fit side-chains REVERT: A 383 ASN cc_start: 0.8130 (m110) cc_final: 0.7700 (p0) REVERT: A 390 GLU cc_start: 0.8615 (OUTLIER) cc_final: 0.8029 (pm20) REVERT: A 504 GLN cc_start: 0.8315 (tm-30) cc_final: 0.7877 (tm-30) REVERT: B 547 GLU cc_start: 0.7660 (tp30) cc_final: 0.7390 (mt-10) outliers start: 16 outliers final: 11 residues processed: 84 average time/residue: 0.1544 time to fit residues: 18.1540 Evaluate side-chains 84 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 12 poor density : 72 time to evaluate : 0.706 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.50 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 62 optimal weight: 1.9990 chunk 66 optimal weight: 1.9990 chunk 68 optimal weight: 0.2980 chunk 40 optimal weight: 1.9990 chunk 28 optimal weight: 0.0050 chunk 52 optimal weight: 0.8980 chunk 20 optimal weight: 0.9980 chunk 60 optimal weight: 0.6980 chunk 43 optimal weight: 7.9990 chunk 70 optimal weight: 0.6980 chunk 42 optimal weight: 0.9990 overall best weight: 0.5194 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7939 moved from start: 0.2768 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.038 6182 Z= 0.228 Angle : 0.492 6.755 8370 Z= 0.245 Chirality : 0.039 0.163 947 Planarity : 0.004 0.040 1056 Dihedral : 4.757 78.708 818 Min Nonbonded Distance : 2.205 Molprobity Statistics. All-atom Clashscore : 7.59 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.24 % Allowed : 10.90 % Favored : 86.87 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.66 (0.31), residues: 725 helix: 2.53 (0.29), residues: 303 sheet: -0.45 (0.48), residues: 105 loop : 0.33 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.003 0.001 HIS A 559 PHE 0.010 0.001 PHE B 452 TYR 0.020 0.001 TYR A 494 ARG 0.002 0.000 ARG B 213 *********************** REFINEMENT MACRO_CYCLE 9 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 78 time to evaluate : 0.641 Fit side-chains REVERT: A 338 ASP cc_start: 0.8251 (m-30) cc_final: 0.8026 (m-30) REVERT: A 383 ASN cc_start: 0.8143 (m110) cc_final: 0.7730 (p0) REVERT: A 390 GLU cc_start: 0.8621 (OUTLIER) cc_final: 0.8032 (pm20) REVERT: A 504 GLN cc_start: 0.8316 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 547 GLU cc_start: 0.7690 (tp30) cc_final: 0.7415 (mt-10) outliers start: 15 outliers final: 14 residues processed: 86 average time/residue: 0.1488 time to fit residues: 18.1108 Evaluate side-chains 92 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 15 poor density : 77 time to evaluate : 0.657 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 387 MET Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 33 optimal weight: 0.7980 chunk 48 optimal weight: 0.8980 chunk 73 optimal weight: 0.5980 chunk 67 optimal weight: 0.2980 chunk 58 optimal weight: 0.9980 chunk 6 optimal weight: 1.9990 chunk 45 optimal weight: 0.5980 chunk 35 optimal weight: 0.6980 chunk 46 optimal weight: 0.3980 chunk 62 optimal weight: 0.1980 chunk 17 optimal weight: 0.9980 overall best weight: 0.4180 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 326 ASN Total number of N/Q/H flips: 1 ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.7928 moved from start: 0.2805 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.003 0.035 6182 Z= 0.200 Angle : 0.486 6.776 8370 Z= 0.242 Chirality : 0.039 0.150 947 Planarity : 0.004 0.041 1056 Dihedral : 4.720 78.215 818 Min Nonbonded Distance : 2.214 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.48 % Favored : 97.52 % Rotamer: Outliers : 2.54 % Allowed : 11.34 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.70 (0.31), residues: 725 helix: 2.57 (0.29), residues: 303 sheet: -0.38 (0.48), residues: 105 loop : 0.32 (0.34), residues: 317 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.007 0.001 TRP A 401 HIS 0.002 0.001 HIS A 559 PHE 0.012 0.001 PHE A 253 TYR 0.021 0.001 TYR A 494 ARG 0.002 0.000 ARG B 455 ********************** REFINEMENT MACRO_CYCLE 10 OF 10 ************************ ------------------------------------------------------------------------------- Update Rama plot phi/psi targets (oldfield only) ************************************************ 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Re-set Ramachandran plot restraints *********************************** favored: oldfield allowed: oldfield outlier: oldfield 1450 Ramachandran restraints generated. 725 Oldfield, 0 Emsley, 725 emsley8k and 0 Phi/Psi/2. ------------------------------------------------------------------------------- Optimize residue side-chains **************************** Evaluate side-chains 93 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 17 poor density : 76 time to evaluate : 0.727 Fit side-chains REVERT: A 383 ASN cc_start: 0.8101 (m110) cc_final: 0.7711 (p0) REVERT: A 390 GLU cc_start: 0.8618 (OUTLIER) cc_final: 0.8030 (pm20) REVERT: A 504 GLN cc_start: 0.8318 (tm-30) cc_final: 0.7857 (tm-30) REVERT: B 547 GLU cc_start: 0.7675 (tp30) cc_final: 0.7452 (mt-10) outliers start: 17 outliers final: 15 residues processed: 85 average time/residue: 0.1542 time to fit residues: 18.4198 Evaluate side-chains 91 residues out of total 679 non-(ALA, GLY, PRO) need fitting. rotamer outliers: 16 poor density : 75 time to evaluate : 0.747 ------------------------------------------------------------------------------- Set rotamer restraints ********************** Chi-restraints excluded: chain A residue 195 MET Chi-restraints excluded: chain A residue 216 VAL Chi-restraints excluded: chain A residue 290 MET Chi-restraints excluded: chain A residue 322 VAL Chi-restraints excluded: chain A residue 361 CYS Chi-restraints excluded: chain A residue 379 ASP Chi-restraints excluded: chain A residue 390 GLU Chi-restraints excluded: chain A residue 433 LEU Chi-restraints excluded: chain A residue 473 ASP Chi-restraints excluded: chain A residue 558 LEU Chi-restraints excluded: chain B residue 130 GLU Chi-restraints excluded: chain B residue 216 VAL Chi-restraints excluded: chain B residue 296 THR Chi-restraints excluded: chain B residue 305 THR Chi-restraints excluded: chain B residue 466 THR Chi-restraints excluded: chain B residue 514 LEU Rotamers are restrained with sigma=1.00 ------------------------------------------------------------------------------- XYZ refinement ************** Weight determination summary: number of chunks: 74 random chunks: chunk 54 optimal weight: 0.7980 chunk 8 optimal weight: 0.3980 chunk 16 optimal weight: 1.9990 chunk 58 optimal weight: 0.9990 chunk 24 optimal weight: 0.0980 chunk 60 optimal weight: 0.4980 chunk 7 optimal weight: 0.8980 chunk 10 optimal weight: 0.0170 chunk 51 optimal weight: 0.5980 chunk 3 optimal weight: 0.0770 chunk 42 optimal weight: 3.9990 overall best weight: 0.2176 ------------------------------------------------------------------------------- NQH flips ********* Analyzing N/Q/H residues for possible flip corrections... Flipped N/Q/H residues before XYZ refinement: A 188 HIS A 326 ASN B 189 GLN B 326 ASN Total number of N/Q/H flips: 4 ------------------------------------------------------------------------------- ADP refinement ************** |-group b-factor refinement (macro cycle = 0; iterations = 0)-----------------| | r_work = 0.3741 r_free = 0.3741 target = 0.143325 restraints weight = None | |-----------------------------------------------------------------------------| |-group b-factor refinement (macro cycle = 1; iterations = 36)----------------| | r_work = 0.3361 r_free = 0.3361 target = 0.113137 restraints weight = 8333.860| |-----------------------------------------------------------------------------| r_work (start): 0.3346 rms_B_bonded: 2.69 r_work: 0.3193 rms_B_bonded: 3.44 restraints_weight: 0.5000 r_work (final): 0.3193 ------------------------------------------------------------------------------- Occupancy refinement ******************** ------------------------------------------------------------------------------- Overall statistics ****************** model-to-map fit, CC_mask: 0.8156 moved from start: 0.2810 Geometry Restraints Library: GeoStd + Monomer Library + CDL v1.2 Deviations from Ideal Values - rmsd, rmsZ for bonds and angles. Bond : 0.002 0.030 6182 Z= 0.148 Angle : 0.472 6.658 8370 Z= 0.234 Chirality : 0.038 0.148 947 Planarity : 0.004 0.041 1056 Dihedral : 4.582 77.603 818 Min Nonbonded Distance : 2.232 Molprobity Statistics. All-atom Clashscore : 7.18 Ramachandran Plot: Outliers : 0.00 % Allowed : 2.34 % Favored : 97.66 % Rotamer: Outliers : 2.09 % Allowed : 11.79 % Favored : 86.12 % Cbeta Deviations : 0.00 % Peptide Plane: Cis-proline : 0.00 % Cis-general : 0.00 % Twisted Proline : 0.00 % Twisted General : 0.00 % Rama-Z (Ramachandran plot Z-score): Interpretation: bad |Rama-Z| > 3; suspicious 2 < |Rama-Z| < 3; good |Rama-Z| < 2. Scores for whole/helix/sheet/loop are scaled independently; therefore, the values are not related in a simple manner. whole: 1.83 (0.31), residues: 725 helix: 2.66 (0.29), residues: 306 sheet: -0.23 (0.49), residues: 103 loop : 0.36 (0.34), residues: 316 Max deviation from planes: Type MaxDev MeanDev LineInFile TRP 0.006 0.001 TRP A 401 HIS 0.002 0.000 HIS B 332 PHE 0.009 0.001 PHE A 253 TYR 0.021 0.001 TYR A 494 ARG 0.002 0.000 ARG B 541 Origin is already at (0, 0, 0), no shifts will be applied =============================================================================== Job complete usr+sys time: 1803.43 seconds wall clock time: 33 minutes 50.57 seconds (2030.57 seconds total)